From 0bf932c45e3da8a7c769d61b93a775400f6a0e4e Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 11 Oct 2024 11:59:55 +1300 Subject: [PATCH 01/12] Changed name to Species to OntologyTerm, removed DbIds not in 2.1 model, matched ObservationUnitLevel etc with model. --- .../BrAPI-Common/ExternalReference.json | 2 +- .../BrAPI-Schema/BrAPI-Common/GeoJSON.json | 12 +--- .../ObservationUnitHierarchyLevel.json | 31 ++++++++++ .../{Species.json => OntologyTerm.json} | 14 +---- .../BrAPI-Common/SourceGermplasm.json | 34 ----------- .../BrAPI-Schema/BrAPI-Common/Variable.json | 7 --- .../BrAPI-Schema/BrAPI-Core/Study.json | 60 +------------------ .../BrAPI-Schema/BrAPI-Core/Trial.json | 14 ----- .../BrAPI-Genotyping/AlleleMatrix.json | 20 +------ .../BrAPI-Schema/BrAPI-Genotyping/Call.json | 7 --- .../BrAPI-Genotyping/Reference.json | 4 +- .../BrAPI-Genotyping/ReferenceSet.json | 4 +- .../BrAPI-Genotyping/VariantSet.json | 40 +++++++------ .../BrAPI-Schema/BrAPI-Germplasm/Cross.json | 6 +- .../BrAPI-Germplasm/CrossParent.json | 9 +-- .../BrAPI-Germplasm/Germplasm.json | 35 +++++------ .../BrAPI-Germplasm/GermplasmAttribute.json | 7 --- .../BrAPI-Germplasm/PedigreeNode.json | 22 ++----- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 18 ++---- .../BrAPI-Schema/BrAPI-Phenotyping/Event.json | 2 +- .../BrAPI-Phenotyping/ObservationUnit.json | 11 +--- .../ObservationUnitLevel.json | 46 +++++--------- .../ObservationUnitLevelRelationship.json | 50 ++++------------ .../BrAPI-Phenotyping/OntologyReference.json | 2 +- .../BrAPI-Schema/BrAPI-Phenotyping/Scale.json | 9 +-- 25 files changed, 132 insertions(+), 334 deletions(-) create mode 100644 Specification/BrAPI-Schema/BrAPI-Common/ObservationUnitHierarchyLevel.json rename Specification/BrAPI-Schema/BrAPI-Common/{Species.json => OntologyTerm.json} (82%) delete mode 100644 Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json index 44f00b41..3332d5ec 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/ExternalReference.json @@ -2,7 +2,7 @@ "$defs": { "ExternalReference": { "properties": { - "externalReferenceDbId": { + "referenceId": { "description": "The external reference ID. Could be a simple string or a URI.", "type": [ "null", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json index 8a496791..64387253 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json @@ -5,13 +5,6 @@ "type": "object", "description": "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", "properties": { - "geoJSONDbId": { - "description": "Unique identifier for the geometry", - "type": [ - "null", - "string" - ] - }, "geometry": { "description": "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed.", "$ref": "GeoJSONGeometry.json#/$defs/GeoJSONGeometry" @@ -46,10 +39,7 @@ "relationshipType": "many-to-one", "referencedAttribute": "coordinates" } - }, - "required": [ - "geoJSONDbId" - ] + } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/GeoJSON.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Common/ObservationUnitHierarchyLevel.json b/Specification/BrAPI-Schema/BrAPI-Common/ObservationUnitHierarchyLevel.json new file mode 100644 index 00000000..12b5f51f --- /dev/null +++ b/Specification/BrAPI-Schema/BrAPI-Common/ObservationUnitHierarchyLevel.json @@ -0,0 +1,31 @@ +{ + "$defs": { + "ObservationUnitHierarchyLevel": { + "description": "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties": { + "levelName": { + "description": "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "type": [ + "null", + "string" + ] + }, + "levelOrder": { + "description": "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", + "type": [ + "null", + "integer" + ] + } + }, + "required": [], + "title": "ObservationUnitHierarchyLevel", + "type": "object", + "brapi-metadata": { + "interface": true + } + } + }, + "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/ObservationUnitHierarchyLevel.json", + "$schema": "http://json-schema.org/draft/2020-12/schema" +} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Species.json b/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json similarity index 82% rename from Specification/BrAPI-Schema/BrAPI-Common/Species.json rename to Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json index 38cab2f7..124a69e9 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Species.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json @@ -1,14 +1,7 @@ { "$defs": { - "Species": { + "OntologyTerm": { "properties": { - "speciesDbId": { - "description": "An ontology term describing an attribute.", - "type": [ - "null", - "string" - ] - }, "term": { "description": "Ontology term - the label of the ontology term the termId is pointing to.", "type": [ @@ -36,9 +29,6 @@ "referencedAttribute": "species" } }, - "required": [ - "specieDbId" - ], "title": "OntologyTerm", "type": "object", "brapi-metadata": { @@ -46,6 +36,6 @@ } } }, - "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/Species.json", + "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/OntologyTerm.json", "$schema": "http://json-schema.org/draft/2020-12/schema" } \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json b/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json deleted file mode 100644 index 36aa1572..00000000 --- a/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "$defs": { - "SourceGermplasm": { - "properties": { - "germplasmName": { - "description": "The human readable name of a `Germplasm`", - "type": [ - "null", - "string" - ] - }, - "reference": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - }, - "referenceSet": { - "description": "Germplasm associated with a reference", - "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", - "relationshipType": "many-to-one", - "referencedAttribute": "sourceGermplasm" - } - }, - "title": "sourceGermplasm", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } - } - }, - "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Common/SourceGermplasm.json", - "$schema": "http://json-schema.org/draft/2020-12/schema" -} \ No newline at end of file diff --git a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json index 76726591..98a8264e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Common/Variable.json +++ b/Specification/BrAPI-Schema/BrAPI-Common/Variable.json @@ -2,13 +2,6 @@ "$defs": { "Variable": { "properties": { - "variableDbId": { - "description": "Unique identifier for the Variable", - "type": [ - "null", - "string" - ] - }, "additionalInfo": { "description": "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", "$ref": "../BrAPI-Common/AdditionalInfo.json#/$defs/AdditionalInfo", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Study.json b/Specification/BrAPI-Schema/BrAPI-Core/Study.json index 7154840a..68c83b51 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Study.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Study.json @@ -100,12 +100,9 @@ }, "growthFacility": { "description": "Short description of the facility in which the study was carried out.", - "relationshipType": "one-to-many", + "relationshipType": "many-to-one", "referencedAttribute": "study", - "items": { - "$ref": "../BrAPI-Core/Study.json#/$defs/GrowthFacility", - "description": "GrowthFacility" - } + "$ref": "../BrAPI-Core/Study.json#/$defs/GrowthFacility" }, "lastUpdate": { "description": "The date and time when this study was last modified", @@ -129,9 +126,8 @@ "observationLevels": { "description": "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", "relationshipType": "one-to-many", - "referencedAttribute": "study", "items": { - "$ref": "../BrAPI-Core/Study.json#/$defs/ObservationLevels", + "$ref": "../BrAPI-Common/ObservationUnitHierarchyLevel.json#/$defs/ObservationUnitHierarchyLevel", "description": "ObservationLevels" }, "title": "ObservationLevels", @@ -394,10 +390,6 @@ }, "ExperimentalDesign": { "properties": { - "experimentalDesignDbId": { - "description": "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology", - "type": "string" - }, "PUI": { "description": "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology.", "type": [ @@ -419,9 +411,6 @@ "referencedAttribute": "experimentalDesign" } }, - "required": [ - "experimentalDesignDbId" - ], "title": "ExperimentalDesign", "type": "object", "brapi-metadata": { @@ -430,10 +419,6 @@ }, "GrowthFacility": { "properties": { - "growthFacilityDbId": { - "description": "Short description of the facility in which the study was carried out.", - "type": "string" - }, "PUI": { "description": "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology.", "type": [ @@ -455,9 +440,6 @@ "referencedAttribute": "growthFacility" } }, - "required": [ - "growthFacilityDbId" - ], "title": "GrowthFacility", "type": "object", "brapi-metadata": { @@ -498,42 +480,6 @@ "brapi-metadata": { "primaryModel": false } - }, - "ObservationLevels": { - "properties": { - "observationLevelsDbId": { - "description": "Observation levels indicate the granularity level at which the measurements are taken. `levelName` defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are at the bottom of the hierarchy (ie plant > 6). ", - "type": "string" - }, - "levelName": { - "description": "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "string" - ] - }, - "levelOrder": { - "description": "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "integer" - ] - }, - "study": { - "description": "Observation levels associated with a study", - "$ref": "../BrAPI-Core/Study.json#/$defs/Study", - "relationshipType": "many-to-one", - "referencedAttribute": "observationLevels" - } - }, - "required": [ - "observationLevelsDbId" - ], - "title": "ObservationUnitHierarchyLevel", - "type": "object", - "brapi-metadata": { - "primaryModel": false - } } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Core/Study.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 9db766c2..28f1ed23 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -192,10 +192,6 @@ }, "DatasetAuthorships": { "properties": { - "datasetAuthorshipsDbId": { - "description": "License and citation information for the data in this trial", - "type": "string" - }, "datasetPUI": { "description": "The DOI or other permanent unique identifier for this published dataset", "type": [ @@ -231,9 +227,6 @@ "referencedAttribute": "datasetAuthorships" } }, - "required": [ - "datasetAuthorshipsDbId" - ], "title": "DatasetAuthorships", "type": "object", "brapi-metadata": { @@ -242,10 +235,6 @@ }, "Publications": { "properties": { - "publicationsDbId": { - "description": "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.", - "type": "string" - }, "publicationPUI": { "type": [ "null", @@ -265,9 +254,6 @@ "referencedAttribute": "publications" } }, - "required": [ - "publicationsDbId" - ], "title": "Publications", "type": "object", "brapi-metadata": { diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json index 2c3064f3..fe22bfef 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/AlleleMatrix.json @@ -16,7 +16,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "alleleMatrix", "items": { - "$ref": "../BrAPI-Genotyping/AlleleMatrix.json#/$defs/DataMatrices", + "$ref": "../BrAPI-Genotyping/AlleleMatrix.json#/$defs/DataMatrix", "description": "DataMatrices" }, "title": "DataMatrices", @@ -96,12 +96,8 @@ "primaryModel": true } }, - "DataMatrices": { + "DataMatrix": { "properties": { - "dataMatricesDbId": { - "description": "This is a single data matrix. It could be the allele matrix or an additional layer of metadata associated with each genotype value.", - "type": "string" - }, "dataMatrix": { "description": "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows.", "items": { @@ -152,9 +148,6 @@ "referencedAttribute": "dataMatrices" } }, - "required": [ - "dataMatricesDbId" - ], "title": "DataMatrix", "type": "object", "brapi-metadata": { @@ -163,10 +156,6 @@ }, "Pagination": { "properties": { - "paginationDbId": { - "description": "Pagination for the matrix", - "type": "string" - }, "dimension": { "description": "The dimension of the matrix being paginated", "enum": [ @@ -208,15 +197,12 @@ ] }, "alleleMatrix": { - "description": "Pgination associated with an alleleMatrix", + "description": "Pagination associated with an alleleMatrix", "$ref": "../BrAPI-Genotyping/AlleleMatrix.json#/$defs/AlleleMatrix", "relationshipType": "many-to-one", "referencedAttribute": "pagination" } }, - "required": [ - "paginationDbId" - ], "title": "Pagination", "type": "object", "brapi-metadata": { diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json index 1343da47..fdb5002a 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Call.json @@ -67,10 +67,6 @@ }, "GenotypeMetadata": { "properties": { - "genotypeMetadataDbId": { - "description": "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended.", - "type": "string" - }, "dataType": { "description": "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", "enum": [ @@ -113,9 +109,6 @@ "referencedAttribute": "genotypeMetadata" } }, - "required": [ - "genotypeMetadataDbId" - ], "title": "GenotypeMetadata", "type": "object", "brapi-metadata": { diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json index 951759ff..912dce94 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/Reference.json @@ -84,7 +84,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "reference", "items": { - "$ref": "../BrAPI-Common/SourceGermplasm.json#/$defs/SourceGermplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", "description": "SourceGermplasm" }, "title": "SourceGermplasm", @@ -104,7 +104,7 @@ "description": "An ontology term describing an attribute.", "relationshipType": "one-to-one", "referencedAttribute": "reference", - "$ref": "../BrAPI-Common/Species.json#/$defs/Species" + "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" }, "variants": { "title": "variants", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json index bbfe7ab4..8cede9b8 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/ReferenceSet.json @@ -78,7 +78,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "referenceSet", "items": { - "$ref": "../BrAPI-Common/SourceGermplasm.json#/$defs/SourceGermplasm", + "$ref": "../BrAPI-Germplasm/Germplasm.json#/$defs/Germplasm", "description": "SourceGermplasm" }, "title": "SourceGermplasm", @@ -98,7 +98,7 @@ "description": "An ontology term describing an attribute.", "relationshipType": "one-to-one", "referencedAttribute": "referenceSet", - "$ref": "../BrAPI-Common/Species.json#/$defs/Species" + "$ref": "../BrAPI-Common/OntologyTerm.json#/$defs/OntologyTerm" }, "references": { "title": "references", diff --git a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json index f6316099..7947a929 100644 --- a/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json +++ b/Specification/BrAPI-Schema/BrAPI-Genotyping/VariantSet.json @@ -63,11 +63,17 @@ "array" ] }, - "availableFormat": { + "availableFormats": { "description": "When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. \n
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)\n
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", - "relationshipType": "one-to-one", - "referencedAttribute": "variantSet", - "$ref": "../BrAPI-Genotyping/VariantSet.json#/$defs/AvailableFormat" + "relationshipType": "many-to-many", + "items": { + "$ref": "../BrAPI-Genotyping/VariantSet.json#/$defs/AvailableFormat" + }, + "type": [ + "null", + "array" + ], + "referencedAttribute": "variantSet" }, "callSetCount": { "description": "The number of CallSets included in this VariantSet", @@ -89,11 +95,17 @@ "array" ] }, - "metadataField": { + "metadataFields": { "description": "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard ", - "relationshipType": "one-to-one", + "relationshipType": "one-to-many", "referencedAttribute": "variantSet", - "$ref": "../BrAPI-Genotyping/VariantSet.json#/$defs/MetadataField" + "items": { + "$ref": "../BrAPI-Genotyping/VariantSet.json#/$defs/MetadataField" + }, + "type": [ + "null", + "array" + ] }, "referenceSet": { "$ref": "ReferenceSet.json#/$defs/ReferenceSet", @@ -296,7 +308,7 @@ "referencedAttribute": "availableFormats" } }, - "title": "AvailableFormats", + "title": "AvailableFormat", "type": "object", "brapi-metadata": { "primaryModel": false @@ -304,13 +316,6 @@ }, "MetadataField": { "properties": { - "metadataFieldDbId": { - "description": "This represents a type of genotyping data or metadata available in this VariantSet", - "type": [ - "null", - "string" - ] - }, "dataType": { "description": "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", "enum": [ @@ -346,10 +351,7 @@ "referencedAttribute": "metadataFields" } }, - "required": [ - "metadataFieldDbId" - ], - "title": "MetadataFields", + "title": "MetadataField", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index 2ff37b76..cac97eda 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -130,7 +130,7 @@ "referencedAttribute": "crossAttributes" } }, - "title": "CrossAttributes", + "title": "CrossAttribute", "type": "object", "brapi-metadata": { "primaryModel": true @@ -161,13 +161,13 @@ ] }, "cross": { - "description": "polunation events associated with a cross", + "description": "Pollination events associated with a cross", "$ref": "../BrAPI-Germplasm/Cross.json#/$defs/Cross", "relationshipType": "many-to-one", "referencedAttribute": "pollinationEvents" } }, - "title": "PollinationEvents", + "title": "PollinationEvent", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json index 181ba952..bbc383a4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/CrossParent.json @@ -2,13 +2,6 @@ "$defs": { "CrossParent": { "properties": { - "crossParentDbId": { - "description": "The ID which uniquely identifies a cross parent", - "type": [ - "null", - "string" - ] - }, "germplasm": { "description": "the germplasm of the cross parent", "relationshipType": "one-to-one", @@ -20,7 +13,7 @@ }, "observationUnit": { "description": "the Observation Unit of the cross parent", - "relationshipType": "one-to-one", + "relationshipType": "many-to-one", "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", "type": [ "null", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index cc1d0e53..d19355a5 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -370,6 +370,18 @@ "null", "array" ] + }, + "reference": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/Reference.json#/$defs/Reference", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" + }, + "referenceSet": { + "description": "Germplasm associated with a reference", + "$ref": "../BrAPI-Genotyping/ReferenceSet.json#/$defs/ReferenceSet", + "relationshipType": "many-to-one", + "referencedAttribute": "sourceGermplasm" } }, "required": [ @@ -386,10 +398,6 @@ }, "Donor": { "properties": { - "donorDbId": { - "description": "the unique identifier for a donor", - "type": "string" - }, "donorAccessionNumber": { "description": "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard.", "type": [ @@ -414,7 +422,7 @@ "required": [ "donorDbId" ], - "title": "Donors", + "title": "Donor", "type": "object", "brapi-metadata": { "primaryModel": false @@ -491,7 +499,7 @@ "referencedAttribute": "storageTypes" } }, - "title": "StorageTypes", + "title": "StorageType", "type": "object", "brapi-metadata": { "primaryModel": false @@ -499,10 +507,6 @@ }, "Synonym": { "properties": { - "synonymDbId": { - "description": "the unique identifier for a synonym", - "type": "string" - }, "synonym": { "description": "Alternative name or ID used to reference this germplasm", "type": [ @@ -524,10 +528,7 @@ "referencedAttribute": "synonyms" } }, - "required": [ - "synonymDbId" - ], - "title": "Synonyms", + "title": "Synonym", "type": "object", "brapi-metadata": { "primaryModel": false @@ -535,10 +536,6 @@ }, "TaxonId": { "properties": { - "taxonDbId": { - "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", - "type": "string" - }, "taxonId": { "description": "The identifier (name, ID, URI) of a particular taxonomy within the source provider", "type": "string" @@ -559,7 +556,7 @@ "taxonDbId", "taxonId" ], - "title": "TaxonIds", + "title": "TaxonId", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json index 91214cd2..fb37543c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/GermplasmAttribute.json @@ -8,13 +8,6 @@ { "type": "object", "properties": { - "germplasmAttributeDbId": { - "description": "The ID which uniquely identifies a germplasm attribute", - "type": [ - "null", - "string" - ] - }, "attributeValues": { "title": "attributeValues", "description": "attributeValues", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index a38e7dc1..62395243 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -126,13 +126,9 @@ }, "GermplasmParent": { "properties": { - "germplasmParentDbId": { - "description": "a unique identifiere for a parent", - "type": "string" - }, "parentGermplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", - "description": "The ID which uniquely identifies a parent germplasm", + "description": "The parent germplasm", "referencedAttribute": "progenyPedigreeNodes", "relationshipType": "many-to-one" }, @@ -148,11 +144,10 @@ } }, "required": [ - "parentDbId", "parentGermplasm", "parentType" ], - "title": "Parents", + "title": "GermplasmParent", "type": "object", "brapi-metadata": { "primaryModel": false @@ -160,13 +155,9 @@ }, "GermplasmChild": { "properties": { - "germplasmChildDbId": { - "description": "a unique identifiere for a progeny", - "type": "string" - }, - "progenyGermplasm": { + "childGermplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", - "description": "The ID which uniquely identifies a parent germplasm", + "description": "The child germplasm", "referencedAttribute": "parentPedigreeNodes", "relationshipType": "many-to-one" }, @@ -182,11 +173,10 @@ } }, "required": [ - "germplasmChildDbId", - "progenyGermplasm", + "childGermplasm", "parentType" ], - "title": "Progeny", + "title": "GermplasmChild", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index dc7f3a54..0f91e815 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -167,19 +167,11 @@ "string" ] }, - "germplasmDbId": { - "description": "The unique DbId of the Germplasm contained in this Seed Lot", - "type": [ - "null", - "string" - ] - }, - "germplasmName": { - "description": "The human readable name of the Germplasm contained in this Seed Lot", - "type": [ - "null", - "string" - ] + "germplasm": { + "$ref": "Germplasm.json#/$defs/Germplasm", + "description": "The ID which uniquely identifies a germplasm", + "referencedAttribute": "parentPedigreeNodes", + "relationshipType": "many-to-one" }, "mixturePercentage": { "description": "The percentage of the given germplasm in the seed lot mixture.", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json index 47aa724a..2b840ee4 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Event.json @@ -189,7 +189,7 @@ "referencedAttribute": "eventParameters" } }, - "title": "EventParameters", + "title": "EventParameter", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json index 7b312820..9a7247b0 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnit.json @@ -210,7 +210,7 @@ }, "observationLevelRelationships": { "description": "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "relationshipType": "one-to-one", + "relationshipType": "one-to-many", "items": { "$ref": "../BrAPI-Phenotyping/ObservationUnitLevelRelationship.json#/$defs/ObservationUnitLevelRelationship" }, @@ -284,10 +284,6 @@ }, "Treatment": { "properties": { - "treatmentDbId": { - "description": "the unique identifier for a treatment", - "type": "string" - }, "factor": { "description": "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor.", "type": [ @@ -309,10 +305,7 @@ "referencedAttribute": "treatments" } }, - "required": [ - "treatmentDbId" - ], - "title": "Treatments", + "title": "Treatment", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevel.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevel.json index 95f669cf..9bc6fc5e 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevel.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevel.json @@ -2,39 +2,23 @@ "$defs": { "ObservationUnitLevel": { "description": "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", - "properties": { - "levelCode": { - "description": "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "type": [ - "null", - "string" - ] + "allOf": [ + { + "$ref": "../BrAPI-Common/ObservationUnitHierarchyLevel.json#/$defs/ObservationUnitHierarchyLevel" }, - "levelName": { - "description": "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "string" - ] - }, - "levelOrder": { - "description": "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "integer" - ] - }, - "observationUnitLevelDbId": { - "description": "The ID which uniquely identifies a observation unit level", - "type": [ - "null", - "string" - ] + { + "type": "object", + "properties": { + "levelCode": { + "description": "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", + "type": [ + "null", + "string" + ] + } + } } - }, - "required": [], - "title": "ObservationUnitLevel", - "type": "object" + ] } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevel.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevelRelationship.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevelRelationship.json index 4ebf7161..fb63808f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevelRelationship.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevelRelationship.json @@ -2,45 +2,21 @@ "$defs": { "ObservationUnitLevelRelationship": { "description": "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", - "properties": { - "levelCode": { - "description": "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. ", - "type": [ - "null", - "string" - ] + "allOf": [ + { + "$ref": "../BrAPI-Phenotyping/ObservationUnitLevel.json#/$defs/ObservationUnitLevel" }, - "levelName": { - "description": "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "string" - ] - }, - "levelOrder": { - "description": "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. ", - "type": [ - "null", - "integer" - ] - }, - "observationUnitDbId": { - "description": "The ID which uniquely identifies an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.", - "type": [ - "null", - "string" - ] - }, - "observationUnitLevelRelationshipDbId": { - "description": "The ID which uniquely identifies a observaton unit level relationship", - "type": [ - "null", - "string" - ] + { + "type": "object", + "properties": { + "observationUnit": { + "description": "The an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response.", + "$ref": "../BrAPI-Phenotyping/ObservationUnit.json#/$defs/ObservationUnit", + "relationshipType": "one-to-one" + } + } } - }, - "title": "ObservationUnitLevelRelationship", - "type": "object" + ] } }, "$id": "https://brapi.org/Specification/BrAPI-Schema/BrAPI-Phenotyping/ObservationUnitLevelRelationship.json", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json index 73131985..a2050bca 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/OntologyReference.json @@ -73,7 +73,7 @@ "referencedAttribute": "documentationLinks" } }, - "title": "DocumentationLinks", + "title": "DocumentationLink", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 55a6b9eb..32c14ffa 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -72,12 +72,9 @@ ] }, "validValues": { - "relationshipType": "one-to-many", + "relationshipType": "one-to-one", "referencedAttribute": "scale", - "items": { - "$ref": "../BrAPI-Phenotyping/Scale.json#/$defs/ValidValue", - "description": "ValidValues" - }, + "$ref": "../BrAPI-Phenotyping/Scale.json#/$defs/ValidValues", "title": "ValidValues", "type": [ "null", @@ -161,7 +158,7 @@ "referencedAttribute": "categories" } }, - "title": "Categories", + "title": "Category", "type": "object", "brapi-metadata": { "primaryModel": false From 2f096156ef573ca935083eb0476aae4c990c3878 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Wed, 30 Oct 2024 19:25:06 +1300 Subject: [PATCH 02/12] fixed content mixture --- .../BrAPI-Schema/BrAPI-Germplasm/SeedLot.json | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json index 0f91e815..0ab0c67f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/SeedLot.json @@ -160,17 +160,14 @@ }, "ContentMixture": { "properties": { - "crossName": { - "description": "The human readable name for a cross contained in this seed lot", - "type": [ - "null", - "string" - ] + "cross": { + "$ref": "Cross.json#/$defs/Cross", + "description": "The cross for the germplasm using in this content mixture", + "relationshipType": "many-to-one" }, "germplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", - "description": "The ID which uniquely identifies a germplasm", - "referencedAttribute": "parentPedigreeNodes", + "description": "The germplasm using in this content mixture", "relationshipType": "many-to-one" }, "mixturePercentage": { From ee5ba3bff9443e1109cdc8d9e2c9ae86ee3305f4 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Mon, 18 Nov 2024 19:56:21 +1300 Subject: [PATCH 03/12] improved entities names, fixed publications --- Specification/BrAPI-Schema/BrAPI-Core/Trial.json | 6 +++--- Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json | 3 ++- .../BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json | 3 ++- Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json | 6 +++--- 4 files changed, 10 insertions(+), 8 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json index 28f1ed23..d4cc0259 100644 --- a/Specification/BrAPI-Schema/BrAPI-Core/Trial.json +++ b/Specification/BrAPI-Schema/BrAPI-Core/Trial.json @@ -99,7 +99,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "trial", "items": { - "$ref": "../BrAPI-Core/Trial.json#/$defs/Publications", + "$ref": "../BrAPI-Core/Trial.json#/$defs/Publication", "description": "Publications" }, "title": "Publications", @@ -233,7 +233,7 @@ "primaryModel": false } }, - "Publications": { + "Publication": { "properties": { "publicationPUI": { "type": [ @@ -254,7 +254,7 @@ "referencedAttribute": "publications" } }, - "title": "Publications", + "title": "Publication", "type": "object", "brapi-metadata": { "primaryModel": false diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index d19355a5..9a7c9528 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -483,7 +483,8 @@ "type": [ "null", "string" - ] + ], + "title": "StorageTypeCode" }, "description": { "description": "A supplemental text description of the storage type", diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json index 34dd2460..57d26cde 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PlannedCross.json @@ -60,7 +60,8 @@ "type": [ "null", "string" - ] + ], + "title": "PlannedCrossStatus" }, "crosses": { "title": "crosses", diff --git a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json index 32c14ffa..436304b0 100644 --- a/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json +++ b/Specification/BrAPI-Schema/BrAPI-Phenotyping/Scale.json @@ -99,7 +99,7 @@ "relationshipType": "one-to-many", "referencedAttribute": "validValues", "items": { - "$ref": "../BrAPI-Phenotyping/Scale.json#/$defs/Category", + "$ref": "../BrAPI-Phenotyping/Scale.json#/$defs/ValidValuesCategory", "description": "Categories" }, "title": "Categories", @@ -135,7 +135,7 @@ "primaryModel": false } }, - "Category": { + "ValidValuesCategory": { "properties": { "label": { "description": "A text label for a category", @@ -158,7 +158,7 @@ "referencedAttribute": "categories" } }, - "title": "Category", + "title": "ValidValuesCategory", "type": "object", "brapi-metadata": { "primaryModel": false From a003c0fcb9de52c1892c2457342965a7fbc1985d Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Sat, 23 Nov 2024 09:11:14 +1300 Subject: [PATCH 04/12] removed pedigree node --- Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index 9a7c9528..fad2002f 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -65,12 +65,6 @@ "referencedAttribute": "germplasm", "relationshipType": "many-to-one" }, - "pedigreeNode": { - "$ref": "PedigreeNode.json#/$defs/PedigreeNode", - "description": "The unique identifier for the node in the pedigree tree associated with a germplasm", - "referencedAttribute": "germplasm", - "relationshipType": "one-to-one" - }, "collection": { "description": "A specific panel/collection/population name this germplasm belongs to.", "type": [ From 89e45a343cef85fce52f5a2b94d836e4985eb3bc Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 15:24:27 +1300 Subject: [PATCH 05/12] added to gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 5a14dc57..bd60213d 100644 --- a/.gitignore +++ b/.gitignore @@ -10,3 +10,5 @@ brapi_openapi.yaml out.yaml Scripts/__pycache__/ brapi_blueprint.apib.json +/generator/.gradle/ +/generator/build \ No newline at end of file From ca904b2a88f5243d0b8391957d7b6c30ce044ef7 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 17:07:40 +1300 Subject: [PATCH 06/12] fixed referencedAttribute --- Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json | 1 - 1 file changed, 1 deletion(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json index 62395243..15f2d26c 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/PedigreeNode.json @@ -56,7 +56,6 @@ "germplasm": { "$ref": "Germplasm.json#/$defs/Germplasm", "description": "The ID which uniquely identifies a germplasm", - "referencedAttribute": "pedigreeNode", "relationshipType": "one-to-one" }, "parents": { From 167dbd7bee053075e2331d9e8370e5a43b4f263d Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 17:39:26 +1300 Subject: [PATCH 07/12] removed missing required dbids --- Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json | 4 ---- 1 file changed, 4 deletions(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json index fad2002f..dc80ae08 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Germplasm.json @@ -413,9 +413,6 @@ "referencedAttribute": "donors" } }, - "required": [ - "donorDbId" - ], "title": "Donor", "type": "object", "brapi-metadata": { @@ -548,7 +545,6 @@ }, "required": [ "sourceName", - "taxonDbId", "taxonId" ], "title": "TaxonId", From 27f3725f3984cf931fb57ba02de5db9b4f441867 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 19:05:37 +1300 Subject: [PATCH 08/12] Add generateAll to CI --- .github/workflows/generate-schema.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index 181e4200..d817022b 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -16,6 +16,9 @@ jobs: - name: Change wrapper permissions working-directory: ./generator/ run: chmod +x ./gradlew - - name: Build with Gradle Wrapper + - name: Validate working-directory: ./generator/ run: ./gradlew validate + - name: Generate OpenAPI, GraphQL and OWL + working-directory: ./generator/ + run: ./gradlew generateAll From a3e953c0c076bc778b44f68be52c7e420d838099 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 19:19:25 +1300 Subject: [PATCH 09/12] CrossAttribute is not primary model --- Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json index cac97eda..22f350df 100644 --- a/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json +++ b/Specification/BrAPI-Schema/BrAPI-Germplasm/Cross.json @@ -133,7 +133,7 @@ "title": "CrossAttribute", "type": "object", "brapi-metadata": { - "primaryModel": true + "primaryModel": false } }, "PollinationEvent": { From e5b875dd66dbe241a9681509996ea7a316319756 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 19:56:43 +1300 Subject: [PATCH 10/12] added OWL metadata --- generator/ont-model-metadata.yaml | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 generator/ont-model-metadata.yaml diff --git a/generator/ont-model-metadata.yaml b/generator/ont-model-metadata.yaml new file mode 100644 index 00000000..cf69f878 --- /dev/null +++ b/generator/ont-model-metadata.yaml @@ -0,0 +1,2 @@ +namespace: http://brapi.org +language: en \ No newline at end of file From d276c641beee4fe31920a5fc261cef8fbf4e8412 Mon Sep 17 00:00:00 2001 From: Guy Davenport Date: Fri, 17 Jan 2025 20:03:05 +1300 Subject: [PATCH 11/12] added a commit for the updated schemas/specs --- .github/workflows/generate-schema.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/generate-schema.yml b/.github/workflows/generate-schema.yml index d817022b..32776ce9 100644 --- a/.github/workflows/generate-schema.yml +++ b/.github/workflows/generate-schema.yml @@ -22,3 +22,4 @@ jobs: - name: Generate OpenAPI, GraphQL and OWL working-directory: ./generator/ run: ./gradlew generateAll + - uses: stefanzweifel/git-auto-commit-action@v5 From fbf1dfd5d360a15f5dbc457d2b47e710d050bd68 Mon Sep 17 00:00:00 2001 From: daveneti <376097+daveneti@users.noreply.github.com> Date: Fri, 17 Jan 2025 07:03:51 +0000 Subject: [PATCH 12/12] Apply automatic changes --- Specification/Generated/brapi_v2_1.graphqls | 7389 +++++++ Specification/Generated/brapi_v2_1.json | 20793 ++++++++++++++++++ Specification/Generated/brapi_v2_1.ttl | 6111 +++++ generator/gradlew | 0 4 files changed, 34293 insertions(+) create mode 100644 Specification/Generated/brapi_v2_1.graphqls create mode 100644 Specification/Generated/brapi_v2_1.json create mode 100644 Specification/Generated/brapi_v2_1.ttl mode change 100644 => 100755 generator/gradlew diff --git a/Specification/Generated/brapi_v2_1.graphqls b/Specification/Generated/brapi_v2_1.graphqls new file mode 100644 index 00000000..5fdbe9eb --- /dev/null +++ b/Specification/Generated/brapi_v2_1.graphqls @@ -0,0 +1,7389 @@ +"Marks the field, argument, input field or enum value as deprecated" +directive @deprecated( + "The reason for the deprecation" + reason: String = "No longer supported" + ) on FIELD_DEFINITION | ARGUMENT_DEFINITION | ENUM_VALUE | INPUT_FIELD_DEFINITION + +"Directs the executor to include this field or fragment only when the `if` argument is true" +directive @include( + "Included when true." + if: Boolean! + ) on FIELD | FRAGMENT_SPREAD | INLINE_FRAGMENT + +"Indicates an Input Object is a OneOf Input Object." +directive @oneOf on INPUT_OBJECT + +"Directs the executor to skip this field or fragment when the `if` argument is true." +directive @skip( + "Skipped when true." + if: Boolean! + ) on FIELD | FRAGMENT_SPREAD | INLINE_FRAGMENT + +"Exposes a URL that specifies the behaviour of this scalar." +directive @specifiedBy( + "The URL that specifies the behaviour of this scalar." + url: String! + ) on SCALAR + +interface Attribute implements Variable { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "General category for the attribute. very similar to Trait class." + attributeCategory: String + "The ID which uniquely identifies this attribute within the given database server" + attributeDbId: String + "A human readable description of this attribute" + attributeDescription: String + "A human readable name for this attribute" + attributeName: String + "The Permanent Unique Identifier of an Attribute, usually in the form of a URI" + attributePUI: String + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: Method + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: Scale + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: Trait +} + +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +interface ObservationUnitHierarchyLevel { + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +interface Variable { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: Method + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: Scale + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: Trait +} + +union GeoJSONGeometry = GeoJSONPoint | GeoJSONPolygon + +"A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." +type AdditionalInfo { + additionalProperties: String +} + +type AlleleMatrix { + "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case." + callSets: [CallSet] + "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + dataMatrices: [DataMatrix] + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "Pagination for the matrix" + pagination: [Pagination] + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String + "A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets." + variantSets: [VariantSet] + "A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix." + variants: [Variant] +} + +type Analysis { + "Unique identifier for this analysis description" + analysisDbId: String + "A human readable name for this analysis" + analysisName: String + "The time at which this record was created, in ISO 8601 format." + created: String + "A human readable description of the analysis" + description: String + "The software run to generate this analysis." + software: [String] + "The type of analysis." + type: String + "The time at which this record was last updated, in ISO 8601 format." + updated: String + "Analysis associated with a variant set" + variantSet: VariantSet +} + +type AvailableFormat { + "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)" + dataFormat: DataFormat + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response." + fileFormat: FileFormat + "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file." + fileURL: String + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String + "Formats associated with a variant set" + variantSet: VariantSet +} + +type BreedingMethod { + "A shortened version of the human readable name for a Breeding Method" + abbreviation: String + "the unique identifier for this breeding method" + breedingMethodDbId: String + "the human readable identifier for this breeding method" + breedingMethodName: String + "human readable description of the breeding method" + description: String + "germplasm" + germplasm: [Germplasm] + "pedigreeNodes" + pedigreeNodes: [PedigreeNode] +} + +type BreedingMethodsListResponse { + data: [BreedingMethod] +} + +type Call { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + """ + The ID of the call set this variant call belongs to. + + If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same. + """ + callSet: CallSet + "Genotype Metadata are additional layers of metadata associated with each genotype." + genotypeMetadata: [GenotypeMetadata] + "The value of this genotype call" + genotypeValue: String + """ + If this field is populated, this variant call's genotype ordering implies the phase of the bases and + is consistent with any other variant calls on the same contig which have the same phase set string. + """ + phaseSet: String + "The ID of the variant this call belongs to." + variant: Variant + "The unique identifier for a VariantSet" + variantSet: VariantSet +} + +type CallSet { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + alleleMatrices: [AlleleMatrix] + "The ID which uniquely identifies a CallSet within the given database server" + callSetDbId: String + "The human readable name which identifies a germplasm within the given database server" + callSetName: String + calls: [Call] + "The date this call set was created" + created: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The Biosample entity the call set data was generated from." + sample: Sample + "The ID which uniquely identifies a study within the given database server" + study: Study + "The time at which this call set was last updated" + updated: String + "The IDs of the variantSets this callSet has calls in." + variantSets: [VariantSet] +} + +type CallSetsListResponse { + data: [CallSet] + page: [CallSet] +} + +type CallSetsSearchResponse { + data: [CallSet] + searchResultsDbId: [CallSet] +} + +type CallsListResponse { + data: [Call] + page: [Call] +} + +type CallsSearchResponse { + data: [Call] + searchResultsDbId: [Call] +} + +type Contact { + """ + The ID which uniquely identifies this contact + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + """ + contactDbId: String + """ + The contacts email address + + MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. + """ + email: String + """ + The name of the institution which this contact is part of + + MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to + """ + instituteName: String + """ + The full name of this contact person + + MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications) + """ + name: String + """ + The Open Researcher and Contributor ID for this contact person (orcid.org) + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + """ + orcid: String + """ + The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) + + MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation + """ + type: String +} + +type ContentMixture { + "The cross for the germplasm using in this content mixture" + cross: Cross + "The germplasm using in this content mixture" + germplasm: Germplasm + "The percentage of the given germplasm in the seed lot mixture." + mixturePercentage: Int + "associated seedLot" + seedLot: SeedLot +} + +type Cross { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Set of custom attributes associated with a cross" + crossAttributes: [CrossAttribute] + "the unique identifier for a cross" + crossDbId: String + "the human readable name for a cross" + crossName: String + "the type of cross" + crossType: CrossType + "the unique identifier for a crossing project" + crossingProject: CrossingProject + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "observationUnits" + observationUnits: [ObservationUnit] + "the first parent used in the cross" + parent1: CrossParent + "the second parent used in the cross" + parent2: CrossParent + "the unique identifier for a planned cross" + plannedCross: PlannedCross + "The list of pollination events that occurred for this cross" + pollinationEvents: [PollinationEvent] +} + +type CrossAttribute { + "a custom attributes associated with a cross" + cross: Cross + "the human readable name of a cross attribute" + crossAttributeName: String + "the value of a cross attribute" + crossAttributeValue: String +} + +type CrossParent { + "the germplasm of the cross parent" + germplasm: Germplasm + "the Observation Unit of the cross parent" + observationUnit: ObservationUnit + "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc." + parentType: ParentType +} + +type CrossesListResponse { + data: [Cross] + page: [Cross] +} + +type CrossingProject { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "the common name of a crop (for multi-crop systems)" + commonCropName: String + "crosses" + crosses: [Cross] + "The unique identifier for a crossing project" + crossingProjectDbId: String + "the description for a crossing project" + crossingProjectDescription: String + "The human readable name for a crossing project" + crossingProjectName: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "pedigreeNodes" + pedigreeNodes: [PedigreeNode] + "plannedCrosses" + plannedCrosses: [PlannedCross] + """ + A list of all the potential parents in the crossing block, available in the crossing project +
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. + """ + potentialParents: [CrossParent] + "the unique identifier for a program" + program: Program +} + +type CrossingProjectsListResponse { + data: [CrossingProject] + page: [CrossingProject] +} + +type CrossingProjectsSearchResponse { + data: [CrossingProject] + searchResultsDbId: [CrossingProject] +} + +type DataLink { + """ + The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + dataFormat: String + """ + The general description of this data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + description: String + """ + The MIME type of the file (ie text/csv, application/excel, application/zip). + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + fileFormat: String + """ + The name of the external data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + name: String + "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow." + provenance: String + "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc" + scientificType: String + """ + URL describing the location of this data file to view or download + + MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. + """ + url: String + """ + The version number for this data + + MIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data). + """ + version: String +} + +type DataMatrix { + "Data matrices associated with an alleleMatrix" + alleleMatrix: AlleleMatrix + "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + dataMatrix: [[String]] + """ + The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word "GT" is reserved for the allele matrix. Examples of other metadata matrices include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + """ + dataMatrixAbbreviation: String + """ + The name of the field represented in this data matrix. The key word "Genotype" is reserved for the allele matrix. Examples of other metadata matrices include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + """ + dataMatrixName: String + "The type of field represented in this data matrix. This is intended to help parse the data out of JSON." + dataType: DataType +} + +type DatasetAuthorships { + "The DOI or other permanent unique identifier for this published dataset" + datasetPUI: String + "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended." + license: String + "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described." + publicReleaseDate: String + "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository." + submissionDate: String + "Dataset authorships associated with a trial" + trial: Trial +} + +type DocumentationLink { + URL: String + "associated ontology reference" + ontologyReference: OntologyReference + type: Type +} + +type Donor { + """ + The accession number assigned by the donor + + MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard. + """ + donorAccessionNumber: String + """ + The institute code for the donor institute +
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. + """ + donorInstituteCode: String + "donoers associated with a germplasm" + germplasm: Germplasm +} + +type EnvironmentParameters { + "Human-readable value of the environment parameter (defined above) constant within the experiment" + description: String + "Human-readable value of the environment parameter (defined above) constant within the experiment" + environmentParametersDbId: String + """ + Name of the environment parameter constant within the experiment + + MIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. + """ + parameterName: String + "URI pointing to an ontology class for the parameter" + parameterPUI: String + "Environment parameters associated with a study" + study: Study + "Unit of the value for this parameter" + unit: String + "URI pointing to an ontology class for the unit" + unitPUI: String + """ + Numerical or categorical value + + MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. + """ + value: String + "URI pointing to an ontology class for the parameter value" + valuePUI: String +} + +type Event { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" + eventDateRange: [EventDateRange] + "Internal database identifier" + eventDbId: String + """ + A detailed, human-readable description of this event +
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. + """ + eventDescription: String + "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI" + eventParameters: [EventParameter] + """ + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + """ + eventType: String + """ + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + """ + eventTypeDbId: String + "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study" + observationUnits: [ObservationUnit] + "The study in which the event occurred" + study: Study +} + +type EventDateRange { + """ + A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + discreteDates: [String] + """ + The end of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + endDate: String + "associated event" + event: Event + """ + The beginning of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + startDate: String +} + +type EventParameter { + """ + The shortened code name of an event parameter +
ICASA "Code_Display" + """ + code: String + "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter." + description: String + "associated event" + event: Event + """ + The full name of an event parameter +
ICASA "Variable_Name" + """ + name: String + """ + The units or data type of the 'value'. +
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. +
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. +
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc +
ICASA "Unit_or_type" + """ + units: String + "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated." + value: String + "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value." + valueDescription: String + "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated." + valuesByDate: [String] +} + +type EventsListResponse { + data: [Event] + page: [Event] +} + +type EventsSearchResponse { + data: [Event] + searchResultsDbId: [Event] +} + +type ExperimentalDesign { + "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology." + PUI: String + "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'." + description: String + "Experimental design associated with a study" + study: Study +} + +type ExternalReference { + "The external reference ID. Could be a simple string or a URI." + referenceId: String + "An identifier for the source system or database of this reference" + referenceSource: String +} + +type GenomeMap { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Additional comments about a `GenomeMap`" + comments: String + "The common name of the `Crop`" + commonCropName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "The number of linkage groups present in a `GenomeMap`" + linkageGroupCount: Int + "The unique identifier for a `GenomeMap`" + mapDbId: String + "The human readable identifier for a `GenomeMap`" + mapName: String + "The DOI or other permanent identifier for a `GenomeMap`" + mapPUI: String + "The number of markers present in a `GenomeMap`" + markerCount: Int + "markerPositions" + markerPositions: [MarkerPosition] + "The date this `GenomeMap` was published" + publishedDate: String + "Full scientific binomial format name. This includes Genus, Species, and Sub-species" + scientificName: String + "The type of map this represents, usually \"Genetic\" or \"Physical\"" + type: String + "The units used to describe the data in a `GenomeMap`" + unit: String +} + +type GenomeMapsListResponse { + data: [GenomeMap] + page: [GenomeMap] +} + +type GenomeMapsSearchResponse { + data: [GenomeMap] + searchResultsDbId: [GenomeMap] +} + +type GenotypeMetadata { + "Genotype metadata associated with a call" + call: Call + "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." + dataType: DataType + """ + The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + """ + fieldAbbreviation: String + """ + The name of the field represented in this Genotype Field. Examples include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + """ + fieldName: String + "The additional metadata value associated with this genotype call" + fieldValue: String +} + +""" +One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + +Copied from RFC 7946 Section 3.1.1 + +A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +type GeoJSON { + "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." + geometry: GeoJSONGeometry + "Geometry associated with an image" + germplasmOrigin: GermplasmOrigin + "Geometry associated with an image" + image: Image + "Geometry associated with an image" + observation: Observation + "Geometry associated with an image" + observationUnit: ObservationUnitPosition + "The literal string \"Feature\"" + type: String +} + +""" +Copied from RFC 7946 Section 3.1.1 + +A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +type GeoJSONPoint { + "A single position" + coordinates: [Float] + "The literal string \"Point\"" + type: String +} + +""" +An array of Linear Rings. Each Linear Ring is an array of Points. + +A Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +type GeoJSONPolygon { + "An array of linear rings" + coordinates: [[[Float]]] + "The literal string \"Polygon\"" + type: String +} + +type Germplasm { + """ + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumber: String + """ + The date a material or germplasm was acquired by the genebank + + MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero]. + """ + acquisitionDate: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "attributeValues" + attributeValues: [GermplasmAttributeValue] + """ + MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. + + 100) Wild + 110) Natural + 120) Semi-natural/wild + 130) Semi-natural/sown + 200) Weedy + 300) Traditional cultivar/landrace + 400) Breeding/research material + 410) Breeders line + 411) Synthetic population + 412) Hybrid + 413) Founder stock/base population + 414) Inbred line (parent of hybrid cultivar) + 415) Segregating population + 416) Clonal selection + 420) Genetic stock + 421) Mutant (e.g. induced/insertion mutants, tilling populations) + 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) + 423) Other genetic stocks (e.g. mapping populations) + 500) Advanced or improved cultivar (conventional breeding methods) + 600) GMO (by genetic engineering) + 999) Other (Elaborate in REMARKS field) + """ + biologicalStatusOfAccessionCode: BiologicalStatusOfAccessionCode + "Supplemental text description for 'biologicalStatusOfAccessionCode'" + biologicalStatusOfAccessionDescription: String + "The unique identifier for the breeding method used to create this germplasm" + breedingMethod: BreedingMethod + "A specific panel/collection/population name this germplasm belongs to." + collection: String + """ + Common name for the crop + + MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: "malting barley", "mas". + """ + commonCropName: String + """ + 3-letter ISO 3166-1 code of the country in which the sample was originally collected + + MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was "collected". + """ + countryOfOriginCode: String + "Human readable name used for display purposes" + defaultDisplayName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "List of donor institutes" + donors: [Donor] + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + """ + Genus name for taxon. Initial uppercase letter required. + + MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required. + + MIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature. + """ + genus: String + """ + The ID which uniquely identifies a germplasm within the given database server +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + """ + germplasmDbId: String + """ + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + """ + germplasmName: String + "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." + germplasmOrigin: [GermplasmOrigin] + """ + The Permanent Unique Identifier which represents a germplasm + + MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + + MIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source + + MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties. + """ + germplasmPUI: String + "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary." + germplasmPreprocessing: String + """ + The code for the institute that maintains the material. + + MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". + """ + instituteCode: String + "The name of the institute that maintains the material" + instituteName: String + "observationUnits" + observationUnits: [ObservationUnit] + "observations" + observations: [Observation] + "parentPedigreeNodes" + parentPedigreeNodes: [PedigreeNode] + """ + The cross name and optional selection history. + + MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'. + """ + pedigree: String + "progenyPedigreeNodes" + progenyPedigreeNodes: [PedigreeNode] + "Germplasm associated with a reference" + reference: Reference + "Germplasm associated with a reference" + referenceSet: ReferenceSet + "samples" + samples: [Sample] + """ + An identifier for the source of the biological material +
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: "mother_accession X father_accession", or, if father is unknown, as "mother_accession X UNKNOWN". For in situ material, the region of provenance may be used when an accession is not available. + """ + seedSource: String + """ + Description of the material source + + MIAPPE V1.1 (DM-56) Material source description - Description of the material source + """ + seedSourceDescription: String + "siblingPedigreeNodes" + siblingPedigreeNodes: [PedigreeNode] + """ + Specific epithet portion of the scientific name in lowercase letters. + + MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: "sp." + + MIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature. + """ + species: String + """ + The authority organization responsible for tracking and maintaining the species name + + MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name. + """ + speciesAuthority: String + "The type of storage this germplasm is kept in at a genebank." + storageTypes: [StorageType] + """ + Subtaxon can be used to store any additional taxonomic identifier. + + MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: "subsp." (for subspecies); "convar." (for convariety); "var." (for variety); "f." (for form); "Group" (for "cultivar group"). + + MIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group). + """ + subtaxa: String + """ + The authority organization responsible for tracking and maintaining the subtaxon information + + MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level. + """ + subtaxaAuthority: String + """ + List of alternative names or IDs used to reference this germplasm + + MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. + """ + synonyms: [Synonym] + """ + The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. + + MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. + """ + taxonIds: [TaxonId] +} + +type GermplasmAttribute { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "General category for the attribute. very similar to Trait class." + attributeCategory: String + "The ID which uniquely identifies this attribute within the given database server" + attributeDbId: String + "A human readable description of this attribute" + attributeDescription: String + "A human readable name for this attribute" + attributeName: String + "The Permanent Unique Identifier of an Attribute, usually in the form of a URI" + attributePUI: String + "attributeValues" + attributeValues: [GermplasmAttributeValue] + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: Method + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: Scale + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: Trait +} + +type GermplasmAttributeValue { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The ID which uniquely identifies this attribute within the given database server" + attribute: GermplasmAttribute + "The ID which uniquely identifies this attribute value within the given database server" + attributeValueDbId: String + "The date the value of this attribute was determined for a given germplasm" + determinedDate: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The ID which uniquely identifies a germplasm within the given database server" + germplasm: Germplasm + "The value of this attribute for a given germplasm" + value: String +} + +type GermplasmAttributeValuesListResponse { + data: [GermplasmAttributeValue] + page: [GermplasmAttributeValue] +} + +type GermplasmAttributeValuesSearchResponse { + data: [GermplasmAttributeValue] + searchResultsDbId: [GermplasmAttributeValue] +} + +type GermplasmAttributesListResponse { + data: [GermplasmAttribute] + page: [GermplasmAttribute] +} + +type GermplasmAttributesSearchResponse { + data: [GermplasmAttribute] + searchResultsDbId: [GermplasmAttribute] +} + +type GermplasmChild { + "The child germplasm" + childGermplasm: Germplasm + """ + The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. + + In a pedigree record, the 'parentType' describes each parent of a particular germplasm. + + In a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. + For example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers + to the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C. + In this way, A could be a male parent to B, but a female parent to C. + """ + parentType: ParentType + "associated pedigreeNode" + pedigreeNode: PedigreeNode +} + +type GermplasmOrigin { + "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + coordinates: [GeoJSON] + "associated germplasm" + germplasm: Germplasm +} + +type GermplasmParent { + "The parent germplasm" + parentGermplasm: Germplasm + """ + The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. + + In a pedigree record, the 'parentType' describes each parent of a particular germplasm. + + In a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. + For example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers + to the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C. + In this way, A could be a male parent to B, but a female parent to C. + """ + parentType: ParentType + "associated pedigreeNode" + pedigreeNode: PedigreeNode +} + +type GermplasmsListResponse { + data: [Germplasm] + page: [Germplasm] +} + +type GermplasmsSearchResponse { + data: [Germplasm] + searchResultsDbId: [Germplasm] +} + +type GrowthFacility { + "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology." + PUI: String + "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out." + description: String + "Growth facility associated with a study" + study: Study +} + +type Image { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'" + copyright: String + "The human readable description of an image." + description: String + "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL." + descriptiveOntologyTerms: [String] + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The unique identifier of an image" + imageDbId: String + "The name of the image file. Might be the same as 'imageName', but could be different." + imageFileName: String + "The size of the image in Bytes." + imageFileSize: Int + "The height of the image in Pixels." + imageHeight: Int + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + imageLocation: GeoJSON + "The human readable name of an image. Might be the same as 'imageFileName', but could be different." + imageName: String + "The date and time the image was taken" + imageTimeStamp: String + "The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server." + imageURL: String + "The width of the image in Pixels." + imageWidth: Int + "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc" + mimeType: String + "The related observation unit identifier, if relevant." + observationUnit: ObservationUnit + "A list of observation Ids this image is associated with, if applicable." + observations: [Observation] +} + +type ImagesListResponse { + data: [Image] + page: [Image] +} + +type ImagesSearchResponse { + data: [Image] + searchResultsDbId: [Image] +} + +type LastUpdate { + "The date and time when this study was last modified" + lastUpdateDbId: String + "Last update associated with a study" + study: Study + timestamp: String + version: String +} + +type List { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The array of DbIds of the BrAPI objects contained in a List" + data: [String] + "Timestamp when the entity was first created" + dateCreated: String + "Timestamp when the entity was last updated" + dateModified: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The unique identifier for a List" + listDbId: String + "Description of a List" + listDescription: String + "Human readable name of a List" + listName: String + "Human readable name of a List Owner. (usually a user or person)" + listOwnerName: String + "The unique identifier for a List Owner. (usually a user or person)" + listOwnerPerson: Person + "The number of elements in a List" + listSize: Int + "The description of where a List originated from" + listSource: String + "A flag to indicate the type of objects that are referenced in a List" + listType: ListType +} + +type ListsListResponse { + data: [List] + page: [List] +} + +type ListsSearchResponse { + data: [List] + searchResultsDbId: [List] +} + +type Location { + "A shortened version of the human readable name for a Location" + abbreviation: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + childLocations: [Location] + "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)" + coordinateDescription: String + "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + coordinates: GeoJSON + """ + [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.' + """ + countryCode: String + """ + The full name of the country where a Location is located +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code. + """ + countryName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)" + environmentType: String + "Describes the level of protection/exposure for things like sun light and wind at a particular Location" + exposure: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + """ + The street address of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + """ + instituteAddress: String + """ + The full name of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + """ + instituteName: String + "The unique identifier for a Location" + locationDbId: String + """ + A human readable name for a Location +
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place. + """ + locationName: String + "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)" + locationType: String + "observationUnits" + observationUnits: [ObservationUnit] + """ + The unique identifier for a Location +
The Parent Location defines the encompassing Location that a smaller Location belongs to. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ + parentLocation: Location + "seedLots" + seedLots: [SeedLot] + "Description of the accessibility of the location (ex. Public, Private)" + siteStatus: String + "Describes the approximate slope (height/distance) of a Location." + slope: String + studies: [Study] + "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)" + topography: String +} + +type LocationsListResponse { + data: [Location] + page: [Location] +} + +type LocationsSearchResponse { + data: [Location] + searchResultsDbId: [Location] +} + +type MarkerPosition { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + """ + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. + """ + linkageGroupName: String + "The ID which uniquely identifies a `GenomeMap`" + map: GenomeMap + "The position of a marker or variant within a `LinkageGroup`" + position: Int + """ + The ID which uniquely identifies a `Variant` within the given database server +
A `Variant` can also represent a Marker + """ + variant: Variant +} + +type MarkerPositionsListResponse { + data: [MarkerPosition] + page: [MarkerPosition] +} + +type MarkerPositionsSearchResponse { + data: [MarkerPosition] + searchResultsDbId: [MarkerPosition] +} + +type MetadataField { + "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." + dataType: DataType + "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"" + fieldAbbreviation: String + "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"" + fieldName: String + "Formats associated with a variant set" + variantSet: VariantSet +} + +type Method { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + """ + Bibliographical reference describing the method. +
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method. + """ + bibliographicalReference: String + """ + Method description +
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number) + """ + description: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation" + formula: String + "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)" + methodClass: String + "Method unique identifier" + methodDbId: String + """ + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + """ + methodName: String + "The Permanent Unique Identifier of a Method, usually in the form of a URI" + methodPUI: String + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference +} + +type MethodsListResponse { + data: [Method] + page: [Method] +} + +type Mutation { + "Create a new BreedingMethod" + createBreedingMethod(breedingMethodInput: BreedingMethodInput): BreedingMethod + "Create a new CrossingProject" + createCrossingProject(commonCropName: String, crossingProjectInput: CrossingProjectInput): CrossingProject + "Create a new Germplasm" + createGermplasm(commonCropName: String, germplasmInput: GermplasmInput): Germplasm + "Create a new GermplasmAttribute" + createGermplasmAttribute(commonCropName: String, germplasmAttributeInput: GermplasmAttributeInput): GermplasmAttribute + "Create a new GermplasmAttributeValue" + createGermplasmAttributeValue(germplasmAttributeValueInput: GermplasmAttributeValueInput): GermplasmAttributeValue + "Create a new Image" + createImage(imageInput: ImageInput): Image + "Create a new List" + createList(listInput: ListInput): List + "Create a new Location" + createLocation(locationInput: LocationInput): Location + "Create a new Method" + createMethod(methodInput: MethodInput): Method + "Create a new Observation" + createObservation(observationInput: ObservationInput): Observation + "Create a new ObservationUnit" + createObservationUnit(observationUnitInput: ObservationUnitInput): ObservationUnit + "Create a new ObservationVariable" + createObservationVariable(commonCropName: String, observationVariableInput: ObservationVariableInput): ObservationVariable + "Create a new Ontology" + createOntology(ontologyInput: OntologyInput): Ontology + "Create a new Person" + createPerson(personInput: PersonInput): Person + "Create a new PlannedCross" + createPlannedCross(plannedCrossInput: PlannedCrossInput): PlannedCross + "Create a new Plate" + createPlate(plateInput: PlateInput): Plate + "Create a new Program" + createProgram(commonCropName: String, programInput: ProgramInput): Program + "Create a new ReferenceSet" + createReferenceSet(commonCropName: String, referenceSetInput: ReferenceSetInput): ReferenceSet + "Create a new Sample" + createSample(sampleInput: SampleInput): Sample + "Create a new Scale" + createScale(scaleInput: ScaleInput): Scale + "Create a new Season" + createSeason(seasonInput: SeasonInput): Season + "Create a new SeedLot" + createSeedLot(seedLotInput: SeedLotInput): SeedLot + "Create a new Study" + createStudy(commonCropName: String, studyInput: StudyInput): Study + "Create a new Trait" + createTrait(traitInput: TraitInput): Trait + "Create a new Trial" + createTrial(commonCropName: String, trialInput: TrialInput): Trial + "Create a new VariantSet" + createVariantSet(variantSetInput: VariantSetInput): VariantSet + "Update the details for an existing BreedingMethod" + updateBreedingMethod(breedingMethodInput: BreedingMethodInput): BreedingMethod + "Update the details for an existing CrossingProject" + updateCrossingProject(commonCropName: String, crossingProjectInput: CrossingProjectInput): CrossingProject + "Update the details for an existing Germplasm" + updateGermplasm(commonCropName: String, germplasmInput: GermplasmInput): Germplasm + "Update the details for an existing GermplasmAttribute" + updateGermplasmAttribute(commonCropName: String, germplasmAttributeInput: GermplasmAttributeInput): GermplasmAttribute + "Update the details for an existing GermplasmAttributeValue" + updateGermplasmAttributeValue(germplasmAttributeValueInput: GermplasmAttributeValueInput): GermplasmAttributeValue + "Update the details for an existing Image" + updateImage(imageInput: ImageInput): Image + "Update the details for an existing List" + updateList(listInput: ListInput): List + "Update the details for an existing Location" + updateLocation(locationInput: LocationInput): Location + "Update the details for an existing Method" + updateMethod(methodInput: MethodInput): Method + "Update the details for an existing Observation" + updateObservation(observationInput: ObservationInput): Observation + "Update the details for an existing ObservationUnit" + updateObservationUnit(observationUnitInput: ObservationUnitInput): ObservationUnit + "Update the details for an existing ObservationVariable" + updateObservationVariable(commonCropName: String, observationVariableInput: ObservationVariableInput): ObservationVariable + "Update the details for an existing Ontology" + updateOntology(ontologyInput: OntologyInput): Ontology + "Update the details for an existing Person" + updatePerson(personInput: PersonInput): Person + "Update the details for an existing PlannedCross" + updatePlannedCross(plannedCrossInput: PlannedCrossInput): PlannedCross + "Update the details for an existing Plate" + updatePlate(plateInput: PlateInput): Plate + "Update the details for an existing Program" + updateProgram(commonCropName: String, programInput: ProgramInput): Program + "Update the details for an existing ReferenceSet" + updateReferenceSet(commonCropName: String, referenceSetInput: ReferenceSetInput): ReferenceSet + "Update the details for an existing Sample" + updateSample(sampleInput: SampleInput): Sample + "Update the details for an existing Scale" + updateScale(scaleInput: ScaleInput): Scale + "Update the details for an existing Season" + updateSeason(seasonInput: SeasonInput): Season + "Update the details for an existing SeedLot" + updateSeedLot(seedLotInput: SeedLotInput): SeedLot + "Update the details for an existing Study" + updateStudy(commonCropName: String, studyInput: StudyInput): Study + "Update the details for an existing Trait" + updateTrait(traitInput: TraitInput): Trait + "Update the details for an existing Trial" + updateTrial(commonCropName: String, trialInput: TrialInput): Trial + "Update the details for an existing VariantSet" + updateVariantSet(variantSetInput: VariantSetInput): VariantSet +} + +type Observation { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The name or identifier of the entity which collected the observation" + collector: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + geoCoordinates: GeoJSON + "The ID which uniquely identifies a germplasm" + germplasm: Germplasm + "images" + images: [Image] + "The ID which uniquely identifies an observation" + observationDbId: String + "The date and time when this observation was made" + observationTimeStamp: String + "The ID which uniquely identifies an observation unit" + observationUnit: ObservationUnit + "The ID which uniquely identifies an observation variable" + observationVariable: ObservationVariable + season: Season + "The ID which uniquely identifies a study within the given database server" + study: Study + "The name or id of the user who uploaded the observation to the database system" + uploadedBy: String + "The value of the data collected as an observation" + value: String +} + +type ObservationUnit { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "the unique identifier for a cross" + cross: Cross + "events" + events: [Event] + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The ID which uniquely identifies a germplasm" + germplasm: Germplasm + "images" + images: [Image] + "The ID which uniquely identifies a location, associated with this study" + location: Location + """ + The ID which uniquely identifies an observation unit + + MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. + """ + observationUnitDbId: String + "A human readable name for an observation unit" + observationUnitName: String + """ + A Permanent Unique Identifier for an observation unit + + MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible. + """ + observationUnitPUI: String + """ + All positional and layout information related to this Observation Unit + + MIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) + or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. + Levels of observation must be consistent with those listed in the Study section. + """ + observationUnitPosition: [ObservationUnitPosition] + "observations" + observations: [Observation] + "The ID which uniquely identifies a program" + program: Program + "samples" + samples: [Sample] + "The unique identifier for the originating Seed Lot" + seedLot: SeedLot + "The ID which uniquely identifies a study within the given database server" + study: Study + """ + List of treatments applied to an observation unit. + + MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. + """ + treatments: [Treatment] + "The ID which uniquely identifies a trial" + trial: Trial +} + +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +type ObservationUnitLevel implements ObservationUnitHierarchyLevel { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +""" +Observation levels indicate the granularity level at which the measurements are taken. `levelName` +defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. +`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are +at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify +this observation unit by each level of the hierarchy where it exists. + +For more information on Observation Levels, please review the Observation Levels documentation. + +**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +""" +type ObservationUnitLevelRelationship { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int + """ + The an observation unit +
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. +
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. + """ + observationUnit: ObservationUnit +} + +type ObservationUnitPosition { + "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" + entryType: EntryType + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + geoCoordinates: [GeoJSON] + """ + The exact level and level code of an observation unit. + + For more information on Observation Levels, please review the Observation Levels documentation. + + MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. + The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). + Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." + """ + observationLevel: ObservationUnitLevel + """ + Observation levels indicate the granularity level at which the measurements are taken. `levelName` + defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. + `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are + at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify + this observation unit by each level of the hierarchy where it exists. + + For more information on Observation Levels, please review the Observation Levels documentation. + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + """ + observationLevelRelationships: [ObservationUnitLevelRelationship] + "associated observation Unit" + observationUnit: ObservationUnit + "The X position coordinate for an observation unit. Different systems may use different coordinate systems." + positionCoordinateX: String + """ + The type of positional coordinate used. Must be one of the following values + + LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + PLANTED_ROW - The physical planted row number + + PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + + GRID_ROW - The row index number of a square grid overlay + + GRID_COL - The column index number of a square grid overlay + + MEASURED_ROW - The distance in meters from a defined 0-th row + + MEASURED_COL - The distance in meters from a defined 0-th column + """ + positionCoordinateXType: PositionCoordinateXType + "The Y position coordinate for an observation unit. Different systems may use different coordinate systems." + positionCoordinateY: String + """ + The type of positional coordinate used. Must be one of the following values + + LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + PLANTED_ROW - The physical planted row number + + PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + + GRID_ROW - The row index number of a square grid overlay + + GRID_COL - The column index number of a square grid overlay + + MEASURED_ROW - The distance in meters from a defined 0-th row + + MEASURED_COL - The distance in meters from a defined 0-th column + """ + positionCoordinateYType: PositionCoordinateYType +} + +type ObservationUnitsListResponse { + data: [ObservationUnit] + page: [ObservationUnit] +} + +type ObservationUnitsSearchResponse { + data: [ObservationUnit] + searchResultsDbId: [ObservationUnit] +} + +type ObservationVariable implements Variable { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: Method + """ + Variable unique identifier + + MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + """ + observationVariableDbId: String + """ + Variable name (usually a short name) + + MIAPPE V1.1 (DM-84) Variable name - Name of the variable. + """ + observationVariableName: String + "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI" + observationVariablePUI: String + "observations" + observations: [Observation] + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: Scale + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + studies: [Study] + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: Trait +} + +type ObservationVariablesListResponse { + data: [ObservationVariable] + page: [ObservationVariable] +} + +type ObservationVariablesSearchResponse { + data: [ObservationVariable] + searchResultsDbId: [ObservationVariable] +} + +type ObservationsListResponse { + data: [Observation] + page: [Observation] +} + +type ObservationsSearchResponse { + data: [Observation] + searchResultsDbId: [Observation] +} + +type OntologiesListResponse { + data: [Ontology] + page: [Ontology] +} + +type Ontology { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Ontology's list of authors (no specific format)" + authors: String + "Ontology copyright" + copyright: String + "Human readable description of Ontology" + description: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Ontology licence" + licence: String + "Ontology database unique identifier" + ontologyDbId: String + "Ontology name" + ontologyName: String + "Ontology version (no specific format)" + version: String +} + +type OntologyReference { + "links to various ontology documentation" + documentationLinks: [DocumentationLink] + "The Ontology for this reference" + ontology: Ontology + "The ID which uniquely identifies a ontology reference" + ontologyReferenceDbId: String + "Ontology version (no specific format)" + version: String +} + +type OntologyTerm { + "Species associated with a reference" + reference: Reference + "Species associated with a referenceSet" + referenceSet: ReferenceSet + "Ontology term - the label of the ontology term the termId is pointing to." + term: String + "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation." + termURI: String +} + +type PageInfo { + currentPage: Int + pageSize: Int + totalCount: Int + totalPages: Int +} + +type Pagination { + "Pagination associated with an alleleMatrix" + alleleMatrix: AlleleMatrix + "The dimension of the matrix being paginated" + dimension: Dimension + "the requested page number (zero indexed)" + page: Int + "the maximum number of elements per page in this dimension of the matrix" + pageSize: Int + "The total number of elements that are available on the server and match the requested query parameters." + totalCount: Int + """ + The total number of pages of elements available on the server. This should be calculated with the following formula. +
totalPages = CEILING( totalCount / requested_page_size) + """ + totalPages: Int +} + +type PedigreeNode { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The unique identifier for the breeding method used to create this germplasm" + breedingMethod: BreedingMethod + "The crossing project used to generate this germplasm" + crossingProject: CrossingProject + "The year the parents were originally crossed" + crossingYear: Int + "Human readable name used for display purposes" + defaultDisplayName: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The code representing the family of this germplasm" + familyCode: String + "The ID which uniquely identifies a germplasm" + germplasm: Germplasm + """ + A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. +
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. +
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. + """ + parents: [GermplasmParent] + "The ID which uniquely identifies a pedigree node" + pedigreeNodeDbId: String + "The string representation of the pedigree for this germplasm in PURDY notation" + pedigreeString: String + """ + A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. +
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows + the type of parent this germplasm is to each of the child germplasm references. +
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. + """ + progeny: [GermplasmChild] + """ + A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. +
Siblings share at least one parent with the given germplasm. +
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. + """ + siblings: [Germplasm] +} + +type PedigreeNodesListResponse { + data: [PedigreeNode] + page: [PedigreeNode] +} + +type PedigreeNodesSearchResponse { + data: [PedigreeNode] + searchResultsDbId: [PedigreeNode] +} + +type Person { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "description of this person" + description: String + "email address for this person" + emailAddress: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Persons first name" + firstName: String + "Persons last name" + lastName: String + lists: [List] + "physical address of this person" + mailingAddress: String + "Persons middle name" + middleName: String + "Unique ID for a person" + personDbId: String + "phone number of this person" + phoneNumber: String + programs: [Program] + "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system." + userID: String +} + +type PersonsListResponse { + data: [Person] + page: [Person] +} + +type PersonsSearchResponse { + data: [Person] + searchResultsDbId: [Person] +} + +type PlannedCross { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "the type of cross" + crossType: CrossType + "crosses" + crosses: [Cross] + "the unique identifier for a crossing project" + crossingProject: CrossingProject + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "the first parent used in the cross" + parent1: CrossParent + "the second parent used in the cross" + parent2: CrossParent + "the unique identifier for a planned cross" + plannedCrossDbId: String + "the human readable name for a planned cross" + plannedCrossName: String + "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')." + status: PlannedCrossStatus +} + +type PlannedCrossesListResponse { + data: [PlannedCross] + page: [PlannedCross] +} + +type PlannedCrossesSearchResponse { + data: [PlannedCross] + searchResultsDbId: [PlannedCross] +} + +type Plate { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "A unique identifier physically attached to a `Plate`" + plateBarcode: String + "The ID which uniquely identifies a `Plate`" + plateDbId: String + "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format" + plateFormat: PlateFormat + "A human readable name for a `Plate`" + plateName: String + "The ID which uniquely identifies a `Program` within the given database server" + program: Program + "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + sampleType: SampleType + "samples" + samples: [Sample] + "The ID which uniquely identifies a `Study` within the given database server" + study: Study + "The ID which uniquely identifies a `Trial` within the given database server" + trial: Trial +} + +type PlatesListResponse { + data: [Plate] + page: [Plate] +} + +type PlatesSearchResponse { + data: [Plate] + searchResultsDbId: [Plate] +} + +type PollinationEvent { + "Pollination events associated with a cross" + cross: Cross + "The unique identifier for this pollination event" + pollinationNumber: String + "True if the pollination was successful" + pollinationSuccessful: Boolean + "The timestamp when the pollination took place" + pollinationTimeStamp: String +} + +type Program { + "A shortened version of the human readable name for a Program" + abbreviation: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Common name for the crop which this program is for" + commonCropName: String + "crossingProjects" + crossingProjects: [CrossingProject] + "A URL to the human readable documentation of an object" + documentationURL: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Information describing the grant or funding source for this program" + fundingInformation: String + "The unique identifier of the program leader" + leadPerson: Person + "The primary objective of the program" + objective: String + "observationUnits" + observationUnits: [ObservationUnit] + "plates" + plates: [Plate] + "The ID which uniquely identifies the program" + programDbId: String + "Human readable name of the program" + programName: String + """ + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding + """ + programType: ProgramType + "samples" + samples: [Sample] + "seedLots" + seedLots: [SeedLot] + trials: [Trial] +} + +type ProgramsListResponse { + data: [Program] + page: [Program] +} + +type ProgramsSearchResponse { + data: [Program] + searchResultsDbId: [Program] +} + +type Publication { + publicationPUI: String + publicationReference: String + "Publications associated with a trial" + trial: Trial +} + +type Query { + "Returns a BreedingMethod object by id" + breedingMethod(breedingMethodDbId: ID, commonCropName: String): BreedingMethod + "Returns BreedingMethod objects" + breedingMethods(breedingMethodsInput: BreedingMethodsInput): BreedingMethodsListResponse + "Returns a CallSet object by id" + callSet(callSetDbId: ID, commonCropName: String): CallSet + "Returns CallSet objects" + callSets(callSetsInput: CallSetsInput, paging: PageInput): CallSetsListResponse + "Returns CallSet objects" + callSetsSearch(callSetInput: CallSetsInput): CallSetsSearchResponse + "Returns Call objects" + calls(callsInput: CallsInput, paging: PageInput): CallsListResponse + "Returns Call objects" + callsSearch(callInput: CallsInput): CallsSearchResponse + "Returns Cross objects" + crosses(crossesInput: CrossesInput, paging: PageInput): CrossesListResponse + "Returns a CrossingProject object by id" + crossingProject(commonCropName: String, crossingProjectDbId: ID): CrossingProject + "Returns CrossingProject objects" + crossingProjects(crossingProjectsInput: CrossingProjectsInput, paging: PageInput): CrossingProjectsListResponse + "Returns CrossingProject objects" + crossingProjectsSearch(crossingProjectInput: CrossingProjectsInput): CrossingProjectsSearchResponse + "Returns Event objects" + events(eventsInput: EventsInput, paging: PageInput): EventsListResponse + "Returns Event objects" + eventsSearch(eventInput: EventsInput): EventsSearchResponse + "Returns a GenomeMap object by id" + genomeMap(commonCropName: String, genomeMapDbId: ID): GenomeMap + "Returns GenomeMap objects" + genomeMaps(genomeMapsInput: GenomeMapsInput, paging: PageInput): GenomeMapsListResponse + "Returns GenomeMap objects" + genomeMapsSearch(genomeMapInput: GenomeMapsInput): GenomeMapsSearchResponse + "Returns a Germplasm object by id" + germplasm(commonCropName: String, germplasmDbId: ID): Germplasm + "Returns a GermplasmAttribute object by id" + germplasmAttribute(commonCropName: String, germplasmAttributeDbId: ID): GermplasmAttribute + "Returns a GermplasmAttributeValue object by id" + germplasmAttributeValue(commonCropName: String, germplasmAttributeValueDbId: ID): GermplasmAttributeValue + "Returns GermplasmAttributeValue objects" + germplasmAttributeValues(germplasmAttributeValuesInput: GermplasmAttributeValuesInput, paging: PageInput): GermplasmAttributeValuesListResponse + "Returns GermplasmAttributeValue objects" + germplasmAttributeValuesSearch(germplasmAttributeValueInput: GermplasmAttributeValuesInput): GermplasmAttributeValuesSearchResponse + "Returns GermplasmAttribute objects" + germplasmAttributes(germplasmAttributesInput: GermplasmAttributesInput, paging: PageInput): GermplasmAttributesListResponse + "Returns GermplasmAttribute objects" + germplasmAttributesSearch(germplasmAttributeInput: GermplasmAttributesInput): GermplasmAttributesSearchResponse + "Returns Germplasm objects" + germplasms(germplasmsInput: GermplasmsInput, paging: PageInput): GermplasmsListResponse + "Returns Germplasm objects" + germplasmsSearch(germplasmInput: GermplasmsInput): GermplasmsSearchResponse + "Returns a Image object by id" + image(commonCropName: String, imageDbId: ID): Image + "Returns Image objects" + images(imagesInput: ImagesInput, paging: PageInput): ImagesListResponse + "Returns Image objects" + imagesSearch(imageInput: ImagesInput): ImagesSearchResponse + "Returns a List object by id" + list(commonCropName: String, listDbId: ID): List + "Returns List objects" + lists(listsInput: ListsInput, paging: PageInput): ListsListResponse + "Returns List objects" + listsSearch(listInput: ListsInput): ListsSearchResponse + "Returns a Location object by id" + location(commonCropName: String, locationDbId: ID): Location + "Returns Location objects" + locations(locationsInput: LocationsInput, paging: PageInput): LocationsListResponse + "Returns Location objects" + locationsSearch(locationInput: LocationsInput): LocationsSearchResponse + "Returns MarkerPosition objects" + markerPositions(markerPositionsInput: MarkerPositionsInput, paging: PageInput): MarkerPositionsListResponse + "Returns MarkerPosition objects" + markerPositionsSearch(markerPositionInput: MarkerPositionsInput): MarkerPositionsSearchResponse + "Returns a Method object by id" + method(commonCropName: String, methodDbId: ID): Method + "Returns Method objects" + methods(methodsInput: MethodsInput, paging: PageInput): MethodsListResponse + "Returns a Observation object by id" + observation(commonCropName: String, observationDbId: ID): Observation + "Returns a ObservationUnit object by id" + observationUnit(commonCropName: String, observationUnitDbId: ID): ObservationUnit + "Returns ObservationUnit objects" + observationUnits(observationUnitsInput: ObservationUnitsInput, paging: PageInput): ObservationUnitsListResponse + "Returns ObservationUnit objects" + observationUnitsSearch(observationUnitInput: ObservationUnitsInput): ObservationUnitsSearchResponse + "Returns a ObservationVariable object by id" + observationVariable(commonCropName: String, observationVariableDbId: ID): ObservationVariable + "Returns ObservationVariable objects" + observationVariables(observationVariablesInput: ObservationVariablesInput, paging: PageInput): ObservationVariablesListResponse + "Returns ObservationVariable objects" + observationVariablesSearch(observationVariableInput: ObservationVariablesInput): ObservationVariablesSearchResponse + "Returns Observation objects" + observations(observationsInput: ObservationsInput, paging: PageInput): ObservationsListResponse + "Returns Observation objects" + observationsSearch(observationInput: ObservationsInput): ObservationsSearchResponse + "Returns Ontology objects" + ontologies(ontologiesInput: OntologiesInput, paging: PageInput): OntologiesListResponse + "Returns a Ontology object by id" + ontology(commonCropName: String, ontologyDbId: ID): Ontology + "Returns a PedigreeNode object by id" + pedigreeNode(commonCropName: String, pedigreeNodeDbId: ID): PedigreeNode + "Returns PedigreeNode objects" + pedigreeNodes(paging: PageInput, pedigreeNodesInput: PedigreeNodesInput): PedigreeNodesListResponse + "Returns PedigreeNode objects" + pedigreeNodesSearch(pedigreeNodeInput: PedigreeNodesInput): PedigreeNodesSearchResponse + "Returns a Person object by id" + person(commonCropName: String, personDbId: ID): Person + "Returns Person objects" + persons(paging: PageInput, personsInput: PersonsInput): PersonsListResponse + "Returns Person objects" + personsSearch(personInput: PersonsInput): PersonsSearchResponse + "Returns PlannedCross objects" + plannedCrosses(paging: PageInput, plannedCrossesInput: PlannedCrossesInput): PlannedCrossesListResponse + "Returns PlannedCross objects" + plannedCrossesSearch(plannedCrossInput: PlannedCrossesInput): PlannedCrossesSearchResponse + "Returns a Plate object by id" + plate(commonCropName: String, plateDbId: ID): Plate + "Returns Plate objects" + plates(paging: PageInput, platesInput: PlatesInput): PlatesListResponse + "Returns Plate objects" + platesSearch(plateInput: PlatesInput): PlatesSearchResponse + "Returns a Program object by id" + program(commonCropName: String, programDbId: ID): Program + "Returns Program objects" + programs(paging: PageInput, programsInput: ProgramsInput): ProgramsListResponse + "Returns Program objects" + programsSearch(programInput: ProgramsInput): ProgramsSearchResponse + "Returns a Reference object by id" + reference(commonCropName: String, referenceDbId: ID): Reference + "Returns a ReferenceSet object by id" + referenceSet(commonCropName: String, referenceSetDbId: ID): ReferenceSet + "Returns ReferenceSet objects" + referenceSets(paging: PageInput, referenceSetsInput: ReferenceSetsInput): ReferenceSetsListResponse + "Returns ReferenceSet objects" + referenceSetsSearch(referenceSetInput: ReferenceSetsInput): ReferenceSetsSearchResponse + "Returns Reference objects" + references(paging: PageInput, referencesInput: ReferencesInput): ReferencesListResponse + "Returns Reference objects" + referencesSearch(referenceInput: ReferencesInput): ReferencesSearchResponse + "Returns a Sample object by id" + sample(commonCropName: String, sampleDbId: ID): Sample + "Returns Sample objects" + samples(paging: PageInput, samplesInput: SamplesInput): SamplesListResponse + "Returns Sample objects" + samplesSearch(sampleInput: SamplesInput): SamplesSearchResponse + "Returns a Scale object by id" + scale(commonCropName: String, scaleDbId: ID): Scale + "Returns Scale objects" + scales(paging: PageInput, scalesInput: ScalesInput): ScalesListResponse + "Returns a Season object by id" + season(commonCropName: String, seasonDbId: ID): Season + "Returns Season objects" + seasons(paging: PageInput, seasonsInput: SeasonsInput): SeasonsListResponse + "Returns Season objects" + seasonsSearch(seasonInput: SeasonsInput): SeasonsSearchResponse + "Returns a SeedLot object by id" + seedLot(commonCropName: String, seedLotDbId: ID): SeedLot + "Returns SeedLot objects" + seedLots(paging: PageInput, seedLotsInput: SeedLotsInput): SeedLotsListResponse + "Returns SeedLot objects" + seedLotsSearch(seedLotInput: SeedLotsInput): SeedLotsSearchResponse + "Returns Study objects" + studies(paging: PageInput, studiesInput: StudiesInput): StudiesListResponse + "Returns Study objects" + studiesSearch(studyInput: StudiesInput): StudiesSearchResponse + "Returns a Study object by id" + study(commonCropName: String, studyDbId: ID): Study + "Returns a Trait object by id" + trait(commonCropName: String, traitDbId: ID): Trait + "Returns Trait objects" + traits(paging: PageInput, traitsInput: TraitsInput): TraitsListResponse + "Returns a Trial object by id" + trial(commonCropName: String, trialDbId: ID): Trial + "Returns Trial objects" + trials(paging: PageInput, trialsInput: TrialsInput): TrialsListResponse + "Returns Trial objects" + trialsSearch(trialInput: TrialsInput): TrialsSearchResponse + "Returns a Variant object by id" + variant(commonCropName: String, variantDbId: ID): Variant + "Returns a VariantSet object by id" + variantSet(commonCropName: String, variantSetDbId: ID): VariantSet + "Returns VariantSet objects" + variantSets(paging: PageInput, variantSetsInput: VariantSetsInput): VariantSetsListResponse + "Returns VariantSet objects" + variantSetsSearch(variantSetInput: VariantSetsInput): VariantSetsSearchResponse + "Returns Variant objects" + variants(paging: PageInput, variantsInput: VariantsInput): VariantsListResponse + "Returns Variant objects" + variantsSearch(variantInput: VariantsInput): VariantsSearchResponse +} + +type Reference { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Common name for the crop" + commonCropName: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases." + isDerived: Boolean + "The length of this `Reference` sequence." + length: Int + "The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)." + md5checksum: String + "The unique identifier for a `Reference`" + referenceDbId: String + "The human readable name of a `Reference` within a `ReferenceSet`." + referenceName: String + "The unique identifier for a `ReferenceSet`" + referenceSet: ReferenceSet + "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`." + sourceAccessions: [String] + "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from." + sourceDivergence: Float + "All known corresponding Germplasm" + sourceGermplasm: [Germplasm] + "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI." + sourceURI: String + "An ontology term describing an attribute." + species: OntologyTerm + "variants" + variants: [Variant] +} + +type ReferenceSet { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`." + assemblyPUI: String + "Common name for the crop" + commonCropName: String + "Optional free text description of this reference set." + description: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`)." + isDerived: Boolean + """ + Order-independent MD5 checksum which identifies this `ReferenceSet`. + + To compute this checksum, make a list of `Reference.md5checksum` for all + `Reference` s in this set. Then sort that list, and take the MD5 hash of + all the strings concatenated together. Express the hash as a lower-case + hexadecimal string. + """ + md5checksum: String + "The unique identifier for a ReferenceSet" + referenceSetDbId: String + "The human readable name of a ReferenceSet" + referenceSetName: String + "references" + references: Reference + "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`." + sourceAccessions: [String] + "All known corresponding Germplasm" + sourceGermplasm: [Germplasm] + "Specifies a FASTA format file/string." + sourceURI: String + "An ontology term describing an attribute." + species: OntologyTerm + "variantSets" + variantSets: [VariantSet] + "variants" + variants: [Variant] +} + +type ReferenceSetsListResponse { + data: [ReferenceSet] + page: [ReferenceSet] +} + +type ReferenceSetsSearchResponse { + data: [ReferenceSet] + searchResultsDbId: [ReferenceSet] +} + +type ReferencesListResponse { + data: [Reference] + page: [Reference] +} + +type ReferencesSearchResponse { + data: [Reference] + searchResultsDbId: [Reference] +} + +type Sample { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + callSets: [CallSet] + "The Column identifier for this `Sample` location in the `Plate`" + column: Int + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The ID which uniquely identifies a `Germplasm`" + germplasm: Germplasm + "The ID which uniquely identifies an `ObservationUnit`" + observationUnit: ObservationUnit + "The ID which uniquely identifies a `Plate` of `Sample`" + plate: Plate + "The ID which uniquely identifies a `Program` within the given database server" + program: Program + "The Row identifier for this `Sample` location in the `Plate`" + row: String + "A unique identifier physically attached to the `Sample`" + sampleBarcode: String + """ + The ID which uniquely identifies a `Sample` +
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. + """ + sampleDbId: String + """ + Description of a `Sample` +
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. + """ + sampleDescription: String + "The ID which uniquely identifies a group of `Samples`" + sampleGroupId: String + "The human readable name of the `Sample`" + sampleName: String + """ + A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc) +
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. + """ + samplePUI: String + """ + The date and time a `Sample` was collected from the field +
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested + """ + sampleTimestamp: String + "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc" + sampleType: String + "The ID which uniquely identifies a `Study` within the given database server" + study: Study + "The name or identifier of the entity which took the `Sample` from the field" + takenBy: String + """ + The type of tissue sampled. ex. 'Leaf', 'Root', etc. +
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology). + """ + tissueType: String + "The ID which uniquely identifies a `Trial` within the given database server" + trial: Trial + "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`." + well: String +} + +type SamplesListResponse { + data: [Sample] + page: [Sample] +} + +type SamplesSearchResponse { + data: [Sample] + searchResultsDbId: [Sample] +} + +type Scale { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + """ +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ """ + dataType: DataType + "For numerical, number of decimal places to be reported" + decimalPlaces: Int + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID." + scaleDbId: String + """ + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + """ + scaleName: String + "The Permanent Unique Identifier of a Scale, usually in the form of a URI" + scalePUI: String + """ + This field can be used to describe the units used for this scale. This should be the abbreviated + form of the units, intended to be displayed with every value using this scale. Usually this only + applies when `dataType` is Numeric, but could also be included for other dataTypes when applicable. + """ + units: String + validValues: ValidValues +} + +type ScalesListResponse { + data: [Scale] + page: [Scale] +} + +type Season { + "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'" + seasonDbId: String + "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc." + seasonName: String + "The 4 digit year of the season." + year: Int +} + +type SeasonsListResponse { + data: [Season] + page: [Season] +} + +type SeasonsSearchResponse { + data: [Season] + searchResultsDbId: [Season] +} + +type SeedLot { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)." + amount: Float + """ + The mixture of germplasm present in the seed lot. +
+ If this seed lot only contains a single germplasm, the response should contain the name + and DbId of that germplasm with a mixturePercentage value of 100 +
+ If the seed lot contains a mixture of different germplasm, the response should contain + the name and DbId every germplasm present. The mixturePercentage field should contain + the ratio of each germplasm in the total mixture. All of the mixturePercentage values + in this array should sum to equal 100. + """ + contentMixture: [ContentMixture] + "The time stamp for when this seed lot was created" + createdDate: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "fromSeedLotTransactions" + fromSeedLotTransactions: [SeedLotTransaction] + "The timestamp for the last update to this Seed Lot (including transactions)" + lastUpdated: String + "The unique identifier for a Location" + location: Location + "observationUnits" + observationUnits: [ObservationUnit] + "The unique DbId of the breeding program this Seed Lot belongs to" + program: Program + "Unique DbId for the Seed Lot" + seedLotDbId: String + "A general description of this Seed Lot" + seedLotDescription: String + "A human readable name for this Seed Lot" + seedLotName: String + "The description of the source where this material was originally collected (wild, nursery, etc)" + sourceCollection: String + "Description the storage location" + storageLocation: String + "toSeedLotTransactions" + toSeedLotTransactions: [SeedLotTransaction] + "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)" + units: String +} + +type SeedLotTransaction { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)." + amount: Float + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "The identifier for the Seed Lot being transferred out of" + fromSeedLot: SeedLot + "The identifier for the Seed Lot being transferred into" + toSeedLot: SeedLot + "Unique DbId for the Seed Lot Transaction" + transactionDbId: String + "A general description of this Seed Lot Transaction" + transactionDescription: String + "The time stamp for when the transaction occurred" + transactionTimestamp: String + "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)" + units: String +} + +type SeedLotsListResponse { + data: [SeedLot] + page: [SeedLot] +} + +type SeedLotsSearchResponse { + data: [SeedLot] + searchResultsDbId: [SeedLot] +} + +type StorageType { + """ + The 2 digit code representing the type of storage this germplasm is kept in at a genebank. + + MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) + + 10) Seed collection + 11) Short term + 12) Medium term + 13) Long term + 20) Field collection + 30) In vitro collection + 40) Cryo-preserved collection + 50) DNA collection + 99) Other (elaborate in REMARKS field) + """ + code: StorageTypeCode + "A supplemental text description of the storage type" + description: String + "associated germplasm" + germplasm: Germplasm +} + +type StudiesListResponse { + data: [Study] + page: [Study] +} + +type StudiesSearchResponse { + data: [Study] + searchResultsDbId: [Study] +} + +type Study { + "A flag to indicate if a Study is currently active and ongoing" + active: Boolean + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + callSets: [CallSet] + "Common name for the crop associated with this study" + commonCropName: String + "List of contact entities associated with this study" + contacts: [Contact] + "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study." + culturalPractices: String + "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data." + dataLinks: [DataLink] + "A URL to the human readable documentation of an object" + documentationURL: String + """ + The date the study ends + + MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended + """ + endDate: String + """ + Environmental parameters that were kept constant throughout the study and did not change between observation units. + + MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + """ + environmentParameters: [EnvironmentParameters] + "events" + events: [Event] + "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" + experimentalDesign: ExperimentalDesign + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "Short description of the facility in which the study was carried out." + growthFacility: GrowthFacility + "The date and time when this study was last modified" + lastUpdate: LastUpdate + "The usage license associated with the study data" + license: String + "The unique identifier for a Location" + location: Location + """ + Observation levels indicate the granularity level at which the measurements are taken. `levelName` + defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. + `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are + at the bottom of the hierarchy (ie plant > 6). + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationLevels: [ObservationUnitHierarchyLevel] + "observationUnits" + observationUnits: [ObservationUnit] + "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study." + observationUnitsDescription: String + """ + The list of Observation Variables being used in this study. + + This list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. + """ + observationVariables: [ObservationVariable] + "observations" + observations: [Observation] + "plates" + plates: [Plate] + "samples" + samples: [Sample] + "List of seasons over which this study was performed." + seasons: [String] + """ + The date this study started + + MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started + """ + startDate: String + "A short human readable code for a study" + studyCode: String + """ + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + """ + studyDbId: String + """ + The description of this study + + MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study + """ + studyDescription: String + """ + The human readable name for a study + + MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study + """ + studyName: String + "A permanent unique identifier associated with this study data. For example, a URI or DOI" + studyPUI: String + "The type of study being performed. ex. \"Yield Trial\", etc" + studyType: String + "The ID which uniquely identifies a trial" + trial: Trial + "variantSets" + variantSets: [VariantSet] +} + +type Synonym { + "associated germplasm" + germplasm: Germplasm + "Alternative name or ID used to reference this germplasm" + synonym: String + "A descriptive classification for this synonym" + type: String +} + +type TaxonId { + "associated germplasm" + germplasm: Germplasm + "The human readable name of the taxonomy provider" + sourceName: String + "The identifier (name, ID, URI) of a particular taxonomy within the source provider" + taxonId: String +} + +type Trait { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention." + alternativeAbbreviations: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"" + attribute: String + """ + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + """ + attributePUI: String + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"" + entity: String + """ + The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI +
A Trait can be decomposed as "Trait" = "Entity" + "Attribute", the Entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" + """ + entityPUI: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "A shortened version of the human readable name for a Trait" + mainAbbreviation: String + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReference + "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Other trait names" + synonyms: [String] + """ + A classification to describe the type of trait and the context it should be considered in. +
examples- "morphological", "phenological", "agronomical", "physiological", "abiotic stress", "biotic stress", "biochemical", "quality traits", "fertility", etc. + """ + traitClass: String + "The ID which uniquely identifies a trait" + traitDbId: String + "The description of a trait" + traitDescription: String + """ + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + """ + traitName: String + "The Permanent Unique Identifier of a Trait, usually in the form of a URI" + traitPUI: String +} + +type TraitsListResponse { + data: [Trait] + page: [Trait] +} + +type Treatment { + """ + The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc + + MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. + """ + factor: String + """ + The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc + + MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. + """ + modality: String + "associated observation Unit" + observationUnit: ObservationUnit +} + +type Trial { + "A flag to indicate if a Trial is currently active and ongoing" + active: Boolean + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + "Common name for the crop associated with this trial" + commonCropName: String + "List of contact entities associated with this trial" + contacts: [Contact] + "License and citation information for the data in this trial" + datasetAuthorships: [DatasetAuthorships] + "A URL to the human readable documentation of an object" + documentationURL: String + "The date this trial ends" + endDate: String + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "observationUnits" + observationUnits: [ObservationUnit] + "plates" + plates: [Plate] + "A program identifier to search for" + program: Program + "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." + publications: [Publication] + "samples" + samples: [Sample] + "The date this trial started" + startDate: String + studies: [Study] + """ + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + """ + trialDbId: String + """ + The human readable description of a trial + + MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail. + """ + trialDescription: String + """ + The human readable name of a trial + + MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation. + """ + trialName: String + "A permanent identifier for a trial. Could be DOI or other URI formatted identifier." + trialPUI: String +} + +type TrialsListResponse { + data: [Trial] + page: [Trial] +} + +type TrialsSearchResponse { + data: [Trial] + searchResultsDbId: [Trial] +} + +type ValidValues { + "List of possible values with optional labels" + categories: [ValidValuesCategory] + "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC." + maximumValue: String + "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC." + minimumValue: String + "associated scale" + scale: Scale +} + +type ValidValuesCategory { + "A text label for a category" + label: String + "associated valid values" + validValues: ValidValues + "The actual value for a category" + value: String +} + +type Variant { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + alleleMatrices: [AlleleMatrix] + "Set of Analysis descriptors for this VariantSet" + analysis: [String] + calls: [Call] + "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)." + ciend: [Int] + """ + In the case of structural variants, start and end of the variant may not + be known with an exact base position. "cipos" provides an interval with + high confidence for the start position. The interval is provided by 0 or + 2 signed integers which are added to the start position. + Based on the use in VCF v4.2 + """ + cipos: [Int] + "The timestamp when this variant was created." + created: String + """ + This field is optional and may be ignored if there is no relevant map or reference to be associated with. +
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated + by `start + referenceBases.length`. + """ + end: Int + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value." + filtersApplied: Boolean + "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record." + filtersFailed: [String] + "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS." + filtersPassed: Boolean + "markerPositions" + markerPositions: [MarkerPosition] + "The unique identifier for a Reference" + reference: Reference + "The reference bases for this variant. They start at the given start position." + referenceBases: String + "The unique identifier for a ReferenceSet" + referenceSet: ReferenceSet + """ + This field is optional and may be ignored if there is no relevant map or reference to be associated with. +
The start position at which this variant occurs (0-based). This corresponds to the first base of the string + of reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning + the join of circular genomes are represented as two variants one on each side of the join (position 0). + """ + start: Int + "Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2" + svlen: Int + "The time at which this variant was last updated." + updated: String + "The ID which uniquely identifies a `Variant`" + variantDbId: String + "A human readable name associated with a `Variant`" + variantNames: [String] + "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." + variantSet: VariantSet + """ + The "variant_type" is used to denote e.g. structural variants. + Examples: + DUP : duplication of sequence following "start" + DEL : deletion of sequence following "start" + """ + variantType: String +} + +type VariantSet { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfo + alleleMatrices: [AlleleMatrix] + "Set of Analysis descriptors for this VariantSet" + analysis: [Analysis] + """ + When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. +
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) +
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. + """ + availableFormats: [AvailableFormat] + "The number of CallSets included in this VariantSet" + callSetCount: Int + callSets: [CallSet] + calls: [Call] + "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI." + externalReferences: [ExternalReference] + """ + The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. +
When possible, these field names and abbreviations should follow the VCF standard + """ + metadataFields: [MetadataField] + "The ID of the reference set that describes the sequences used by the variants in this set." + referenceSet: ReferenceSet + "The ID of the dataset this variant set belongs to." + study: Study + "The number of Variants included in this VariantSet" + variantCount: Int + "The unique identifier for a VariantSet" + variantSetDbId: String + "The human readable name for a VariantSet" + variantSetName: String + "variants" + variants: [Variant] +} + +type VariantSetsListResponse { + data: [VariantSet] + page: [VariantSet] +} + +type VariantSetsSearchResponse { + data: [VariantSet] + searchResultsDbId: [VariantSet] +} + +type VariantsListResponse { + data: [Variant] + page: [Variant] +} + +type VariantsSearchResponse { + data: [Variant] + searchResultsDbId: [Variant] +} + +""" +MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. + +100) Wild +110) Natural +120) Semi-natural/wild +130) Semi-natural/sown +200) Weedy +300) Traditional cultivar/landrace +400) Breeding/research material +410) Breeders line +411) Synthetic population +412) Hybrid +413) Founder stock/base population +414) Inbred line (parent of hybrid cultivar) +415) Segregating population +416) Clonal selection +420) Genetic stock +421) Mutant (e.g. induced/insertion mutants, tilling populations) +422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) +423) Other genetic stocks (e.g. mapping populations) +500) Advanced or improved cultivar (conventional breeding methods) +600) GMO (by genetic engineering) +999) Other (Elaborate in REMARKS field) +""" +enum BiologicalStatusOfAccessionCode { + N100 + N110 + N120 + N130 + N200 + N300 + N400 + N410 + N411 + N412 + N413 + N414 + N415 + N416 + N420 + N421 + N422 + N423 + N500 + N600 + N999 +} + +enum CrossStatus { + DONE + SKIPPED + TODO +} + +"The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'." +enum CrossType { + BIPARENTAL + BULK + BULK_OPEN_POLLINATED + BULK_SELFED + DOUBLE_HAPLOID + OPEN_POLLINATED + SELF +} + +"dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)" +enum DataFormat { + DartSeq + Hapmap + JSON + VCF + tabular +} + +"The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." +enum DataType { + boolean + float + integer + string +} + +"The dimension of the matrix being paginated" +enum Dimension { + CALLSETS + VARIANTS +} + +"The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" +enum EntryType { + CHECK + FILLER + TEST +} + +"fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response." +enum FileFormat { + application_excel + application_json + application_zip + text_csv + text_tsv +} + +"The type of objects that are referenced in a List" +enum ListType { + germplasm + markers + observationUnits + observationVariables + observations + programs + samples + studies + trials + variants +} + +"The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. " +enum ParentType { + CLONAL + FEMALE + MALE + POPULATION + SELF +} + +"The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')." +enum PlannedCrossStatus { + DONE + SKIPPED + TODO +} + +"Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format" +enum PlateFormat { + PLATE_96 + TUBES +} + +""" +The type of positional coordinate used. Must be one of the following values + +LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + +LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + +PLANTED_ROW - The physical planted row number + +PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + +GRID_ROW - The row index number of a square grid overlay + +GRID_COL - The column index number of a square grid overlay + +MEASURED_ROW - The distance in meters from a defined 0-th row + +MEASURED_COL - The distance in meters from a defined 0-th column +""" +enum PositionCoordinateXType { + GRID_COL + GRID_ROW + LATITUDE + LONGITUDE + MEASURED_COL + MEASURED_ROW + PLANTED_INDIVIDUAL + PLANTED_ROW +} + +""" +The type of positional coordinate used. Must be one of the following values + +LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + +LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + +PLANTED_ROW - The physical planted row number + +PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + +GRID_ROW - The row index number of a square grid overlay + +GRID_COL - The column index number of a square grid overlay + +MEASURED_ROW - The distance in meters from a defined 0-th row + +MEASURED_COL - The distance in meters from a defined 0-th column +""" +enum PositionCoordinateYType { + GRID_COL + GRID_ROW + LATITUDE + LONGITUDE + MEASURED_COL + MEASURED_ROW + PLANTED_INDIVIDUAL + PLANTED_ROW +} + +""" +The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding +""" +enum ProgramType { + PROJECT + STANDARD +} + +"The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" +enum SampleType { + DNA + MIXED + RNA + TISSUE +} + +""" +The 2 digit code representing the type of storage this germplasm is kept in at a genebank. + +MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) + +10) Seed collection +11) Short term +12) Medium term +13) Long term +20) Field collection +30) In vitro collection +40) Cryo-preserved collection +50) DNA collection +99) Other (elaborate in REMARKS field) +""" +enum StorageTypeCode { + N10 + N11 + N12 + N13 + N20 + N30 + N40 + N50 + N99 +} + +""" +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+""" +enum TraitDataType { + Code + Date + Duration + Nominal + Numerical + Ordinal + Text +} + +enum Type { + OBO + RDF + WEBPAGE +} + +"A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." +input AdditionalInfoInput { + additionalProperties: String +} + +input AlleleMatrixInput { + "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case." + callSets: [CallSetInput] + "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + dataMatrices: [DataMatrixInput] + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "Pagination for the matrix" + pagination: [PaginationInput] + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String + "A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets." + variantSets: [VariantSetInput] + "A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix." + variants: [VariantInput] +} + +input AnalysisInput { + "Unique identifier for this analysis description" + analysisDbId: String + "A human readable name for this analysis" + analysisName: String + "The time at which this record was created, in ISO 8601 format." + created: String + "A human readable description of the analysis" + description: String + "The software run to generate this analysis." + software: [String] + "The type of analysis." + type: String + "The time at which this record was last updated, in ISO 8601 format." + updated: String + "Analysis associated with a variant set" + variantSet: VariantSetInput +} + +input AvailableFormatInput { + "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)" + dataFormat: DataFormat + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response." + fileFormat: FileFormat + "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file." + fileURL: String + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String + "Formats associated with a variant set" + variantSet: VariantSetInput +} + +input BreedingMethodInput { + "A shortened version of the human readable name for a Breeding Method" + abbreviation: String + "the unique identifier for this breeding method" + breedingMethodDbId: String + "the human readable identifier for this breeding method" + breedingMethodName: String + "human readable description of the breeding method" + description: String + "germplasm" + germplasm: [GermplasmInput] + "pedigreeNodes" + pedigreeNodes: [PedigreeNodeInput] +} + +input BreedingMethodsInput { + "A shortened version of the human readable name for a Breeding Method" + abbreviation: String + "the unique identifier for this breeding method" + breedingMethodDbId: String + "the human readable identifier for this breeding method" + breedingMethodName: String + "human readable description of the breeding method" + description: String + "germplasm" + germplasm: [GermplasmInput] + "pedigreeNodes" + pedigreeNodes: [PedigreeNodeInput] +} + +input CallInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + """ + The ID of the call set this variant call belongs to. + + If this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same. + """ + callSet: CallSetInput + "Genotype Metadata are additional layers of metadata associated with each genotype." + genotypeMetadata: [GenotypeMetadataInput] + "The value of this genotype call" + genotypeValue: String + """ + If this field is populated, this variant call's genotype ordering implies the phase of the bases and + is consistent with any other variant calls on the same contig which have the same phase set string. + """ + phaseSet: String + "The ID of the variant this call belongs to." + variant: VariantInput + "The unique identifier for a VariantSet" + variantSet: VariantSetInput +} + +input CallSetInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + alleleMatrices: [AlleleMatrixInput] + "The ID which uniquely identifies a CallSet within the given database server" + callSetDbId: String + "The human readable name which identifies a germplasm within the given database server" + callSetName: String + calls: [CallInput] + "The date this call set was created" + created: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The Biosample entity the call set data was generated from." + sample: SampleInput + "The ID which uniquely identifies a study within the given database server" + study: StudyInput + "The time at which this call set was last updated" + updated: String + "The IDs of the variantSets this callSet has calls in." + variantSets: [VariantSetInput] +} + +input CallSetsInput { + "A list of IDs which uniquely identify `CallSets` within the given database server" + callSetDbIds: [String] + "A list of human readable names associated with `CallSets`" + callSetNames: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "A list of IDs which uniquely identify `Samples` within the given database server" + sampleDbIds: [String] + "A list of human readable names associated with `Samples`" + sampleNames: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] + "A list of IDs which uniquely identify `VariantSets` within the given database server" + variantSetDbIds: [String] +} + +input CallsInput { + "A list of IDs which uniquely identify `CallSets` within the given database server" + callSetDbIds: [String] + "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)" + expandHomozygotes: Boolean + "The string used as a separator for phased allele calls." + sepPhased: String + "The string used as a separator for unphased allele calls." + sepUnphased: String + "The string used as a representation for missing data." + unknownString: String + "A list of IDs which uniquely identify `Variant` within the given database server" + variantDbIds: [String] + "A list of IDs which uniquely identify `VariantSets` within the given database server" + variantSetDbIds: [String] +} + +input ContactInput { + """ + The ID which uniquely identifies this contact + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + """ + contactDbId: String + """ + The contacts email address + + MIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person. + """ + email: String + """ + The name of the institution which this contact is part of + + MIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to + """ + instituteName: String + """ + The full name of this contact person + + MIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications) + """ + name: String + """ + The Open Researcher and Contributor ID for this contact person (orcid.org) + + MIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended. + """ + orcid: String + """ + The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.) + + MIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation + """ + type: String +} + +input ContentMixtureInput { + "The cross for the germplasm using in this content mixture" + cross: CrossInput + "The germplasm using in this content mixture" + germplasm: GermplasmInput + "The percentage of the given germplasm in the seed lot mixture." + mixturePercentage: Int + "associated seedLot" + seedLot: SeedLotInput +} + +input CrossAttributeInput { + "a custom attributes associated with a cross" + cross: CrossInput + "the human readable name of a cross attribute" + crossAttributeName: String + "the value of a cross attribute" + crossAttributeValue: String +} + +input CrossInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Set of custom attributes associated with a cross" + crossAttributes: [CrossAttributeInput] + "the unique identifier for a cross" + crossDbId: String + "the human readable name for a cross" + crossName: String + "the type of cross" + crossType: CrossType + "the unique identifier for a crossing project" + crossingProject: CrossingProjectInput + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "observationUnits" + observationUnits: [ObservationUnitInput] + "the first parent used in the cross" + parent1: CrossParentInput + "the second parent used in the cross" + parent2: CrossParentInput + "the unique identifier for a planned cross" + plannedCross: PlannedCrossInput + "The list of pollination events that occurred for this cross" + pollinationEvents: [PollinationEventInput] +} + +input CrossParentInput { + "the germplasm of the cross parent" + germplasm: GermplasmInput + "the Observation Unit of the cross parent" + observationUnit: ObservationUnitInput + "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc." + parentType: ParentType +} + +input CrossesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "Search for Cross with this unique id" + crossDbIds: [String] + "Search for Cross with this human readable name" + crossNames: [String] + "Search for Crossing Projects with this unique id" + crossingProjectDbIds: [String] + "The human readable name for a crossing project" + crossingProjectNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] +} + +input CrossingProjectInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "the common name of a crop (for multi-crop systems)" + commonCropName: String + "crosses" + crosses: [CrossInput] + "The unique identifier for a crossing project" + crossingProjectDbId: String + "the description for a crossing project" + crossingProjectDescription: String + "The human readable name for a crossing project" + crossingProjectName: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "pedigreeNodes" + pedigreeNodes: [PedigreeNodeInput] + "plannedCrosses" + plannedCrosses: [PlannedCrossInput] + """ + A list of all the potential parents in the crossing block, available in the crossing project +
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object. + """ + potentialParents: [CrossParentInput] + "the unique identifier for a program" + program: ProgramInput +} + +input CrossingProjectsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "Search for Crossing Projects with this unique id" + crossingProjectDbIds: [String] + "The human readable name for a crossing project" + crossingProjectNames: [String] + "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object." + includePotentialParents: Boolean + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] +} + +input DataLinkInput { + """ + The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy) + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + dataFormat: String + """ + The general description of this data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + description: String + """ + The MIME type of the file (ie text/csv, application/excel, application/zip). + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + fileFormat: String + """ + The name of the external data link + + MIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file. + """ + name: String + "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow." + provenance: String + "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc" + scientificType: String + """ + URL describing the location of this data file to view or download + + MIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission. + """ + url: String + """ + The version number for this data + + MIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data). + """ + version: String +} + +input DataMatrixInput { + "Data matrices associated with an alleleMatrix" + alleleMatrix: AlleleMatrixInput + "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows." + dataMatrix: [[String]] + """ + The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word "GT" is reserved for the allele matrix. Examples of other metadata matrices include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + """ + dataMatrixAbbreviation: String + """ + The name of the field represented in this data matrix. The key word "Genotype" is reserved for the allele matrix. Examples of other metadata matrices include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + """ + dataMatrixName: String + "The type of field represented in this data matrix. This is intended to help parse the data out of JSON." + dataType: DataType +} + +input DatasetAuthorshipsInput { + "The DOI or other permanent unique identifier for this published dataset" + datasetPUI: String + "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended." + license: String + "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described." + publicReleaseDate: String + "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository." + submissionDate: String + "Dataset authorships associated with a trial" + trial: TrialInput +} + +input DocumentationLinkInput { + URL: String + "associated ontology reference" + ontologyReference: OntologyReferenceInput + type: Type +} + +input DonorInput { + """ + The accession number assigned by the donor + + MCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard. + """ + donorAccessionNumber: String + """ + The institute code for the donor institute +
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard. + """ + donorInstituteCode: String + "donoers associated with a germplasm" + germplasm: GermplasmInput +} + +input EnvironmentParametersInput { + "Human-readable value of the environment parameter (defined above) constant within the experiment" + description: String + "Human-readable value of the environment parameter (defined above) constant within the experiment" + environmentParametersDbId: String + """ + Name of the environment parameter constant within the experiment + + MIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. + """ + parameterName: String + "URI pointing to an ontology class for the parameter" + parameterPUI: String + "Environment parameters associated with a study" + study: StudyInput + "Unit of the value for this parameter" + unit: String + "URI pointing to an ontology class for the unit" + unitPUI: String + """ + Numerical or categorical value + + MIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment. + """ + value: String + "URI pointing to an ontology class for the parameter value" + valuePUI: String +} + +input EventDateRangeInput { + """ + A list of dates when the event occurred +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + discreteDates: [String] + """ + The end of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + endDate: String + "associated event" + event: EventInput + """ + The beginning of a continuous or regularly repetitive event +
MIAPPE V1.1 (DM-68) Event date - Date and time of the event. + """ + startDate: String +} + +input EventInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)" + eventDateRange: [EventDateRangeInput] + "Internal database identifier" + eventDbId: String + """ + A detailed, human-readable description of this event +
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. + """ + eventDescription: String + "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI" + eventParameters: [EventParameterInput] + """ + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + """ + eventType: String + """ + An identifier for this event type, in the form of an ontology class reference +
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other +
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology). + """ + eventTypeDbId: String + "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study" + observationUnits: [ObservationUnitInput] + "The study in which the event occurred" + study: StudyInput +} + +input EventParameterInput { + """ + The shortened code name of an event parameter +
ICASA "Code_Display" + """ + code: String + "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter." + description: String + "associated event" + event: EventInput + """ + The full name of an event parameter +
ICASA "Variable_Name" + """ + name: String + """ + The units or data type of the 'value'. +
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. +
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. +
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc +
ICASA "Unit_or_type" + """ + units: String + "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated." + value: String + "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value." + valueDescription: String + "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated." + valuesByDate: [String] +} + +input EventsInput { + "Filter based on an Event start date." + dateRangeEnd: String + "Filter based on an Event start date." + dateRangeStart: String + "Filter based on an Event DbId." + eventDbIds: [String] + "Filter based on an Event Type" + eventTypes: [String] + "The ID which uniquely identifies an observation unit." + observationUnitDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] +} + +input ExperimentalDesignInput { + "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology." + PUI: String + "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'." + description: String + "Experimental design associated with a study" + study: StudyInput +} + +input ExternalReferenceInput { + "The external reference ID. Could be a simple string or a URI." + referenceId: String + "An identifier for the source system or database of this reference" + referenceSource: String +} + +input GenomeMapInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Additional comments about a `GenomeMap`" + comments: String + "The common name of the `Crop`" + commonCropName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "The number of linkage groups present in a `GenomeMap`" + linkageGroupCount: Int + "The unique identifier for a `GenomeMap`" + mapDbId: String + "The human readable identifier for a `GenomeMap`" + mapName: String + "The DOI or other permanent identifier for a `GenomeMap`" + mapPUI: String + "The number of markers present in a `GenomeMap`" + markerCount: Int + "markerPositions" + markerPositions: [MarkerPositionInput] + "The date this `GenomeMap` was published" + publishedDate: String + "Full scientific binomial format name. This includes Genus, Species, and Sub-species" + scientificName: String + "The type of map this represents, usually \"Genetic\" or \"Physical\"" + type: String + "The units used to describe the data in a `GenomeMap`" + unit: String +} + +input GenomeMapsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The ID which uniquely identifies a `GenomeMap`" + mapDbIds: [String] + "The DOI or other permanent identifier for a `GenomeMap`" + mapPUI: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "Full scientific binomial format name. This includes Genus, Species, and Sub-species" + scientificName: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] + "The type of map, usually \"Genetic\" or \"Physical\"" + types: [String] +} + +input GenotypeMetadataInput { + "Genotype metadata associated with a call" + call: CallInput + "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." + dataType: DataType + """ + The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: "GQ", "RD", and "HQ" +
This maps to a FORMAT field in the VCF file standard. + """ + fieldAbbreviation: String + """ + The name of the field represented in this Genotype Field. Examples include: "Genotype Quality", "Read Depth", and "Haplotype Quality" +
This maps to a FORMAT field in the VCF file standard. + """ + fieldName: String + "The additional metadata value associated with this genotype call" + fieldValue: String +} + +input GeoJSONGeometryInput { + "Field for possible type 'GeoJSONPointInput'" + geoJSONPointInput: GeoJSONPointInput + "Field for possible type 'GeoJSONPolygonInput'" + geoJSONPolygonInput: GeoJSONPolygonInput +} + +""" +One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + +Copied from RFC 7946 Section 3.1.1 + +A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +input GeoJSONInput { + "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." + geometry: GeoJSONGeometryInput + "Geometry associated with an image" + germplasmOrigin: GermplasmOriginInput + "Geometry associated with an image" + image: ImageInput + "Geometry associated with an image" + observation: ObservationInput + "Geometry associated with an image" + observationUnit: ObservationUnitPositionInput + "The literal string \"Feature\"" + type: String +} + +""" +Copied from RFC 7946 Section 3.1.1 + +A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +input GeoJSONPointInput { + "A single position" + coordinates: [Float] + "The literal string \"Point\"" + type: String +} + +""" +An array of Linear Rings. Each Linear Ring is an array of Points. + +A Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or +easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. +""" +input GeoJSONPolygonInput { + "An array of linear rings" + coordinates: [[[Float]]] + "The literal string \"Polygon\"" + type: String +} + +input GeoJSONSearchAreaInput { + "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed." + geometry: GeoJSONGeometryInput + "Geometry associated with an image" + germplasmOrigin: GermplasmOriginInput + "Geometry associated with an image" + image: ImageInput + "Geometry associated with an image" + observation: ObservationInput + "Geometry associated with an image" + observationUnit: ObservationUnitPositionInput + "The literal string \"Feature\"" + type: String +} + +input GermplasmAttributeInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "General category for the attribute. very similar to Trait class." + attributeCategory: String + "The ID which uniquely identifies this attribute within the given database server" + attributeDbId: String + "A human readable description of this attribute" + attributeDescription: String + "A human readable name for this attribute" + attributeName: String + "The Permanent Unique Identifier of an Attribute, usually in the form of a URI" + attributePUI: String + "attributeValues" + attributeValues: [GermplasmAttributeValueInput] + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: MethodInput + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReferenceInput + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: ScaleInput + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: TraitInput +} + +input GermplasmAttributeValueInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The ID which uniquely identifies this attribute within the given database server" + attribute: GermplasmAttributeInput + "The ID which uniquely identifies this attribute value within the given database server" + attributeValueDbId: String + "The date the value of this attribute was determined for a given germplasm" + determinedDate: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The ID which uniquely identifies a germplasm within the given database server" + germplasm: GermplasmInput + "The value of this attribute for a given germplasm" + value: String +} + +input GermplasmAttributeValuesInput { + "List of Germplasm Attribute IDs to search for" + attributeDbIds: [String] + "List of human readable Germplasm Attribute names to search for" + attributeNames: [String] + "List of Germplasm Attribute Value IDs to search for" + attributeValueDbIds: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of scale data types to filter search results" + dataTypes: [TraitDataType] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "List of methods to filter search results" + methodDbIds: [String] + "List of ontology IDs to search for" + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "List of scales to filter search results" + scaleDbIds: [String] + "List of trait classes to filter search results" + traitClasses: [String] + "List of trait unique ID to filter search results" + traitDbIds: [String] +} + +input GermplasmAttributesInput { + "General category for the attribute. very similar to Trait class." + attributeCategories: [String] + "List of Germplasm Attribute IDs to search for" + attributeDbIds: [String] + "List of human readable Germplasm Attribute names to search for" + attributeNames: [String] + "The Permanent Unique Identifier of an Attribute, usually in the form of a URI" + attributePUIs: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of scale data types to filter search results" + dataTypes: [TraitDataType] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "List of methods to filter search results" + methodDbIds: [String] + """ + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + """ + methodNames: [String] + "The Permanent Unique Identifier of a Method, usually in the form of a URI" + methodPUIs: [String] + "List of ontology IDs to search for" + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier for a Scale" + scaleDbIds: [String] + """ + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + """ + scaleNames: [String] + "The Permanent Unique Identifier of a Scale, usually in the form of a URI" + scalePUIs: [String] + """ + **Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 +
The unique ID of a studies to filter on + """ + studyDbId: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + """ + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + """ + traitAttributePUIs: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"" + traitAttributes: [String] + "List of trait classes to filter search results" + traitClasses: [String] + "The unique identifier for a Trait" + traitDbIds: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"" + traitEntities: [String] + """ + The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" + """ + traitEntityPUIs: [String] + """ + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + """ + traitNames: [String] + "The Permanent Unique Identifier of a Trait, usually in the form of a URI" + traitPUIs: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input GermplasmChildInput { + "The child germplasm" + childGermplasm: GermplasmInput + """ + The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. + + In a pedigree record, the 'parentType' describes each parent of a particular germplasm. + + In a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. + For example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers + to the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C. + In this way, A could be a male parent to B, but a female parent to C. + """ + parentType: ParentType + "associated pedigreeNode" + pedigreeNode: PedigreeNodeInput +} + +input GermplasmInput { + """ + The unique identifier for a material or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumber: String + """ + The date a material or germplasm was acquired by the genebank + + MCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or "00" [double zero]. + """ + acquisitionDate: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "attributeValues" + attributeValues: [GermplasmAttributeValueInput] + """ + MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. + + 100) Wild + 110) Natural + 120) Semi-natural/wild + 130) Semi-natural/sown + 200) Weedy + 300) Traditional cultivar/landrace + 400) Breeding/research material + 410) Breeders line + 411) Synthetic population + 412) Hybrid + 413) Founder stock/base population + 414) Inbred line (parent of hybrid cultivar) + 415) Segregating population + 416) Clonal selection + 420) Genetic stock + 421) Mutant (e.g. induced/insertion mutants, tilling populations) + 422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) + 423) Other genetic stocks (e.g. mapping populations) + 500) Advanced or improved cultivar (conventional breeding methods) + 600) GMO (by genetic engineering) + 999) Other (Elaborate in REMARKS field) + """ + biologicalStatusOfAccessionCode: BiologicalStatusOfAccessionCode + "Supplemental text description for 'biologicalStatusOfAccessionCode'" + biologicalStatusOfAccessionDescription: String + "The unique identifier for the breeding method used to create this germplasm" + breedingMethod: BreedingMethodInput + "A specific panel/collection/population name this germplasm belongs to." + collection: String + """ + Common name for the crop + + MCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: "malting barley", "mas". + """ + commonCropName: String + """ + 3-letter ISO 3166-1 code of the country in which the sample was originally collected + + MCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was "collected". + """ + countryOfOriginCode: String + "Human readable name used for display purposes" + defaultDisplayName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "List of donor institutes" + donors: [DonorInput] + "Filter by External References" + externalReferences: [ExternalReferenceInput] + """ + Genus name for taxon. Initial uppercase letter required. + + MCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required. + + MIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature. + """ + genus: String + """ + The ID which uniquely identifies a germplasm within the given database server +
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + """ + germplasmDbId: String + """ + Name of the germplasm. It can be the preferred name and does not have to be unique. + + MCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space. + """ + germplasmName: String + "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm." + germplasmOrigin: [GermplasmOriginInput] + """ + The Permanent Unique Identifier which represents a germplasm + + MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below. + + MIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source + + MCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties. + """ + germplasmPUI: String + "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary." + germplasmPreprocessing: String + """ + The code for the institute that maintains the material. + + MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". + """ + instituteCode: String + "The name of the institute that maintains the material" + instituteName: String + "observationUnits" + observationUnits: [ObservationUnitInput] + "observations" + observations: [ObservationInput] + "parentPedigreeNodes" + parentPedigreeNodes: [PedigreeNodeInput] + """ + The cross name and optional selection history. + + MCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'. + """ + pedigree: String + "progenyPedigreeNodes" + progenyPedigreeNodes: [PedigreeNodeInput] + "Germplasm associated with a reference" + reference: ReferenceInput + "Germplasm associated with a reference" + referenceSet: ReferenceSetInput + "samples" + samples: [SampleInput] + """ + An identifier for the source of the biological material +
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: "mother_accession X father_accession", or, if father is unknown, as "mother_accession X UNKNOWN". For in situ material, the region of provenance may be used when an accession is not available. + """ + seedSource: String + """ + Description of the material source + + MIAPPE V1.1 (DM-56) Material source description - Description of the material source + """ + seedSourceDescription: String + "siblingPedigreeNodes" + siblingPedigreeNodes: [PedigreeNodeInput] + """ + Specific epithet portion of the scientific name in lowercase letters. + + MCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: "sp." + + MIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature. + """ + species: String + """ + The authority organization responsible for tracking and maintaining the species name + + MCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name. + """ + speciesAuthority: String + "The type of storage this germplasm is kept in at a genebank." + storageTypes: [StorageTypeInput] + """ + Subtaxon can be used to store any additional taxonomic identifier. + + MCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: "subsp." (for subspecies); "convar." (for convariety); "var." (for variety); "f." (for form); "Group" (for "cultivar group"). + + MIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group). + """ + subtaxa: String + """ + The authority organization responsible for tracking and maintaining the subtaxon information + + MCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level. + """ + subtaxaAuthority: String + """ + List of alternative names or IDs used to reference this germplasm + + MCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon. + """ + synonyms: [SynonymInput] + """ + The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as "ncbiTaxon" preferably with a purl. The rank of this ID should be species. + + MIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended. + """ + taxonIds: [TaxonIdInput] +} + +input GermplasmOriginInput { + "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + coordinates: [GeoJSONInput] + "associated germplasm" + germplasm: GermplasmInput +} + +input GermplasmParentInput { + "The parent germplasm" + parentGermplasm: GermplasmInput + """ + The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. + + In a pedigree record, the 'parentType' describes each parent of a particular germplasm. + + In a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. + For example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers + to the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C. + In this way, A could be a male parent to B, but a female parent to C. + """ + parentType: ParentType + "associated pedigreeNode" + pedigreeNode: PedigreeNodeInput +} + +input GermplasmsInput { + """ + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumbers: [String] + "List of the full binomial name (scientific name) to identify a germplasm" + binomialNames: [String] + "A specific panel/collection/population name this germplasm belongs to." + collections: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "A familyCode representing the family this germplasm belongs to." + familyCodes: [String] + "List of Genus names to identify germplasm" + genus: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "List of Permanent Unique Identifiers to identify germplasm" + germplasmPUIs: [String] + """ + The code for the institute that maintains the material. +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". + """ + instituteCodes: [String] + "Search for Germplasm with these parents" + parentDbIds: [String] + "Search for Germplasm with these children" + progenyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "List of Species names to identify germplasm" + species: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "List of alternative names or IDs used to reference this germplasm" + synonyms: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input GrowthFacilityInput { + "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology." + PUI: String + "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out." + description: String + "Growth facility associated with a study" + study: StudyInput +} + +input ImageInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'" + copyright: String + "The human readable description of an image." + description: String + "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL." + descriptiveOntologyTerms: [String] + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The unique identifier of an image" + imageDbId: String + "The name of the image file. Might be the same as 'imageName', but could be different." + imageFileName: String + "The size of the image in Bytes." + imageFileSize: Int + "The height of the image in Pixels." + imageHeight: Int + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + imageLocation: GeoJSONInput + "The human readable name of an image. Might be the same as 'imageFileName', but could be different." + imageName: String + "The date and time the image was taken" + imageTimeStamp: String + "The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server." + imageURL: String + "The width of the image in Pixels." + imageWidth: Int + "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc" + mimeType: String + "The related observation unit identifier, if relevant." + observationUnit: ObservationUnitInput + "A list of observation Ids this image is associated with, if applicable." + observations: [ObservationInput] +} + +input ImagesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL." + descriptiveOntologyTerms: [String] + "A list of image Ids to search for" + imageDbIds: [String] + "Image file names to search for." + imageFileNames: [String] + "A maximum image file size to search for." + imageFileSizeMax: Int + "A minimum image file size to search for." + imageFileSizeMin: Int + "A maximum image height to search for." + imageHeightMax: Int + "A minimum image height to search for." + imageHeightMin: Int + imageLocation: GeoJSONSearchAreaInput + "Human readable names to search for." + imageNames: [String] + "The latest timestamp to search for." + imageTimeStampRangeEnd: String + "The earliest timestamp to search for." + imageTimeStampRangeStart: String + "A maximum image width to search for." + imageWidthMax: Int + "A minimum image width to search for." + imageWidthMin: Int + "A set of image file types to search for." + mimeTypes: [String] + "A list of observation Ids this image is associated with to search for" + observationDbIds: [String] + "A set of observation unit identifiers to search for." + observationUnitDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] +} + +input LastUpdateInput { + "The date and time when this study was last modified" + lastUpdateDbId: String + "Last update associated with a study" + study: StudyInput + timestamp: String + version: String +} + +input ListInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The array of DbIds of the BrAPI objects contained in a List" + data: [String] + "Timestamp when the entity was first created" + dateCreated: String + "Timestamp when the entity was last updated" + dateModified: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The unique identifier for a List" + listDbId: String + "Description of a List" + listDescription: String + "Human readable name of a List" + listName: String + "Human readable name of a List Owner. (usually a user or person)" + listOwnerName: String + "The unique identifier for a List Owner. (usually a user or person)" + listOwnerPerson: PersonInput + "The number of elements in a List" + listSize: Int + "The description of where a List originated from" + listSource: String + "A flag to indicate the type of objects that are referenced in a List" + listType: ListType +} + +input ListsInput { + "Define the end for an interval of time and only include Lists that are created within this interval." + dateCreatedRangeEnd: String + "Define the beginning for an interval of time and only include Lists that are created within this interval." + dateCreatedRangeStart: String + "Define the end for an interval of time and only include Lists that are modified within this interval." + dateModifiedRangeEnd: String + "Define the beginning for an interval of time and only include Lists that are modified within this interval." + dateModifiedRangeStart: String + "An array of primary database identifiers to identify a set of Lists" + listDbIds: [String] + "An array of human readable names to identify a set of Lists" + listNames: [String] + "An array of names for the people or entities who are responsible for a set of Lists" + listOwnerNames: [String] + "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists" + listOwnerPersonDbIds: [String] + "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)" + listSources: [String] + listType: ListType +} + +input LocationInput { + "A shortened version of the human readable name for a Location" + abbreviation: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + childLocations: [LocationInput] + "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)" + coordinateDescription: String + "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown." + coordinateUncertainty: String + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + coordinates: GeoJSONInput + """ + [ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.' + """ + countryCode: String + """ + The full name of the country where a Location is located +
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code. + """ + countryName: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)" + environmentType: String + "Describes the level of protection/exposure for things like sun light and wind at a particular Location" + exposure: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + """ + The street address of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + """ + instituteAddress: String + """ + The full name of the institute at a particular Location +
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study. + """ + instituteName: String + "The unique identifier for a Location" + locationDbId: String + """ + A human readable name for a Location +
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place. + """ + locationName: String + "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)" + locationType: String + "observationUnits" + observationUnits: [ObservationUnitInput] + """ + The unique identifier for a Location +
The Parent Location defines the encompassing Location that a smaller Location belongs to. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ + parentLocation: LocationInput + "seedLots" + seedLots: [SeedLotInput] + "Description of the accessibility of the location (ex. Public, Private)" + siteStatus: String + "Describes the approximate slope (height/distance) of a Location." + slope: String + studies: [StudyInput] + "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)" + topography: String +} + +input LocationsInput { + "A list of shortened human readable names for a set of Locations" + abbreviations: [String] + "The maximum altitude to search for" + altitudeMax: Float + "The minimum altitude to search for" + altitudeMin: Float + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + coordinates: GeoJSONSearchAreaInput + "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec" + countryCodes: [String] + "The full name of the country to search for" + countryNames: [String] + "The street address of the institute to search for" + instituteAddresses: [String] + "The name of the institute to search for" + instituteNames: [String] + "The location ids to search for" + locationDbIds: [String] + "A human readable names to search for" + locationNames: [String] + "The type of location this represents (ex. Breeding Location, Storage Location, etc)" + locationTypes: [String] + """ + The unique identifier for a Location +
The Parent Location defines the encompassing location that this location belongs to. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ + parentLocationDbIds: [String] + """ + A human readable name for a location +
The Parent Location defines the encompassing location that this location belongs to. + For example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields. + """ + parentLocationNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] +} + +input MarkerPositionInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + """ + The Uniquely Identifiable name of a `LinkageGroup` +
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable. + """ + linkageGroupName: String + "The ID which uniquely identifies a `GenomeMap`" + map: GenomeMapInput + "The position of a marker or variant within a `LinkageGroup`" + position: Int + """ + The ID which uniquely identifies a `Variant` within the given database server +
A `Variant` can also represent a Marker + """ + variant: VariantInput +} + +input MarkerPositionsInput { + "A list of Uniquely Identifiable linkage group names" + linkageGroupNames: [String] + "A list of IDs which uniquely identify `GenomeMaps` within the given database server" + mapDbIds: [String] + "The maximum position of markers in a given map" + maxPosition: Int + "The minimum position of markers in a given map" + minPosition: Int + "A list of IDs which uniquely identify `Variants` within the given database server" + variantDbIds: [String] +} + +input MetadataFieldInput { + "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON." + dataType: DataType + "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"" + fieldAbbreviation: String + "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"" + fieldName: String + "Formats associated with a variant set" + variantSet: VariantSetInput +} + +input MethodInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + """ + Bibliographical reference describing the method. +
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method. + """ + bibliographicalReference: String + """ + Method description +
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number) + """ + description: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation" + formula: String + "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)" + methodClass: String + "Method unique identifier" + methodDbId: String + """ + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + """ + methodName: String + "The Permanent Unique Identifier of a Method, usually in the form of a URI" + methodPUI: String + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReferenceInput +} + +input MethodsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The unique identifier for an observation variable." + observationVariableDbIds: [String] + """ + The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology + + Use `GET /ontologies` to find the list of available ontologies on a server. + """ + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier for a method." + scaleDbIds: [String] +} + +input ObservationInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The name or identifier of the entity which collected the observation" + collector: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + geoCoordinates: GeoJSONInput + "The ID which uniquely identifies a germplasm" + germplasm: GermplasmInput + "images" + images: [ImageInput] + "The ID which uniquely identifies an observation" + observationDbId: String + "The date and time when this observation was made" + observationTimeStamp: String + "The ID which uniquely identifies an observation unit" + observationUnit: ObservationUnitInput + "The ID which uniquely identifies an observation variable" + observationVariable: ObservationVariableInput + season: SeasonInput + "The ID which uniquely identifies a study within the given database server" + study: StudyInput + "The name or id of the user who uploaded the observation to the database system" + uploadedBy: String + "The value of the data collected as an observation" + value: String +} + +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +input ObservationUnitHierarchyLevelInput { + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +input ObservationUnitInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "the unique identifier for a cross" + cross: CrossInput + "events" + events: [EventInput] + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The ID which uniquely identifies a germplasm" + germplasm: GermplasmInput + "images" + images: [ImageInput] + "The ID which uniquely identifies a location, associated with this study" + location: LocationInput + """ + The ID which uniquely identifies an observation unit + + MIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. + """ + observationUnitDbId: String + "A human readable name for an observation unit" + observationUnitName: String + """ + A Permanent Unique Identifier for an observation unit + + MIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible. + """ + observationUnitPUI: String + """ + All positional and layout information related to this Observation Unit + + MIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) + or level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. + Levels of observation must be consistent with those listed in the Study section. + """ + observationUnitPosition: [ObservationUnitPositionInput] + "observations" + observations: [ObservationInput] + "The ID which uniquely identifies a program" + program: ProgramInput + "samples" + samples: [SampleInput] + "The unique identifier for the originating Seed Lot" + seedLot: SeedLotInput + "The ID which uniquely identifies a study within the given database server" + study: StudyInput + """ + List of treatments applied to an observation unit. + + MIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit. + """ + treatments: [TreatmentInput] + "The ID which uniquely identifies a trial" + trial: TrialInput +} + +""" +The exact level and level code of an observation unit. + +For more information on Observation Levels, please review the Observation Levels documentation. + +MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. +The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). +Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." +""" +input ObservationUnitLevelInput { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int +} + +""" +Observation levels indicate the granularity level at which the measurements are taken. `levelName` +defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. +`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are +at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify +this observation unit by each level of the hierarchy where it exists. + +For more information on Observation Levels, please review the Observation Levels documentation. + +**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** +""" +input ObservationUnitLevelRelationshipInput { + """ + An ID code or number to represent a real thing that may or may not be an an observation unit. +
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded. +
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. + """ + levelCode: String + """ + A name for this level + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelName: String + """ + `levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers + are at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + levelOrder: Int + """ + The an observation unit +
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. +
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response. + """ + observationUnit: ObservationUnitInput +} + +input ObservationUnitPositionInput { + "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"" + entryType: EntryType + """ + One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system. + + Copied from RFC 7946 Section 3.1.1 + + A position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or + easting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element. + """ + geoCoordinates: [GeoJSONInput] + """ + The exact level and level code of an observation unit. + + For more information on Observation Levels, please review the Observation Levels documentation. + + MIAPPE V1.1 DM-71 Observation unit type "Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. + The observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). + Alternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead." + """ + observationLevel: ObservationUnitLevelInput + """ + Observation levels indicate the granularity level at which the measurements are taken. `levelName` + defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. + `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are + at the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify + this observation unit by each level of the hierarchy where it exists. + + For more information on Observation Levels, please review the Observation Levels documentation. + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + """ + observationLevelRelationships: [ObservationUnitLevelRelationshipInput] + "associated observation Unit" + observationUnit: ObservationUnitInput + "The X position coordinate for an observation unit. Different systems may use different coordinate systems." + positionCoordinateX: String + """ + The type of positional coordinate used. Must be one of the following values + + LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + PLANTED_ROW - The physical planted row number + + PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + + GRID_ROW - The row index number of a square grid overlay + + GRID_COL - The column index number of a square grid overlay + + MEASURED_ROW - The distance in meters from a defined 0-th row + + MEASURED_COL - The distance in meters from a defined 0-th column + """ + positionCoordinateXType: PositionCoordinateXType + "The Y position coordinate for an observation unit. Different systems may use different coordinate systems." + positionCoordinateY: String + """ + The type of positional coordinate used. Must be one of the following values + + LONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + LATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details + + PLANTED_ROW - The physical planted row number + + PLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row + + GRID_ROW - The row index number of a square grid overlay + + GRID_COL - The column index number of a square grid overlay + + MEASURED_ROW - The distance in meters from a defined 0-th row + + MEASURED_COL - The distance in meters from a defined 0-th column + """ + positionCoordinateYType: PositionCoordinateYType +} + +input ObservationUnitsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + """ + Use this parameter to include a list of observations embedded in each ObservationUnit object. + + CAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to. + """ + includeObservations: Boolean + "The location ids to search for" + locationDbIds: [String] + "A human readable names to search for" + locationNames: [String] + "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships" + observationLevelRelationships: [ObservationUnitLevelRelationshipInput] + "Searches for values in ObservationUnit->observationUnitPosition->observationLevel" + observationLevels: [ObservationUnitLevelInput] + "The unique id of an observation unit" + observationUnitDbIds: [String] + "The human readable identifier for an Observation Unit" + observationUnitNames: [String] + "The DbIds of Variables to search for" + observationVariableDbIds: [String] + "The names of Variables to search for" + observationVariableNames: [String] + "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" + observationVariablePUIs: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)" + seasonDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input ObservationVariableInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Crop name (examples: \"Maize\", \"Wheat\")" + commonCropName: String + "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])" + contextOfUse: [String] + "Variable default value. (examples: \"red\", \"2.3\", etc.)" + defaultValue: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "Growth stage at which measurement is made (examples: \"flowering\")" + growthStage: String + "Name of institution submitting the variable" + institution: String + "2 letter ISO 639-1 code for the language of submission of the variable." + language: String + """ + A description of the way an Observation should be collected. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Method "estimation" or "drone image processing". + """ + method: MethodInput + """ + Variable unique identifier + + MIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation. + """ + observationVariableDbId: String + """ + Variable name (usually a short name) + + MIAPPE V1.1 (DM-84) Variable name - Name of the variable. + """ + observationVariableName: String + "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI" + observationVariablePUI: String + "observations" + observations: [ObservationInput] + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReferenceInput + """ + A Scale describes the units and acceptable values for an ObservationVariable. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Scale "inches" or "pixels". + """ + scale: ScaleInput + "Name of scientist submitting the variable." + scientist: String + "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + studies: [StudyInput] + "Timestamp when the Variable was added (ISO 8601)" + submissionTimestamp: String + "Other variable names" + synonyms: [String] + """ + A Trait describes what property is being observed. +
For example, an ObservationVariable might be defined with a Trait of "plant height", a Scale of "meters", and a Method of "tape measure". This variable would be distinct from a variable with the Trait "Leaf length" or "Flower height". + """ + trait: TraitInput +} + +input ObservationVariablesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of scale data types to filter search results" + dataTypes: [TraitDataType] + "List of methods to filter search results" + methodDbIds: [String] + """ + Human readable name for the method +
MIAPPE V1.1 (DM-88) Method Name of the method of observation + """ + methodNames: [String] + "The Permanent Unique Identifier of a Method, usually in the form of a URI" + methodPUIs: [String] + "The DbIds of Variables to search for" + observationVariableDbIds: [String] + "The names of Variables to search for" + observationVariableNames: [String] + "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" + observationVariablePUIs: [String] + "List of ontology IDs to search for" + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier for a Scale" + scaleDbIds: [String] + """ + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + """ + scaleNames: [String] + "The Permanent Unique Identifier of a Scale, usually in the form of a URI" + scalePUIs: [String] + """ + **Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 +
The unique ID of a studies to filter on + """ + studyDbId: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + """ + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + """ + traitAttributePUIs: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"" + traitAttributes: [String] + "List of trait classes to filter search results" + traitClasses: [String] + "The unique identifier for a Trait" + traitDbIds: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"" + traitEntities: [String] + """ + The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" + """ + traitEntityPUIs: [String] + """ + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + """ + traitNames: [String] + "The Permanent Unique Identifier of a Trait, usually in the form of a URI" + traitPUIs: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input ObservationsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "The location ids to search for" + locationDbIds: [String] + "A human readable names to search for" + locationNames: [String] + "The unique id of an Observation" + observationDbIds: [String] + "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships" + observationLevelRelationships: [ObservationUnitLevelRelationshipInput] + "Searches for values in ObservationUnit->observationUnitPosition->observationLevel" + observationLevels: [ObservationUnitLevelInput] + "Timestamp range end" + observationTimeStampRangeEnd: String + "Timestamp range start" + observationTimeStampRangeStart: String + "The unique id of an Observation Unit" + observationUnitDbIds: [String] + "The DbIds of Variables to search for" + observationVariableDbIds: [String] + "The names of Variables to search for" + observationVariableNames: [String] + "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" + observationVariablePUIs: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)" + seasonDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input OntologiesInput { + """ + The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology + + Use `GET /ontologies` to find the list of available ontologies on a server. + """ + ontologyDbIds: [String] + "The human readable identifier for an ontology definition." + ontologyNames: [String] +} + +input OntologyInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Ontology's list of authors (no specific format)" + authors: String + "Ontology copyright" + copyright: String + "Human readable description of Ontology" + description: String + "A URL to the human readable documentation of an object" + documentationURL: String + "Ontology licence" + licence: String + "Ontology database unique identifier" + ontologyDbId: String + "Ontology name" + ontologyName: String + "Ontology version (no specific format)" + version: String +} + +input OntologyReferenceInput { + "links to various ontology documentation" + documentationLinks: [DocumentationLinkInput] + "The Ontology for this reference" + ontology: OntologyInput + "The ID which uniquely identifies a ontology reference" + ontologyReferenceDbId: String + "Ontology version (no specific format)" + version: String +} + +input OntologyTermInput { + "Species associated with a reference" + reference: ReferenceInput + "Species associated with a referenceSet" + referenceSet: ReferenceSetInput + "Ontology term - the label of the ontology term the termId is pointing to." + term: String + "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation." + termURI: String +} + +input PageInput { + page: Int + pageSize: Int +} + +input PaginationInput { + "Pagination associated with an alleleMatrix" + alleleMatrix: AlleleMatrixInput + "The dimension of the matrix being paginated" + dimension: Dimension + "the requested page number (zero indexed)" + page: Int + "the maximum number of elements per page in this dimension of the matrix" + pageSize: Int + "The total number of elements that are available on the server and match the requested query parameters." + totalCount: Int + """ + The total number of pages of elements available on the server. This should be calculated with the following formula. +
totalPages = CEILING( totalCount / requested_page_size) + """ + totalPages: Int +} + +input PedigreeNodeInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The unique identifier for the breeding method used to create this germplasm" + breedingMethod: BreedingMethodInput + "The crossing project used to generate this germplasm" + crossingProject: CrossingProjectInput + "The year the parents were originally crossed" + crossingYear: Int + "Human readable name used for display purposes" + defaultDisplayName: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The code representing the family of this germplasm" + familyCode: String + "The ID which uniquely identifies a germplasm" + germplasm: GermplasmInput + """ + A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. +
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. +
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response. + """ + parents: [GermplasmParentInput] + "The ID which uniquely identifies a pedigree node" + pedigreeNodeDbId: String + "The string representation of the pedigree for this germplasm in PURDY notation" + pedigreeString: String + """ + A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes. +
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows + the type of parent this germplasm is to each of the child germplasm references. +
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response. + """ + progeny: [GermplasmChildInput] + """ + A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes. +
Siblings share at least one parent with the given germplasm. +
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response. + """ + siblings: [GermplasmInput] +} + +input PedigreeNodesInput { + """ + A collection of unique identifiers for materials or germplasm within a genebank + + MCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. "PI 113869"). + """ + accessionNumbers: [String] + "List of the full binomial name (scientific name) to identify a germplasm" + binomialNames: [String] + "A specific panel/collection/population name this germplasm belongs to." + collections: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "A familyCode representing the family this germplasm belongs to." + familyCodes: [String] + "List of Genus names to identify germplasm" + genus: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "List of Permanent Unique Identifiers to identify germplasm" + germplasmPUIs: [String] + "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree" + includeFullTree: Boolean + "If this parameter is true, include the array of parents in the response" + includeParents: Boolean + "If this parameter is true, include the array of progeny in the response" + includeProgeny: Boolean + "If this parameter is true, include the array of siblings in the response" + includeSiblings: Boolean + """ + The code for the institute that maintains the material. +
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with "obsolete" codes, see "Common formatting rules (v)". + """ + instituteCodes: [String] + "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)" + pedigreeDepth: Int + "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)" + progenyDepth: Int + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "List of Species names to identify germplasm" + species: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "List of alternative names or IDs used to reference this germplasm" + synonyms: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input PersonInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "description of this person" + description: String + "email address for this person" + emailAddress: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "Persons first name" + firstName: String + "Persons last name" + lastName: String + lists: [ListInput] + "physical address of this person" + mailingAddress: String + "Persons middle name" + middleName: String + "Unique ID for a person" + personDbId: String + "phone number of this person" + phoneNumber: String + programs: [ProgramInput] + "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system." + userID: String +} + +input PersonsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "email address for this person" + emailAddresses: [String] + "Persons first name" + firstNames: [String] + "Persons last name" + lastNames: [String] + "physical address of this person" + mailingAddresses: [String] + "Persons middle name" + middleNames: [String] + "Unique ID for this person" + personDbIds: [String] + "phone number of this person" + phoneNumbers: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system." + userIDs: [String] +} + +input PlannedCrossInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "the type of cross" + crossType: CrossType + "crosses" + crosses: [CrossInput] + "the unique identifier for a crossing project" + crossingProject: CrossingProjectInput + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "the first parent used in the cross" + parent1: CrossParentInput + "the second parent used in the cross" + parent2: CrossParentInput + "the unique identifier for a planned cross" + plannedCrossDbId: String + "the human readable name for a planned cross" + plannedCrossName: String + "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')." + status: PlannedCrossStatus +} + +input PlannedCrossesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "Search for Crossing Projects with this unique id" + crossingProjectDbIds: [String] + "The human readable name for a crossing project" + crossingProjectNames: [String] + "Search for Planned Cross with this unique id" + plannedCrossDbIds: [String] + "Search for Planned Cross with this human readable name" + plannedCrossNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')." + statuses: [CrossStatus] +} + +input PlateInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "A unique identifier physically attached to a `Plate`" + plateBarcode: String + "The ID which uniquely identifies a `Plate`" + plateDbId: String + "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format" + plateFormat: PlateFormat + "A human readable name for a `Plate`" + plateName: String + "The ID which uniquely identifies a `Program` within the given database server" + program: ProgramInput + "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc" + sampleType: SampleType + "samples" + samples: [SampleInput] + "The ID which uniquely identifies a `Study` within the given database server" + study: StudyInput + "The ID which uniquely identifies a `Trial` within the given database server" + trial: TrialInput +} + +input PlatesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The ID which uniquely identifies a germplasm" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "The ID which uniquely identifies an observation unit" + observationUnitDbIds: [String] + "A unique identifier physically attached to the plate" + plateBarcodes: [String] + "The ID which uniquely identifies a plate of samples" + plateDbIds: [String] + "The human readable name of a plate of samples" + plateNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The ID which uniquely identifies a sample" + sampleDbIds: [String] + "The unique identifier for a group of related Samples" + sampleGroupDbIds: [String] + "The human readable name of the sample" + sampleNames: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input PollinationEventInput { + "Pollination events associated with a cross" + cross: CrossInput + "The unique identifier for this pollination event" + pollinationNumber: String + "True if the pollination was successful" + pollinationSuccessful: Boolean + "The timestamp when the pollination took place" + pollinationTimeStamp: String +} + +input ProgramInput { + "A shortened version of the human readable name for a Program" + abbreviation: String + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Common name for the crop which this program is for" + commonCropName: String + "crossingProjects" + crossingProjects: [CrossingProjectInput] + "A URL to the human readable documentation of an object" + documentationURL: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "Information describing the grant or funding source for this program" + fundingInformation: String + "The unique identifier of the program leader" + leadPerson: PersonInput + "The primary objective of the program" + objective: String + "observationUnits" + observationUnits: [ObservationUnitInput] + "plates" + plates: [PlateInput] + "The ID which uniquely identifies the program" + programDbId: String + "Human readable name of the program" + programName: String + """ + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding + """ + programType: ProgramType + "samples" + samples: [SampleInput] + "seedLots" + seedLots: [SeedLotInput] + trials: [TrialInput] +} + +input ProgramsInput { + "A list of shortened human readable names for a set of Programs" + abbreviations: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The person DbIds of the program leader to search for" + leadPersonDbIds: [String] + "The names of the program leader to search for" + leadPersonNames: [String] + "A program objective to search for" + objectives: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + """ + The type of program entity this object represents +
'STANDARD' represents a standard, permanent breeding program +
'PROJECT' represents a short term project, usually with a set time limit based on funding + """ + programTypes: [ProgramType] +} + +input PublicationInput { + publicationPUI: String + publicationReference: String + "Publications associated with a trial" + trial: TrialInput +} + +input ReferenceInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Common name for the crop" + commonCropName: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases." + isDerived: Boolean + "The length of this `Reference` sequence." + length: Int + "The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)." + md5checksum: String + "The unique identifier for a `Reference`" + referenceDbId: String + "The human readable name of a `Reference` within a `ReferenceSet`." + referenceName: String + "The unique identifier for a `ReferenceSet`" + referenceSet: ReferenceSetInput + "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`." + sourceAccessions: [String] + "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from." + sourceDivergence: Float + "All known corresponding Germplasm" + sourceGermplasm: [GermplasmInput] + "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI." + sourceURI: String + "An ontology term describing an attribute." + species: OntologyTermInput + "variants" + variants: [VariantInput] +} + +input ReferenceSetInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`." + assemblyPUI: String + "Common name for the crop" + commonCropName: String + "Optional free text description of this reference set." + description: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`)." + isDerived: Boolean + """ + Order-independent MD5 checksum which identifies this `ReferenceSet`. + + To compute this checksum, make a list of `Reference.md5checksum` for all + `Reference` s in this set. Then sort that list, and take the MD5 hash of + all the strings concatenated together. Express the hash as a lower-case + hexadecimal string. + """ + md5checksum: String + "The unique identifier for a ReferenceSet" + referenceSetDbId: String + "The human readable name of a ReferenceSet" + referenceSetName: String + "references" + references: ReferenceInput + "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`." + sourceAccessions: [String] + "All known corresponding Germplasm" + sourceGermplasm: [GermplasmInput] + "Specifies a FASTA format file/string." + sourceURI: String + "An ontology term describing an attribute." + species: OntologyTermInput + "variantSets" + variantSets: [VariantSetInput] + "variants" + variants: [VariantInput] +} + +input ReferenceSetsInput { + "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match)." + accessions: [String] + "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match)." + assemblyPUIs: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match)." + md5checksums: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The `ReferenceSets` to search." + referenceSetDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input ReferencesInput { + "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match)." + accessions: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases." + isDerived: Boolean + "The minimum length of this `References` sequence." + maxLength: Int + "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match)." + md5checksums: [String] + "The minimum length of this `References` sequence." + minLength: Int + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "A list of IDs which uniquely identify `References` within the given database server" + referenceDbIds: [String] + "A list of IDs which uniquely identify `ReferenceSets` within the given database server" + referenceSetDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input SampleInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + callSets: [CallSetInput] + "The Column identifier for this `Sample` location in the `Plate`" + column: Int + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The ID which uniquely identifies a `Germplasm`" + germplasm: GermplasmInput + "The ID which uniquely identifies an `ObservationUnit`" + observationUnit: ObservationUnitInput + "The ID which uniquely identifies a `Plate` of `Sample`" + plate: PlateInput + "The ID which uniquely identifies a `Program` within the given database server" + program: ProgramInput + "The Row identifier for this `Sample` location in the `Plate`" + row: String + "A unique identifier physically attached to the `Sample`" + sampleBarcode: String + """ + The ID which uniquely identifies a `Sample` +
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample. + """ + sampleDbId: String + """ + Description of a `Sample` +
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing. + """ + sampleDescription: String + "The ID which uniquely identifies a group of `Samples`" + sampleGroupId: String + "The human readable name of the `Sample`" + sampleName: String + """ + A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc) +
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. + """ + samplePUI: String + """ + The date and time a `Sample` was collected from the field +
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested + """ + sampleTimestamp: String + "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc" + sampleType: String + "The ID which uniquely identifies a `Study` within the given database server" + study: StudyInput + "The name or identifier of the entity which took the `Sample` from the field" + takenBy: String + """ + The type of tissue sampled. ex. 'Leaf', 'Root', etc. +
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology). + """ + tissueType: String + "The ID which uniquely identifies a `Trial` within the given database server" + trial: TrialInput + "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`." + well: String +} + +input SamplesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The ID which uniquely identifies a `Germplasm`" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "The ID which uniquely identifies an `ObservationUnit`" + observationUnitDbIds: [String] + "The ID which uniquely identifies a `Plate` of `Samples`" + plateDbIds: [String] + "The human readable name of a `Plate` of `Samples`" + plateNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The ID which uniquely identifies a `Sample`" + sampleDbIds: [String] + "The unique identifier for a group of related `Samples`" + sampleGroupDbIds: [String] + "The human readable name of the `Sample`" + sampleNames: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input ScaleInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + """ +

Class of the scale, entries can be

+

"Code" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. "75VD" means "75 %" of the plant is infected and the plant is very delayed.

+

"Date" - The date class is for events expressed in a time format, See ISO 8601

+

"Duration" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

+

"Nominal" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

+

"Numerical" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

+

"Ordinal" - Ordinal scales are scales composed of ordered categories

+

"Text" - A free text is used to express the trait.

+ """ + dataType: DataType + "For numerical, number of decimal places to be reported" + decimalPlaces: Int + "Filter by External References" + externalReferences: [ExternalReferenceInput] + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReferenceInput + "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID." + scaleDbId: String + """ + Name of the scale +
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable + """ + scaleName: String + "The Permanent Unique Identifier of a Scale, usually in the form of a URI" + scalePUI: String + """ + This field can be used to describe the units used for this scale. This should be the abbreviated + form of the units, intended to be displayed with every value using this scale. Usually this only + applies when `dataType` is Numeric, but could also be included for other dataTypes when applicable. + """ + units: String + validValues: ValidValuesInput +} + +input ScalesInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The unique identifier for an observation variable." + observationVariableDbIds: [String] + """ + The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology + + Use `GET /ontologies` to find the list of available ontologies on a server. + """ + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier for a scale." + scaleDbIds: [String] +} + +input SeasonInput { + "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'" + seasonDbId: String + "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc." + seasonName: String + "The 4 digit year of the season." + year: Int +} + +input SeasonsInput { + "The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'." + seasonDbIds: [String] + "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\"." + seasonNames: [String] + "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\"." + seasons: [String] + "The 4 digit year of a season. Example \"2017\"" + years: [String] +} + +input SeedLotInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)." + amount: Float + """ + The mixture of germplasm present in the seed lot. +
+ If this seed lot only contains a single germplasm, the response should contain the name + and DbId of that germplasm with a mixturePercentage value of 100 +
+ If the seed lot contains a mixture of different germplasm, the response should contain + the name and DbId every germplasm present. The mixturePercentage field should contain + the ratio of each germplasm in the total mixture. All of the mixturePercentage values + in this array should sum to equal 100. + """ + contentMixture: [ContentMixtureInput] + "The time stamp for when this seed lot was created" + createdDate: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "fromSeedLotTransactions" + fromSeedLotTransactions: [SeedLotTransactionInput] + "The timestamp for the last update to this Seed Lot (including transactions)" + lastUpdated: String + "The unique identifier for a Location" + location: LocationInput + "observationUnits" + observationUnits: [ObservationUnitInput] + "The unique DbId of the breeding program this Seed Lot belongs to" + program: ProgramInput + "Unique DbId for the Seed Lot" + seedLotDbId: String + "A general description of this Seed Lot" + seedLotDescription: String + "A human readable name for this Seed Lot" + seedLotName: String + "The description of the source where this material was originally collected (wild, nursery, etc)" + sourceCollection: String + "Description the storage location" + storageLocation: String + "toSeedLotTransactions" + toSeedLotTransactions: [SeedLotTransactionInput] + "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)" + units: String +} + +input SeedLotTransactionInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)." + amount: Float + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "The identifier for the Seed Lot being transferred out of" + fromSeedLot: SeedLotInput + "The identifier for the Seed Lot being transferred into" + toSeedLot: SeedLotInput + "Unique DbId for the Seed Lot Transaction" + transactionDbId: String + "A general description of this Seed Lot Transaction" + transactionDescription: String + "The time stamp for when the transaction occurred" + transactionTimestamp: String + "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)" + units: String +} + +input SeedLotsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "Search for Cross with this unique id" + crossDbIds: [String] + "Search for Cross with this human readable name" + crossNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "Unique id for a seed lot on this server" + seedLotDbIds: [String] +} + +input StorageTypeInput { + """ + The 2 digit code representing the type of storage this germplasm is kept in at a genebank. + + MCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) + + 10) Seed collection + 11) Short term + 12) Medium term + 13) Long term + 20) Field collection + 30) In vitro collection + 40) Cryo-preserved collection + 50) DNA collection + 99) Other (elaborate in REMARKS field) + """ + code: StorageTypeCode + "A supplemental text description of the storage type" + description: String + "associated germplasm" + germplasm: GermplasmInput +} + +input StudiesInput { + "A flag to indicate if a Study is currently active and ongoing" + active: Boolean + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of IDs which uniquely identify germplasm to search for" + germplasmDbIds: [String] + "List of human readable names to identify germplasm to search for" + germplasmNames: [String] + "The location ids to search for" + locationDbIds: [String] + "A human readable names to search for" + locationNames: [String] + "The DbIds of Variables to search for" + observationVariableDbIds: [String] + "The names of Variables to search for" + observationVariableNames: [String] + "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" + observationVariablePUIs: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The ID which uniquely identifies a season" + seasonDbIds: [String] + "A short human readable code for a study" + studyCodes: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "Permanent unique identifier associated with study data. For example, a URI or DOI" + studyPUIs: [String] + "The type of study being performed. ex. \"Yield Trial\", etc" + studyTypes: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] +} + +input StudyInput { + "A flag to indicate if a Study is currently active and ongoing" + active: Boolean + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + callSets: [CallSetInput] + "Common name for the crop associated with this study" + commonCropName: String + "List of contact entities associated with this study" + contacts: [ContactInput] + "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study." + culturalPractices: String + "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data." + dataLinks: [DataLinkInput] + "A URL to the human readable documentation of an object" + documentationURL: String + """ + The date the study ends + + MIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended + """ + endDate: String + """ + Environmental parameters that were kept constant throughout the study and did not change between observation units. + + MIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below). + """ + environmentParameters: [EnvironmentParametersInput] + "events" + events: [EventInput] + "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology" + experimentalDesign: ExperimentalDesignInput + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "Short description of the facility in which the study was carried out." + growthFacility: GrowthFacilityInput + "The date and time when this study was last modified" + lastUpdate: LastUpdateInput + "The usage license associated with the study data" + license: String + "The unique identifier for a Location" + location: LocationInput + """ + Observation levels indicate the granularity level at which the measurements are taken. `levelName` + defines the level, `levelOrder` defines where that level exists in the hierarchy of levels. + `levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are + at the bottom of the hierarchy (ie plant > 6). + + **Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** + + For more information on Observation Levels, please review the Observation Levels documentation. + """ + observationLevels: [ObservationUnitHierarchyLevelInput] + "observationUnits" + observationUnits: [ObservationUnitInput] + "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study." + observationUnitsDescription: String + """ + The list of Observation Variables being used in this study. + + This list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. + """ + observationVariables: [ObservationVariableInput] + "observations" + observations: [ObservationInput] + "plates" + plates: [PlateInput] + "samples" + samples: [SampleInput] + "List of seasons over which this study was performed." + seasons: [String] + """ + The date this study started + + MIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started + """ + startDate: String + "A short human readable code for a study" + studyCode: String + """ + The ID which uniquely identifies a study within the given database server + + MIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution. + """ + studyDbId: String + """ + The description of this study + + MIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study + """ + studyDescription: String + """ + The human readable name for a study + + MIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study + """ + studyName: String + "A permanent unique identifier associated with this study data. For example, a URI or DOI" + studyPUI: String + "The type of study being performed. ex. \"Yield Trial\", etc" + studyType: String + "The ID which uniquely identifies a trial" + trial: TrialInput + "variantSets" + variantSets: [VariantSetInput] +} + +input SynonymInput { + "associated germplasm" + germplasm: GermplasmInput + "Alternative name or ID used to reference this germplasm" + synonym: String + "A descriptive classification for this synonym" + type: String +} + +input TaxonIdInput { + "associated germplasm" + germplasm: GermplasmInput + "The human readable name of the taxonomy provider" + sourceName: String + "The identifier (name, ID, URI) of a particular taxonomy within the source provider" + taxonId: String +} + +input TraitInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention." + alternativeAbbreviations: [String] + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"" + attribute: String + """ + The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI +
A trait can be decomposed as "Trait" = "Entity" + "Attribute", the attribute is the observed feature (or characteristic) of the entity e.g., for "grain colour", attribute = "colour" + """ + attributePUI: String + "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"" + entity: String + """ + The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI +
A Trait can be decomposed as "Trait" = "Entity" + "Attribute", the Entity is the part of the plant that the trait refers to e.g., for "grain colour", entity = "grain" + """ + entityPUI: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "A shortened version of the human readable name for a Trait" + mainAbbreviation: String + """ + MIAPPE V1.1 + + (DM-85) Variable accession number - Accession number of the variable in the Crop Ontology + + (DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology). + + (DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology). + """ + ontologyReference: OntologyReferenceInput + "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)" + status: String + "Other trait names" + synonyms: [String] + """ + A classification to describe the type of trait and the context it should be considered in. +
examples- "morphological", "phenological", "agronomical", "physiological", "abiotic stress", "biotic stress", "biochemical", "quality traits", "fertility", etc. + """ + traitClass: String + "The ID which uniquely identifies a trait" + traitDbId: String + "The description of a trait" + traitDescription: String + """ + The human readable name of a trait +
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation + """ + traitName: String + "The Permanent Unique Identifier of a Trait, usually in the form of a URI" + traitPUI: String +} + +input TraitsInput { + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The unique identifier for an observation variable." + observationVariableDbIds: [String] + """ + The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology + + Use `GET /ontologies` to find the list of available ontologies on a server. + """ + ontologyDbIds: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier for a trait." + traitDbIds: [String] +} + +input TreatmentInput { + """ + The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc + + MIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor. + """ + factor: String + """ + The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc + + MIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. + """ + modality: String + "associated observation Unit" + observationUnit: ObservationUnitInput +} + +input TrialInput { + "A flag to indicate if a Trial is currently active and ongoing" + active: Boolean + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + "Common name for the crop associated with this trial" + commonCropName: String + "List of contact entities associated with this trial" + contacts: [ContactInput] + "License and citation information for the data in this trial" + datasetAuthorships: [DatasetAuthorshipsInput] + "A URL to the human readable documentation of an object" + documentationURL: String + "The date this trial ends" + endDate: String + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "observationUnits" + observationUnits: [ObservationUnitInput] + "plates" + plates: [PlateInput] + "A program identifier to search for" + program: ProgramInput + "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended." + publications: [PublicationInput] + "samples" + samples: [SampleInput] + "The date this trial started" + startDate: String + studies: [StudyInput] + """ + The ID which uniquely identifies a trial + + MIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution. + """ + trialDbId: String + """ + The human readable description of a trial + + MIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail. + """ + trialDescription: String + """ + The human readable name of a trial + + MIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation. + """ + trialName: String + "A permanent identifier for a trial. Could be DOI or other URI formatted identifier." + trialPUI: String +} + +input TrialsInput { + "A flag to indicate if a Trial is currently active and ongoing" + active: Boolean + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "List of contact entities associated with this trial" + contactDbIds: [String] + "The location ids to search for" + locationDbIds: [String] + "A human readable names to search for" + locationNames: [String] + "The DbIds of Variables to search for" + observationVariableDbIds: [String] + "The names of Variables to search for" + observationVariableNames: [String] + "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI" + observationVariablePUIs: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + """ + The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`. + + Return a Trial entity if any of the following cases are true + + - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null + + - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate` + + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null + + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` + """ + searchDateRangeEnd: String + """ + The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`. + + Return a Trial entity if any of the following cases are true + + - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null + + - `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate` + + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null + + - `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate` + """ + searchDateRangeStart: String + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] + "A permanent identifier for a trial. Could be DOI or other URI formatted identifier." + trialPUIs: [String] +} + +input ValidValuesCategoryInput { + "A text label for a category" + label: String + "associated valid values" + validValues: ValidValuesInput + "The actual value for a category" + value: String +} + +input ValidValuesInput { + "List of possible values with optional labels" + categories: [ValidValuesCategoryInput] + "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC." + maximumValue: String + "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC." + minimumValue: String + "associated scale" + scale: ScaleInput +} + +input VariantInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + alleleMatrices: [AlleleMatrixInput] + "Set of Analysis descriptors for this VariantSet" + analysis: [String] + calls: [CallInput] + "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)." + ciend: [Int] + """ + In the case of structural variants, start and end of the variant may not + be known with an exact base position. "cipos" provides an interval with + high confidence for the start position. The interval is provided by 0 or + 2 signed integers which are added to the start position. + Based on the use in VCF v4.2 + """ + cipos: [Int] + "The timestamp when this variant was created." + created: String + """ + This field is optional and may be ignored if there is no relevant map or reference to be associated with. +
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated + by `start + referenceBases.length`. + """ + end: Int + "Filter by External References" + externalReferences: [ExternalReferenceInput] + "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value." + filtersApplied: Boolean + "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record." + filtersFailed: [String] + "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS." + filtersPassed: Boolean + "markerPositions" + markerPositions: [MarkerPositionInput] + "The unique identifier for a Reference" + reference: ReferenceInput + "The reference bases for this variant. They start at the given start position." + referenceBases: String + "The unique identifier for a ReferenceSet" + referenceSet: ReferenceSetInput + """ + This field is optional and may be ignored if there is no relevant map or reference to be associated with. +
The start position at which this variant occurs (0-based). This corresponds to the first base of the string + of reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning + the join of circular genomes are represented as two variants one on each side of the join (position 0). + """ + start: Int + "Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2" + svlen: Int + "The time at which this variant was last updated." + updated: String + "The ID which uniquely identifies a `Variant`" + variantDbId: String + "A human readable name associated with a `Variant`" + variantNames: [String] + "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted." + variantSet: VariantSetInput + """ + The "variant_type" is used to denote e.g. structural variants. + Examples: + DUP : duplication of sequence following "start" + DEL : deletion of sequence following "start" + """ + variantType: String +} + +input VariantSetInput { + "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification." + additionalInfo: AdditionalInfoInput + alleleMatrices: [AlleleMatrixInput] + "Set of Analysis descriptors for this VariantSet" + analysis: [AnalysisInput] + """ + When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. +
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc) +
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response. + """ + availableFormats: [AvailableFormatInput] + "The number of CallSets included in this VariantSet" + callSetCount: Int + callSets: [CallSetInput] + calls: [CallInput] + "Filter by External References" + externalReferences: [ExternalReferenceInput] + """ + The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. +
When possible, these field names and abbreviations should follow the VCF standard + """ + metadataFields: [MetadataFieldInput] + "The ID of the reference set that describes the sequences used by the variants in this set." + referenceSet: ReferenceSetInput + "The ID of the dataset this variant set belongs to." + study: StudyInput + "The number of Variants included in this VariantSet" + variantCount: Int + "The unique identifier for a VariantSet" + variantSetDbId: String + "The human readable name for a VariantSet" + variantSetName: String + "variants" + variants: [VariantInput] +} + +input VariantSetsInput { + "The unique identifier representing a CallSet" + callSetDbIds: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + "The unique identifier representing a genotype Reference" + referenceDbIds: [String] + "The unique identifier representing a genotype ReferenceSet" + referenceSetDbIds: [String] + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] + "The unique identifier representing a Variant" + variantDbIds: [String] + "The unique identifier representing a VariantSet" + variantSetDbIds: [String] +} + +input VariantsInput { + """ + **Deprecated in v2.1** Parameter unnecessary. Github issue number #474 +
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects. + """ + callSetDbIds: [String] + """ + The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names. + + Use this parameter to only return results associated with the given crops. + + Use `GET /commoncropnames` to find the list of available crops on a server. + """ + commonCropNames: [String] + "The end of the window (0-based, exclusive) for which overlapping variants should be returned." + end: Int + """ + A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. + + Use this parameter to only return results associated with the given programs. + + Use `GET /programs` to find the list of available programs on a server. + """ + programDbIds: [String] + """ + Use this parameter to only return results associated with the given program names. Program names are not required to be unique. + + Use `GET /programs` to find the list of available programs on a server. + """ + programNames: [String] + """ + **Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472 +
Only return variants on this reference. + """ + referenceDbId: String + "The unique identifier representing a genotype `Reference`" + referenceDbIds: [String] + "The unique identifier representing a genotype `ReferenceSet`" + referenceSetDbIds: [String] + "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0)." + start: Int + "List of study identifiers to search for" + studyDbIds: [String] + "List of study names to filter search results" + studyNames: [String] + "The ID which uniquely identifies a trial to search for" + trialDbIds: [String] + "The human readable name of a trial to search for" + trialNames: [String] + "A list of IDs which uniquely identify `Variants`" + variantDbIds: [String] + "A list of IDs which uniquely identify `VariantSets`" + variantSetDbIds: [String] +} diff --git a/Specification/Generated/brapi_v2_1.json b/Specification/Generated/brapi_v2_1.json new file mode 100644 index 00000000..b62b6ad5 --- /dev/null +++ b/Specification/Generated/brapi_v2_1.json @@ -0,0 +1,20793 @@ +{ + "openapi" : "3.0.1", + "info" : { + "title" : "BrAPI", + "version" : "0.0.0" + }, + "paths" : { + "/breedingMethods" : { + "get" : { + "tags" : [ "BreedingMethods" ], + "summary" : "Get a filtered list of BreedingMethod", + "description" : "Get a list of BreedingMethod", + "parameters" : [ ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/calls" : { + "get" : { + "tags" : [ "Calls" ], + "summary" : "Get a filtered list of Call", + "description" : "Get a list of Call", + "parameters" : [ { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variant` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "expandHomozygote", + "in" : "query", + "description" : "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "sepPhased", + "in" : "query", + "description" : "The string used as a separator for phased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sepUnphased", + "in" : "query", + "description" : "The string used as a separator for unphased allele calls.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "unknownString", + "in" : "query", + "description" : "The string used as a representation for missing data.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/callSets" : { + "get" : { + "tags" : [ "CallSets" ], + "summary" : "Get a filtered list of CallSet", + "description" : "Get a list of CallSet", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Samples` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleName", + "in" : "query", + "description" : "A list of human readable names associated with `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "callSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `CallSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "callSetName", + "in" : "query", + "description" : "A list of human readable names associated with `CallSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/crosses" : { + "get" : { + "tags" : [ "Crosses" ], + "summary" : "Get a filtered list of Cross", + "description" : "Get a list of Cross", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossDbId", + "in" : "query", + "description" : "Search for Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossName", + "in" : "query", + "description" : "Search for Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Crosses" ], + "summary" : "Create new Cross", + "description" : "Add new Cross to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/CrossNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/crossingProjects" : { + "get" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Get a filtered list of CrossingProject", + "description" : "Get a list of CrossingProject", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "includePotentialParent", + "in" : "query", + "description" : "If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Create new CrossingProject", + "description" : "Add new CrossingProject to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/CrossingProjectNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/events" : { + "get" : { + "tags" : [ "Events" ], + "summary" : "Get a filtered list of Event", + "description" : "Get a list of Event", + "parameters" : [ { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an observation unit.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "eventDbId", + "in" : "query", + "description" : "Filter based on an Event DbId.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "eventType", + "in" : "query", + "description" : "Filter based on an Event Type", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dateRangeStart", + "in" : "query", + "description" : "Filter based on an Event start date.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dateRangeEnd", + "in" : "query", + "description" : "Filter based on an Event start date.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/EventListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/genomeMaps" : { + "get" : { + "tags" : [ "GenomeMaps" ], + "summary" : "Get a filtered list of GenomeMap", + "description" : "Get a list of GenomeMap", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "mapDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `GenomeMap`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "mapPUI", + "in" : "query", + "description" : "The DOI or other permanent identifier for a `GenomeMap`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scientificName", + "in" : "query", + "description" : "Full scientific binomial format name. This includes Genus, Species, and Sub-species", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "type", + "in" : "query", + "description" : "The type of map, usually \"Genetic\" or \"Physical\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasms" : { + "get" : { + "tags" : [ "Germplasms" ], + "summary" : "Get a filtered list of Germplasm", + "description" : "Get a list of Germplasm", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmPUI", + "in" : "query", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "accessionNumber", + "in" : "query", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "collection", + "in" : "query", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "familyCode", + "in" : "query", + "description" : "A familyCode representing the family this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "instituteCode", + "in" : "query", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "binomialName", + "in" : "query", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "genu", + "in" : "query", + "description" : "List of Genus names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "species", + "in" : "query", + "description" : "List of Species names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "synonym", + "in" : "query", + "description" : "List of alternative names or IDs used to reference this germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "parentDbId", + "in" : "query", + "description" : "Search for Germplasm with these parents", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "progenyDbId", + "in" : "query", + "description" : "Search for Germplasm with these children", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Germplasms" ], + "summary" : "Create new Germplasm", + "description" : "Add new Germplasm to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/GermplasmNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasmAttributes" : { + "get" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Get a filtered list of GermplasmAttribute", + "description" : "Get a list of GermplasmAttribute", + "parameters" : [ { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "List of ontology IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodName", + "in" : "query", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a Scale", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleName", + "in" : "query", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scalePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dataType", + "in" : "query", + "description" : "List of scale data types to filter search results", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, { + "name" : "traitClass", + "in" : "query", + "description" : "List of trait classes to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a Trait", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitName", + "in" : "query", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitAttribute", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitAttributePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitEntity", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitEntityPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeDbId", + "in" : "query", + "description" : "List of Germplasm Attribute IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeName", + "in" : "query", + "description" : "List of human readable Germplasm Attribute names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Attribute, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeCategory", + "in" : "query", + "description" : "General category for the attribute. very similar to Trait class.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Create new GermplasmAttribute", + "description" : "Add new GermplasmAttribute to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/GermplasmAttributeNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasmAttributeValues" : { + "get" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Get a filtered list of GermplasmAttributeValue", + "description" : "Get a list of GermplasmAttributeValue", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeValueDbId", + "in" : "query", + "description" : "List of Germplasm Attribute Value IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeDbId", + "in" : "query", + "description" : "List of Germplasm Attribute IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "attributeName", + "in" : "query", + "description" : "List of human readable Germplasm Attribute names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "List of ontology IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleDbId", + "in" : "query", + "description" : "List of scales to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitDbId", + "in" : "query", + "description" : "List of trait unique ID to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitClass", + "in" : "query", + "description" : "List of trait classes to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dataType", + "in" : "query", + "description" : "List of scale data types to filter search results", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Create new GermplasmAttributeValue", + "description" : "Add new GermplasmAttributeValue to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/GermplasmAttributeValueNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/images" : { + "get" : { + "tags" : [ "Images" ], + "summary" : "Get a filtered list of Image", + "description" : "Get a list of Image", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "descriptiveOntologyTerm", + "in" : "query", + "description" : "A list of terms to formally describe the image to search for. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageFileName", + "in" : "query", + "description" : "Image file names to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageFileSizeMax", + "in" : "query", + "description" : "A maximum image file size to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "imageFileSizeMin", + "in" : "query", + "description" : "A minimum image file size to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "imageHeightMax", + "in" : "query", + "description" : "A maximum image height to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "imageHeightMin", + "in" : "query", + "description" : "A minimum image height to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "imageLocation", + "in" : "query", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSONSearchArea" + } + }, { + "name" : "imageName", + "in" : "query", + "description" : "Human readable names to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageTimeStampRangeEnd", + "in" : "query", + "description" : "The latest timestamp to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageTimeStampRangeStart", + "in" : "query", + "description" : "The earliest timestamp to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageWidthMax", + "in" : "query", + "description" : "A maximum image width to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "imageWidthMin", + "in" : "query", + "description" : "A minimum image width to search for.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "mimeType", + "in" : "query", + "description" : "A set of image file types to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationDbId", + "in" : "query", + "description" : "A list of observation Ids this image is associated with to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "imageDbId", + "in" : "query", + "description" : "A list of image Ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "A set of observation unit identifiers to search for.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Images" ], + "summary" : "Create new Image", + "description" : "Add new Image to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ImageNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/lists" : { + "get" : { + "tags" : [ "Lists" ], + "summary" : "Get a filtered list of List", + "description" : "Get a list of List", + "parameters" : [ { + "name" : "dateCreatedRangeStart", + "in" : "query", + "description" : "Define the beginning for an interval of time and only include Lists that are created within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dateCreatedRangeEnd", + "in" : "query", + "description" : "Define the end for an interval of time and only include Lists that are created within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dateModifiedRangeStart", + "in" : "query", + "description" : "Define the beginning for an interval of time and only include Lists that are modified within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dateModifiedRangeEnd", + "in" : "query", + "description" : "Define the end for an interval of time and only include Lists that are modified within this interval.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listDbId", + "in" : "query", + "description" : "An array of primary database identifiers to identify a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listName", + "in" : "query", + "description" : "An array of human readable names to identify a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listOwnerName", + "in" : "query", + "description" : "An array of names for the people or entities who are responsible for a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listOwnerPersonDbId", + "in" : "query", + "description" : "An array of primary database identifiers to identify people or entities who are responsible for a set of Lists", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listSource", + "in" : "query", + "description" : "An array of terms identifying lists from different sources (ie 'USER', 'SYSTEM', etc)", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "listType", + "in" : "query", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/ListType" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Lists" ], + "summary" : "Create new List", + "description" : "Add new List to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ListNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/locations" : { + "get" : { + "tags" : [ "Locations" ], + "summary" : "Get a filtered list of Location", + "description" : "Get a list of Location", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "abbreviation", + "in" : "query", + "description" : "A list of shortened human readable names for a set of Locations", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "altitudeMin", + "in" : "query", + "description" : "The minimum altitude to search for", + "required" : false, + "schema" : { + "type" : "number" + } + }, { + "name" : "altitudeMax", + "in" : "query", + "description" : "The maximum altitude to search for", + "required" : false, + "schema" : { + "type" : "number" + } + }, { + "name" : "countryCode", + "in" : "query", + "description" : "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "countryName", + "in" : "query", + "description" : "The full name of the country to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "coordinate", + "in" : "query", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSONSearchArea" + } + }, { + "name" : "instituteAddress", + "in" : "query", + "description" : "The street address of the institute to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "instituteName", + "in" : "query", + "description" : "The name of the institute to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationType", + "in" : "query", + "description" : "The type of location this represents (ex. Breeding Location, Storage Location, etc)", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "parentLocationDbId", + "in" : "query", + "description" : "The unique identifier for a Location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "parentLocationName", + "in" : "query", + "description" : "A human readable name for a location\n
The Parent Location defines the encompassing location that this location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Locations" ], + "summary" : "Create new Location", + "description" : "Add new Location to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/LocationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/markerPositions" : { + "get" : { + "tags" : [ "MarkerPositions" ], + "summary" : "Get a filtered list of MarkerPosition", + "description" : "Get a list of MarkerPosition", + "parameters" : [ { + "name" : "mapDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `GenomeMaps` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "linkageGroupName", + "in" : "query", + "description" : "A list of Uniquely Identifiable linkage group names", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "minPosition", + "in" : "query", + "description" : "The minimum position of markers in a given map", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "maxPosition", + "in" : "query", + "description" : "The maximum position of markers in a given map", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/methods" : { + "get" : { + "tags" : [ "Methods" ], + "summary" : "Get a filtered list of Method", + "description" : "Get a list of Method", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a method.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Methods" ], + "summary" : "Create new Method", + "description" : "Add new Method to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/MethodNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observations" : { + "get" : { + "tags" : [ "Observations" ], + "summary" : "Get a filtered list of Observation", + "description" : "Get a list of Observation", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationDbId", + "in" : "query", + "description" : "The unique id of an Observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an Observation Unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, { + "name" : "observationLevelRelationship", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, { + "name" : "observationTimeStampRangeEnd", + "in" : "query", + "description" : "Timestamp range end", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationTimeStampRangeStart", + "in" : "query", + "description" : "Timestamp range start", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Observations" ], + "summary" : "Create new Observation", + "description" : "Add new Observation to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ObservationNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observationUnits" : { + "get" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Get a filtered list of ObservationUnit", + "description" : "Get a list of ObservationUnit", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The unique id of an observation unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitName", + "in" : "query", + "description" : "The human readable identifier for an Observation Unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationLevel", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevel", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, { + "name" : "observationLevelRelationship", + "in" : "query", + "description" : "Searches for values in ObservationUnit->observationUnitPosition->observationLevelRelationships", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, { + "name" : "includeObservation", + "in" : "query", + "description" : "Use this parameter to include a list of observations embedded in each ObservationUnit object. \n\nCAUTION - Use this parameter at your own risk. It may return large, unpaginated lists of observation data. Only set this value to True if you are sure you need to.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "seasonDbId", + "in" : "query", + "description" : "The year or Phenotyping campaign of a multi-annual study (trees, grape, ...)", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Create new ObservationUnit", + "description" : "Add new ObservationUnit to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ObservationUnitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observationVariables" : { + "get" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Get a filtered list of ObservationVariable", + "description" : "Get a list of ObservationVariable", + "parameters" : [ { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `studyDbIds`. Github issue number #483 \n
The unique ID of a studies to filter on", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "List of ontology IDs to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodDbId", + "in" : "query", + "description" : "List of methods to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodName", + "in" : "query", + "description" : "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "methodPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Method, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a Scale", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleName", + "in" : "query", + "description" : "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scalePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Scale, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "dataType", + "in" : "query", + "description" : "List of scale data types to filter search results", + "required" : false, + "schema" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, { + "name" : "traitClass", + "in" : "query", + "description" : "List of trait classes to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a Trait", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitName", + "in" : "query", + "description" : "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitAttribute", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitAttributePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitEntity", + "in" : "query", + "description" : "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitEntityPUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" ", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Create new ObservationVariable", + "description" : "Add new ObservationVariable to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ObservationVariableNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/ontologies" : { + "get" : { + "tags" : [ "Ontologies" ], + "summary" : "Get a filtered list of Ontology", + "description" : "Get a list of Ontology", + "parameters" : [ { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyName", + "in" : "query", + "description" : "The human readable identifier for an ontology definition.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Ontologies" ], + "summary" : "Create new Ontology", + "description" : "Add new Ontology to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/OntologyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "pedigrees" : { + "get" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Get a filtered list of PedigreeNode", + "description" : "Get a list of PedigreeNode", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmPUI", + "in" : "query", + "description" : "List of Permanent Unique Identifiers to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "accessionNumber", + "in" : "query", + "description" : "A collection of unique identifiers for materials or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\").", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "collection", + "in" : "query", + "description" : "A specific panel/collection/population name this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "familyCode", + "in" : "query", + "description" : "A familyCode representing the family this germplasm belongs to.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "instituteCode", + "in" : "query", + "description" : "The code for the institute that maintains the material. \n
MCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "binomialName", + "in" : "query", + "description" : "List of the full binomial name (scientific name) to identify a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "genu", + "in" : "query", + "description" : "List of Genus names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "species", + "in" : "query", + "description" : "List of Species names to identify germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "synonym", + "in" : "query", + "description" : "List of alternative names or IDs used to reference this germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "includeParent", + "in" : "query", + "description" : "If this parameter is true, include the array of parents in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "includeSibling", + "in" : "query", + "description" : "If this parameter is true, include the array of siblings in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "includeProgeny", + "in" : "query", + "description" : "If this parameter is true, include the array of progeny in the response", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "includeFullTree", + "in" : "query", + "description" : "If this parameter is true, recursively include ALL of the nodes available in this pedigree tree", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "pedigreeDepth", + "in" : "query", + "description" : "Recursively include this number of levels up the tree in the response (parents, grand-parents, great-grand-parents, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "progenyDepth", + "in" : "query", + "description" : "Recursively include this number of levels down the tree in the response (children, grand-children, great-grand-children, etc)", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Create new PedigreeNode", + "description" : "Add new PedigreeNode to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/PedigreeNode" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/persons" : { + "get" : { + "tags" : [ "Persons" ], + "summary" : "Get a filtered list of Person", + "description" : "Get a list of Person", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "emailAddress", + "in" : "query", + "description" : "email address for this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "firstName", + "in" : "query", + "description" : "Persons first name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "lastName", + "in" : "query", + "description" : "Persons last name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "mailingAddress", + "in" : "query", + "description" : "physical address of this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "middleName", + "in" : "query", + "description" : "Persons middle name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "personDbId", + "in" : "query", + "description" : "Unique ID for this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "phoneNumber", + "in" : "query", + "description" : "phone number of this person", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "userID", + "in" : "query", + "description" : "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Persons" ], + "summary" : "Create new Person", + "description" : "Add new Person to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/PersonNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/plannedCrosses" : { + "get" : { + "tags" : [ "PlannedCrosses" ], + "summary" : "Get a filtered list of PlannedCross", + "description" : "Get a list of PlannedCross", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectDbId", + "in" : "query", + "description" : "Search for Crossing Projects with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossingProjectName", + "in" : "query", + "description" : "The human readable name for a crossing project", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plannedCrossDbId", + "in" : "query", + "description" : "Search for Planned Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plannedCrossName", + "in" : "query", + "description" : "Search for Planned Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "status", + "in" : "query", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "required" : false, + "schema" : { + "type" : "string", + "enum" : [ "TODO", "DONE", "SKIPPED" ] + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "PlannedCrosses" ], + "summary" : "Create new PlannedCross", + "description" : "Add new PlannedCross to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/PlannedCross" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/plates" : { + "get" : { + "tags" : [ "Plates" ], + "summary" : "Get a filtered list of Plate", + "description" : "Get a list of Plate", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an observation unit", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plateDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a plate of samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plateName", + "in" : "query", + "description" : "The human readable name of a plate of samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plateBarcode", + "in" : "query", + "description" : "A unique identifier physically attached to the plate", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a sample", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleName", + "in" : "query", + "description" : "The human readable name of the sample", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleGroupDbId", + "in" : "query", + "description" : "The unique identifier for a group of related Samples", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a germplasm", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Plates" ], + "summary" : "Create new Plate", + "description" : "Add new Plate to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/PlateNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/programs" : { + "get" : { + "tags" : [ "Programs" ], + "summary" : "Get a filtered list of Program", + "description" : "Get a list of Program", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "abbreviation", + "in" : "query", + "description" : "A list of shortened human readable names for a set of Programs", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "leadPersonDbId", + "in" : "query", + "description" : "The person DbIds of the program leader to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "leadPersonName", + "in" : "query", + "description" : "The names of the program leader to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "objectife", + "in" : "query", + "description" : "A program objective to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programType", + "in" : "query", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "required" : false, + "schema" : { + "type" : "string", + "enum" : [ "STANDARD", "PROJECT" ] + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Programs" ], + "summary" : "Create new Program", + "description" : "Add new Program to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ProgramNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/references" : { + "get" : { + "tags" : [ "References" ], + "summary" : "Get a filtered list of Reference", + "description" : "Get a list of Reference", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "accession", + "in" : "query", + "description" : "If specified, return the references for which the `accession` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "md5checksum", + "in" : "query", + "description" : "If specified, return the references for which the `md5checksum` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `References` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `ReferenceSets` within the given database server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "isDerived", + "in" : "query", + "description" : "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases.", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "minLength", + "in" : "query", + "description" : "The minimum length of this `References` sequence.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "maxLength", + "in" : "query", + "description" : "The minimum length of this `References` sequence.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/referenceSets" : { + "get" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Get a filtered list of ReferenceSet", + "description" : "Get a list of ReferenceSet", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "accession", + "in" : "query", + "description" : "If set, return the reference sets for which the `accession` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "assemblyPUI", + "in" : "query", + "description" : "If set, return the reference sets for which the `assemblyId` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "md5checksum", + "in" : "query", + "description" : "If set, return the reference sets for which the `md5checksum` matches this string (case-sensitive, exact match).", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The `ReferenceSets` to search.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Create new ReferenceSet", + "description" : "Add new ReferenceSet to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ReferenceSetNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/samples" : { + "get" : { + "tags" : [ "Samples" ], + "summary" : "Get a filtered list of Sample", + "description" : "Get a list of Sample", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationUnitDbId", + "in" : "query", + "description" : "The ID which uniquely identifies an `ObservationUnit`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plateDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Plate` of `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "plateName", + "in" : "query", + "description" : "The human readable name of a `Plate` of `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Sample`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleName", + "in" : "query", + "description" : "The human readable name of the `Sample`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "sampleGroupDbId", + "in" : "query", + "description" : "The unique identifier for a group of related `Samples`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a `Germplasm`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Samples" ], + "summary" : "Create new Sample", + "description" : "Add new Sample to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/SampleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/scales" : { + "get" : { + "tags" : [ "Scales" ], + "summary" : "Get a filtered list of Scale", + "description" : "Get a list of Scale", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "scaleDbId", + "in" : "query", + "description" : "The unique identifier for a scale.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Scales" ], + "summary" : "Create new Scale", + "description" : "Add new Scale to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/ScaleNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/seasons" : { + "get" : { + "tags" : [ "Seasons" ], + "summary" : "Get a filtered list of Season", + "description" : "Get a list of Season", + "parameters" : [ { + "name" : "seasonDbId", + "in" : "query", + "description" : "The unique identifier for a season. For backward compatibility it can be a string like '2012', '1957-2004'.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "season", + "in" : "query", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "seasonName", + "in" : "query", + "description" : "The term to describe a given season. Example \"Spring\" OR \"May\" OR \"Planting_Time_7\".", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "year", + "in" : "query", + "description" : "The 4 digit year of a season. Example \"2017\"", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Seasons" ], + "summary" : "Create new Season", + "description" : "Add new Season to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/Season" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/seedLots" : { + "get" : { + "tags" : [ "SeedLots" ], + "summary" : "Get a filtered list of SeedLot", + "description" : "Get a list of SeedLot", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "seedLotDbId", + "in" : "query", + "description" : "Unique id for a seed lot on this server", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossDbId", + "in" : "query", + "description" : "Search for Cross with this unique id", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "crossName", + "in" : "query", + "description" : "Search for Cross with this human readable name", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "SeedLots" ], + "summary" : "Create new SeedLot", + "description" : "Add new SeedLot to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/SeedLotNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/studies" : { + "get" : { + "tags" : [ "Studies" ], + "summary" : "Get a filtered list of Study", + "description" : "Get a list of Study", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmDbId", + "in" : "query", + "description" : "List of IDs which uniquely identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "germplasmName", + "in" : "query", + "description" : "List of human readable names to identify germplasm to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "actife", + "in" : "query", + "description" : "A flag to indicate if a Study is currently active and ongoing", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "seasonDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a season", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyType", + "in" : "query", + "description" : "The type of study being performed. ex. \"Yield Trial\", etc", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyCode", + "in" : "query", + "description" : "A short human readable code for a study", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyPUI", + "in" : "query", + "description" : "Permanent unique identifier associated with study data. For example, a URI or DOI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Studies" ], + "summary" : "Create new Study", + "description" : "Add new Study to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/StudyNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/traits" : { + "get" : { + "tags" : [ "Traits" ], + "summary" : "Get a filtered list of Trait", + "description" : "Get a list of Trait", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "ontologyDbId", + "in" : "query", + "description" : "The unique identifier for an ontology definition. Use this parameter to filter results based on a specific ontology \n\n Use `GET /ontologies` to find the list of available ontologies on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "traitDbId", + "in" : "query", + "description" : "The unique identifier for a trait.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The unique identifier for an observation variable.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Traits" ], + "summary" : "Create new Trait", + "description" : "Add new Trait to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/TraitNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/trials" : { + "get" : { + "tags" : [ "Trials" ], + "summary" : "Get a filtered list of Trial", + "description" : "Get a list of Trial", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationDbId", + "in" : "query", + "description" : "The location ids to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "locationName", + "in" : "query", + "description" : "A human readable names to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableDbId", + "in" : "query", + "description" : "The DbIds of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariableName", + "in" : "query", + "description" : "The names of Variables to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "observationVariablePUI", + "in" : "query", + "description" : "The Permanent Unique Identifier of an Observation Variable, usually in the form of a URI", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "actife", + "in" : "query", + "description" : "A flag to indicate if a Trial is currently active and ongoing", + "required" : false, + "schema" : { + "type" : "boolean" + } + }, { + "name" : "contactDbId", + "in" : "query", + "description" : "List of contact entities associated with this trial", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "searchDateRangeStart", + "in" : "query", + "description" : "The start of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "searchDateRangeEnd", + "in" : "query", + "description" : "The end of the overlapping search date range. `searchDateRangeStart` must be before `searchDateRangeEnd`.\n\nReturn a Trial entity if any of the following cases are true\n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is null \n\n- `searchDateRangeStart` is before `trial.endDate` AND `searchDateRangeEnd` is after `trial.startDate`\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is null\n\n- `searchDateRangeEnd` is after `trial.startDate` AND `searchDateRangeStart` is before `trial.endDate`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialPUI", + "in" : "query", + "description" : "A permanent identifier for a trial. Could be DOI or other URI formatted identifier.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "post" : { + "tags" : [ "Trials" ], + "summary" : "Create new Trial", + "description" : "Add new Trial to database", + "parameters" : [ { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "requestBody" : { + "content" : { + "application/json" : { + "schema" : { + "type" : "array", + "$ref" : "#/components/schemas/TrialNewRequest" + } + } + } + }, + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/variants" : { + "get" : { + "tags" : [ "Variants" ], + "summary" : "Get a filtered list of Variant", + "description" : "Get a list of Variant", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "callSetDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Parameter unnecessary. Github issue number #474 \n
Only return variant calls which belong to call sets with these IDs. If unspecified, return all variants and no variant call objects.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "end", + "in" : "query", + "description" : "The end of the window (0-based, exclusive) for which overlapping variants should be returned.", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "referenceDbId", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `referenceDbIds`. Github issue number #472\n
Only return variants on this reference.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `Reference`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype `ReferenceSet`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "start", + "in" : "query", + "description" : "The beginning of the window (0-based, inclusive) for which overlapping variants should be returned. Genomic positions are non-negative integers less than reference length. Requests spanning the join of circular genomes are represented as two requests one on each side of the join (position 0).", + "required" : false, + "schema" : { + "type" : "integer", + "format" : "int32" + } + }, { + "name" : "variantDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `Variants`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantSetDbId", + "in" : "query", + "description" : "A list of IDs which uniquely identify `VariantSets`", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/variantSets" : { + "get" : { + "tags" : [ "VariantSets" ], + "summary" : "Get a filtered list of VariantSet", + "description" : "Get a list of VariantSet", + "parameters" : [ { + "name" : "commonCropName", + "in" : "query", + "description" : "The BrAPI Common Crop Name is the simple, generalized, widely accepted name of the organism being researched. It is most often used in multi-crop systems where digital resources need to be divided at a high level. Things like 'Maize', 'Wheat', and 'Rice' are examples of common crop names.\n\nUse this parameter to only return results associated with the given crops. \n\nUse `GET /commoncropnames` to find the list of available crops on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programDbId", + "in" : "query", + "description" : "A BrAPI Program represents the high level organization or group who is responsible for conducting trials and studies. Things like Breeding Programs and Funded Projects are considered BrAPI Programs. \n\nUse this parameter to only return results associated with the given programs. \n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "programName", + "in" : "query", + "description" : "Use this parameter to only return results associated with the given program names. Program names are not required to be unique.\n\nUse `GET /programs` to find the list of available programs on a server.", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyDbId", + "in" : "query", + "description" : "List of study identifiers to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "studyName", + "in" : "query", + "description" : "List of study names to filter search results", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialDbId", + "in" : "query", + "description" : "The ID which uniquely identifies a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "trialName", + "in" : "query", + "description" : "The human readable name of a trial to search for", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "callSetDbId", + "in" : "query", + "description" : "The unique identifier representing a CallSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantDbId", + "in" : "query", + "description" : "The unique identifier representing a Variant", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "variantSetDbId", + "in" : "query", + "description" : "The unique identifier representing a VariantSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype Reference", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "name" : "referenceSetDbId", + "in" : "query", + "description" : "The unique identifier representing a genotype ReferenceSet", + "required" : false, + "schema" : { + "type" : "string" + } + }, { + "$ref" : "#/components/properties/externalReferenceID" + }, { + "$ref" : "#/components/properties/externalReferenceId" + }, { + "$ref" : "#/components/properties/externalReferenceSource" + }, { + "$ref" : "#/components/properties/page" + }, { + "$ref" : "#/components/properties/pageSize" + }, { + "$ref" : "#/components/properties/authorizationHeader" + } ], + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/breedingMethods/{breedingMethodDbId}" : { + "get" : { + "tags" : [ "BreedingMethods" ], + "summary" : "Get the details of a specific BreedingMethod", + "description" : "Get details for a BreedingMethod", + "responses" : { + "200" : { + "$ref" : "#/components/responses/BreedingMethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/callSets/{callSetDbId}" : { + "get" : { + "tags" : [ "CallSets" ], + "summary" : "Get the details of a specific CallSet", + "description" : "Get details for a CallSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/crossingProjects/{crossingProjectDbId}" : { + "get" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Get the details of a specific CrossingProject", + "description" : "Get details for a CrossingProject", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Update the details for an existing CrossingProject", + "description" : "Update the details for an existing CrossingProject", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/genomeMaps/{genomeMapDbId}" : { + "get" : { + "tags" : [ "GenomeMaps" ], + "summary" : "Get the details of a specific GenomeMap", + "description" : "Get details for a GenomeMap", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasms/{germplasmDbId}" : { + "get" : { + "tags" : [ "Germplasms" ], + "summary" : "Get the details of a specific Germplasm", + "description" : "Get details for a Germplasm", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Germplasms" ], + "summary" : "Update the details for an existing Germplasm", + "description" : "Update the details for an existing Germplasm", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasmAttributes/{attributeDbId}" : { + "get" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Get the details of a specific GermplasmAttribute", + "description" : "Get details for a GermplasmAttribute", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Update the details for an existing GermplasmAttribute", + "description" : "Update the details for an existing GermplasmAttribute", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/germplasmAttributeValues/{attributeValueDbId}" : { + "get" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Get the details of a specific GermplasmAttributeValue", + "description" : "Get details for a GermplasmAttributeValue", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Update the details for an existing GermplasmAttributeValue", + "description" : "Update the details for an existing GermplasmAttributeValue", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/images/{imageDbId}" : { + "get" : { + "tags" : [ "Images" ], + "summary" : "Get the details of a specific Image", + "description" : "Get details for a Image", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Images" ], + "summary" : "Update the details for an existing Image", + "description" : "Update the details for an existing Image", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/lists/{listDbId}" : { + "get" : { + "tags" : [ "Lists" ], + "summary" : "Get the details of a specific List", + "description" : "Get details for a List", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Lists" ], + "summary" : "Update the details for an existing List", + "description" : "Update the details for an existing List", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/locations/{locationDbId}" : { + "get" : { + "tags" : [ "Locations" ], + "summary" : "Get the details of a specific Location", + "description" : "Get details for a Location", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Locations" ], + "summary" : "Update the details for an existing Location", + "description" : "Update the details for an existing Location", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/methods/{methodDbId}" : { + "get" : { + "tags" : [ "Methods" ], + "summary" : "Get the details of a specific Method", + "description" : "Get details for a Method", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Methods" ], + "summary" : "Update the details for an existing Method", + "description" : "Update the details for an existing Method", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MethodSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observations/{observationDbId}" : { + "get" : { + "tags" : [ "Observations" ], + "summary" : "Get the details of a specific Observation", + "description" : "Get details for a Observation", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Observations" ], + "summary" : "Update the details for an existing Observation", + "description" : "Update the details for an existing Observation", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observationUnits/{observationUnitDbId}" : { + "get" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Get the details of a specific ObservationUnit", + "description" : "Get details for a ObservationUnit", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Update the details for an existing ObservationUnit", + "description" : "Update the details for an existing ObservationUnit", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/observationVariables/{observationVariableDbId}" : { + "get" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Get the details of a specific ObservationVariable", + "description" : "Get details for a ObservationVariable", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Update the details for an existing ObservationVariable", + "description" : "Update the details for an existing ObservationVariable", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/ontologies/{ontologyDbId}" : { + "get" : { + "tags" : [ "Ontologies" ], + "summary" : "Get the details of a specific Ontology", + "description" : "Get details for a Ontology", + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Ontologies" ], + "summary" : "Update the details for an existing Ontology", + "description" : "Update the details for an existing Ontology", + "responses" : { + "200" : { + "$ref" : "#/components/responses/OntologySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "pedigrees/{pedigreeNodeDbId}" : { + "get" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Get the details of a specific PedigreeNode", + "description" : "Get details for a PedigreeNode", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Update the details for an existing PedigreeNode", + "description" : "Update the details for an existing PedigreeNode", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/persons/{personDbId}" : { + "get" : { + "tags" : [ "Persons" ], + "summary" : "Get the details of a specific Person", + "description" : "Get details for a Person", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Persons" ], + "summary" : "Update the details for an existing Person", + "description" : "Update the details for an existing Person", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/plannedCrosses/{plannedCrossDbId}" : { + "put" : { + "tags" : [ "PlannedCrosses" ], + "summary" : "Update the details for an existing PlannedCross", + "description" : "Update the details for an existing PlannedCross", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/plates/{plateDbId}" : { + "get" : { + "tags" : [ "Plates" ], + "summary" : "Get the details of a specific Plate", + "description" : "Get details for a Plate", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Plates" ], + "summary" : "Update the details for an existing Plate", + "description" : "Update the details for an existing Plate", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/programs/{programDbId}" : { + "get" : { + "tags" : [ "Programs" ], + "summary" : "Get the details of a specific Program", + "description" : "Get details for a Program", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Programs" ], + "summary" : "Update the details for an existing Program", + "description" : "Update the details for an existing Program", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/references/{referenceDbId}" : { + "get" : { + "tags" : [ "References" ], + "summary" : "Get the details of a specific Reference", + "description" : "Get details for a Reference", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/referenceSets/{referenceSetDbId}" : { + "get" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Get the details of a specific ReferenceSet", + "description" : "Get details for a ReferenceSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Update the details for an existing ReferenceSet", + "description" : "Update the details for an existing ReferenceSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/samples/{sampleDbId}" : { + "get" : { + "tags" : [ "Samples" ], + "summary" : "Get the details of a specific Sample", + "description" : "Get details for a Sample", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Samples" ], + "summary" : "Update the details for an existing Sample", + "description" : "Update the details for an existing Sample", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/scales/{scaleDbId}" : { + "get" : { + "tags" : [ "Scales" ], + "summary" : "Get the details of a specific Scale", + "description" : "Get details for a Scale", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Scales" ], + "summary" : "Update the details for an existing Scale", + "description" : "Update the details for an existing Scale", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ScaleSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/seasons/{seasonDbId}" : { + "get" : { + "tags" : [ "Seasons" ], + "summary" : "Get the details of a specific Season", + "description" : "Get details for a Season", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Seasons" ], + "summary" : "Update the details for an existing Season", + "description" : "Update the details for an existing Season", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/seedLots/{seedLotDbId}" : { + "get" : { + "tags" : [ "SeedLots" ], + "summary" : "Get the details of a specific SeedLot", + "description" : "Get details for a SeedLot", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "SeedLots" ], + "summary" : "Update the details for an existing SeedLot", + "description" : "Update the details for an existing SeedLot", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/studies/{studyDbId}" : { + "get" : { + "tags" : [ "Studies" ], + "summary" : "Get the details of a specific Study", + "description" : "Get details for a Study", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Studies" ], + "summary" : "Update the details for an existing Study", + "description" : "Update the details for an existing Study", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudySingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/traits/{traitDbId}" : { + "get" : { + "tags" : [ "Traits" ], + "summary" : "Get the details of a specific Trait", + "description" : "Get details for a Trait", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Traits" ], + "summary" : "Update the details for an existing Trait", + "description" : "Update the details for an existing Trait", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TraitSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/trials/{trialDbId}" : { + "get" : { + "tags" : [ "Trials" ], + "summary" : "Get the details of a specific Trial", + "description" : "Get details for a Trial", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "Trials" ], + "summary" : "Update the details for an existing Trial", + "description" : "Update the details for an existing Trial", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/variants/{variantDbId}" : { + "get" : { + "tags" : [ "Variants" ], + "summary" : "Get the details of a specific Variant", + "description" : "Get details for a Variant", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/variantSets/{variantSetDbId}" : { + "get" : { + "tags" : [ "VariantSets" ], + "summary" : "Get the details of a specific VariantSet", + "description" : "Get details for a VariantSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + }, + "put" : { + "tags" : [ "VariantSets" ], + "summary" : "Update the details for an existing VariantSet", + "description" : "Update the details for an existing VariantSet", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetSingleResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/calls" : { + "post" : { + "tags" : [ "Calls" ], + "summary" : "Submit a search request for `Call`", + "description" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/callSets" : { + "post" : { + "tags" : [ "CallSets" ], + "summary" : "Submit a search request for `CallSet`", + "description" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/crossingProjects" : { + "post" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Submit a search request for `CrossingProject`", + "description" : "Submit a search request for `CrossingProject`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/crossingProject/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/events" : { + "post" : { + "tags" : [ "Events" ], + "summary" : "Submit a search request for `Event`", + "description" : "Submit a search request for `Event`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/event/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/EventListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/genomeMaps" : { + "post" : { + "tags" : [ "GenomeMaps" ], + "summary" : "Submit a search request for `GenomeMap`", + "description" : "Submit a search request for `GenomeMap`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/genomeMap/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasms" : { + "post" : { + "tags" : [ "Germplasms" ], + "summary" : "Submit a search request for `Germplasm`", + "description" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasmAttributes" : { + "post" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Submit a search request for `GermplasmAttribute`", + "description" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasmAttributeValues" : { + "post" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Submit a search request for `GermplasmAttributeValue`", + "description" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/images" : { + "post" : { + "tags" : [ "Images" ], + "summary" : "Submit a search request for `Image`", + "description" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/lists" : { + "post" : { + "tags" : [ "Lists" ], + "summary" : "Submit a search request for `List`", + "description" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/locations" : { + "post" : { + "tags" : [ "Locations" ], + "summary" : "Submit a search request for `Location`", + "description" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/markerPositions" : { + "post" : { + "tags" : [ "MarkerPositions" ], + "summary" : "Submit a search request for `MarkerPosition`", + "description" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observations" : { + "post" : { + "tags" : [ "Observations" ], + "summary" : "Submit a search request for `Observation`", + "description" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observationUnits" : { + "post" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Submit a search request for `ObservationUnit`", + "description" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observationVariables" : { + "post" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Submit a search request for `ObservationVariable`", + "description" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/pedigreeNodes" : { + "post" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Submit a search request for `PedigreeNode`", + "description" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/persons" : { + "post" : { + "tags" : [ "Persons" ], + "summary" : "Submit a search request for `Person`", + "description" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/plannedCrosses" : { + "post" : { + "tags" : [ "PlannedCrosses" ], + "summary" : "Submit a search request for `PlannedCross`", + "description" : "Submit a search request for `PlannedCross`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plannedCross/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/plates" : { + "post" : { + "tags" : [ "Plates" ], + "summary" : "Submit a search request for `Plate`", + "description" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/programs" : { + "post" : { + "tags" : [ "Programs" ], + "summary" : "Submit a search request for `Program`", + "description" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/references" : { + "post" : { + "tags" : [ "References" ], + "summary" : "Submit a search request for `Reference`", + "description" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/referenceSets" : { + "post" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Submit a search request for `ReferenceSet`", + "description" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/samples" : { + "post" : { + "tags" : [ "Samples" ], + "summary" : "Submit a search request for `Sample`", + "description" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/seasons" : { + "post" : { + "tags" : [ "Seasons" ], + "summary" : "Submit a search request for `Season`", + "description" : "Submit a search request for `Season`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/season/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/seedLots" : { + "post" : { + "tags" : [ "SeedLots" ], + "summary" : "Submit a search request for `SeedLot`", + "description" : "Submit a search request for `SeedLot`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/seedLot/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/studies" : { + "post" : { + "tags" : [ "Studies" ], + "summary" : "Submit a search request for `Study`", + "description" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/trials" : { + "post" : { + "tags" : [ "Trials" ], + "summary" : "Submit a search request for `Trial`", + "description" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/variants" : { + "post" : { + "tags" : [ "Variants" ], + "summary" : "Submit a search request for `Variant`", + "description" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/variantSets" : { + "post" : { + "tags" : [ "VariantSets" ], + "summary" : "Submit a search request for `VariantSet`", + "description" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "202" : { + "$ref" : "#/components/responses/202AcceptedSearchResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/calls/{callDbId}" : { + "get" : { + "tags" : [ "Calls" ], + "summary" : "Submit a search request for `Call`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/call/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Call` search request
\nClients should submit a search request using the corresponding `POST /search/call` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/callSets/{callSetDbId}" : { + "get" : { + "tags" : [ "CallSets" ], + "summary" : "Submit a search request for `CallSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/callSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `CallSet` search request
\nClients should submit a search request using the corresponding `POST /search/callSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CallSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/crossingProjects/{crossingProjectDbId}" : { + "get" : { + "tags" : [ "CrossingProjects" ], + "summary" : "Submit a search request for `CrossingProject`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/crossingProject/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `CrossingProject` search request
\nClients should submit a search request using the corresponding `POST /search/crossingProject` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/CrossingProjectListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/events/{eventDbId}" : { + "get" : { + "tags" : [ "Events" ], + "summary" : "Submit a search request for `Event`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/event/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Event` search request
\nClients should submit a search request using the corresponding `POST /search/event` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/EventListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/genomeMaps/{genomeMapDbId}" : { + "get" : { + "tags" : [ "GenomeMaps" ], + "summary" : "Submit a search request for `GenomeMap`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/genomeMap/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `GenomeMap` search request
\nClients should submit a search request using the corresponding `POST /search/genomeMap` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GenomeMapListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasms/{germplasmDbId}" : { + "get" : { + "tags" : [ "Germplasms" ], + "summary" : "Submit a search request for `Germplasm`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasm/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Germplasm` search request
\nClients should submit a search request using the corresponding `POST /search/germplasm` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasmAttributes/{attributeDbId}" : { + "get" : { + "tags" : [ "GermplasmAttributes" ], + "summary" : "Submit a search request for `GermplasmAttribute`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttribute/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `GermplasmAttribute` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttribute` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/germplasmAttributeValues/{attributeValueDbId}" : { + "get" : { + "tags" : [ "GermplasmAttributeValues" ], + "summary" : "Submit a search request for `GermplasmAttributeValue`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/germplasmAttributeValue/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `GermplasmAttributeValue` search request
\nClients should submit a search request using the corresponding `POST /search/germplasmAttributeValue` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/GermplasmAttributeValueListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/images/{imageDbId}" : { + "get" : { + "tags" : [ "Images" ], + "summary" : "Submit a search request for `Image`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/image/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Image` search request
\nClients should submit a search request using the corresponding `POST /search/image` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ImageListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/lists/{listDbId}" : { + "get" : { + "tags" : [ "Lists" ], + "summary" : "Submit a search request for `List`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/list/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `List` search request
\nClients should submit a search request using the corresponding `POST /search/list` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ListListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/locations/{locationDbId}" : { + "get" : { + "tags" : [ "Locations" ], + "summary" : "Submit a search request for `Location`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/location/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Location` search request
\nClients should submit a search request using the corresponding `POST /search/location` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/LocationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/markerPositions/{markerPositionDbId}" : { + "get" : { + "tags" : [ "MarkerPositions" ], + "summary" : "Submit a search request for `MarkerPosition`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/markerPosition/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `MarkerPosition` search request
\nClients should submit a search request using the corresponding `POST /search/markerPosition` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/MarkerPositionListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observations/{observationDbId}" : { + "get" : { + "tags" : [ "Observations" ], + "summary" : "Submit a search request for `Observation`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observation/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Observation` search request
\nClients should submit a search request using the corresponding `POST /search/observation` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observationUnits/{observationUnitDbId}" : { + "get" : { + "tags" : [ "ObservationUnits" ], + "summary" : "Submit a search request for `ObservationUnit`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationUnit/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ObservationUnit` search request
\nClients should submit a search request using the corresponding `POST /search/observationUnit` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationUnitListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/observationVariables/{observationVariableDbId}" : { + "get" : { + "tags" : [ "ObservationVariables" ], + "summary" : "Submit a search request for `ObservationVariable`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/observationVariable/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ObservationVariable` search request
\nClients should submit a search request using the corresponding `POST /search/observationVariable` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ObservationVariableListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/pedigreeNodes/{pedigreeNodeDbId}" : { + "get" : { + "tags" : [ "PedigreeNodes" ], + "summary" : "Submit a search request for `PedigreeNode`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/pedigreeNode/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `PedigreeNode` search request
\nClients should submit a search request using the corresponding `POST /search/pedigreeNode` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PedigreeNodeListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/persons/{personDbId}" : { + "get" : { + "tags" : [ "Persons" ], + "summary" : "Submit a search request for `Person`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/person/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Person` search request
\nClients should submit a search request using the corresponding `POST /search/person` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PersonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/plannedCrosses/{plannedCrossDbId}" : { + "get" : { + "tags" : [ "PlannedCrosses" ], + "summary" : "Submit a search request for `PlannedCross`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plannedCross/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `PlannedCross` search request
\nClients should submit a search request using the corresponding `POST /search/plannedCross` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlannedCrossListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/plates/{plateDbId}" : { + "get" : { + "tags" : [ "Plates" ], + "summary" : "Submit a search request for `Plate`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/plate/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Plate` search request
\nClients should submit a search request using the corresponding `POST /search/plate` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/PlateListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/programs/{programDbId}" : { + "get" : { + "tags" : [ "Programs" ], + "summary" : "Submit a search request for `Program`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/program/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Program` search request
\nClients should submit a search request using the corresponding `POST /search/program` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ProgramListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/references/{referenceDbId}" : { + "get" : { + "tags" : [ "References" ], + "summary" : "Submit a search request for `Reference`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/reference/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Reference` search request
\nClients should submit a search request using the corresponding `POST /search/reference` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/referenceSets/{referenceSetDbId}" : { + "get" : { + "tags" : [ "ReferenceSets" ], + "summary" : "Submit a search request for `ReferenceSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/referenceSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `ReferenceSet` search request
\nClients should submit a search request using the corresponding `POST /search/referenceSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/ReferenceSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/samples/{sampleDbId}" : { + "get" : { + "tags" : [ "Samples" ], + "summary" : "Submit a search request for `Sample`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/sample/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Sample` search request
\nClients should submit a search request using the corresponding `POST /search/sample` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SampleListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/seasons/{seasonDbId}" : { + "get" : { + "tags" : [ "Seasons" ], + "summary" : "Submit a search request for `Season`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/season/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Season` search request
\nClients should submit a search request using the corresponding `POST /search/season` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeasonListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/seedLots/{seedLotDbId}" : { + "get" : { + "tags" : [ "SeedLots" ], + "summary" : "Submit a search request for `SeedLot`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/seedLot/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `SeedLot` search request
\nClients should submit a search request using the corresponding `POST /search/seedLot` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/SeedLotListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/studies/{studyDbId}" : { + "get" : { + "tags" : [ "Studies" ], + "summary" : "Submit a search request for `Study`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/study/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Study` search request
\nClients should submit a search request using the corresponding `POST /search/study` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/StudyListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/trials/{trialDbId}" : { + "get" : { + "tags" : [ "Trials" ], + "summary" : "Submit a search request for `Trial`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/trial/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Trial` search request
\nClients should submit a search request using the corresponding `POST /search/trial` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/TrialListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/variants/{variantDbId}" : { + "get" : { + "tags" : [ "Variants" ], + "summary" : "Submit a search request for `Variant`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variant/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `Variant` search request
\nClients should submit a search request using the corresponding `POST /search/variant` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + }, + "/search/variantSets/{variantSetDbId}" : { + "get" : { + "tags" : [ "VariantSets" ], + "summary" : "Submit a search request for `VariantSet`
\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse the corresponding `GET /search/variantSet/{searchResultsDbId}` to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "description" : "Get the results of a `VariantSet` search request
\nClients should submit a search request using the corresponding `POST /search/variantSet` endpoint.\nSearch requests allow a client to send a complex query for data. However, the server may not respond with the search results immediately. \nIf a server needs more time to process the request, it might respond with a `searchResultsDbId`. \nUse this endpoint to retrieve the results of the search.
\nReview the Search Services documentation for additional implementation details.", + "responses" : { + "200" : { + "$ref" : "#/components/responses/VariantSetListResponse" + }, + "400" : { + "$ref" : "#/components/responses/400BadRequest" + }, + "401" : { + "$ref" : "#/components/responses/401Unauthorized" + }, + "403" : { + "$ref" : "#/components/responses/403Forbidden" + } + } + } + } + }, + "components" : { + "schemas" : { + "AdditionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "AlleleMatrix" : { + "type" : "object", + "properties" : { + "callSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataMatrices" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DataMatrix" + } + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "pagination" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Pagination" + } + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "callSetDbIds", "variantSetDbIds" ] + }, + "Analysis" : { + "type" : "object", + "properties" : { + "analysisDbId" : { + "type" : "string" + }, + "analysisName" : { + "type" : "string" + }, + "created" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "software" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "type" : { + "type" : "string" + }, + "updated" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "required" : [ "analysisDbId" ] + }, + "Attribute" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "attributeName", "methodName", "scaleDbId", "scaleName", "traitName" ] + }, + "AvailableFormat" : { + "type" : "object", + "properties" : { + "dataFormat" : { + "type" : "string", + "description" : "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)", + "enum" : [ "DartSeq", "VCF", "Hapmap", "tabular", "JSON" ] + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "fileFormat" : { + "type" : "string", + "description" : "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response.", + "enum" : [ "text/csv", "text/tsv", "application/excel", "application/zip", "application/json" ] + }, + "fileURL" : { + "type" : "string" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + } + }, + "BreedingMethod" : { + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "germplasm" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + }, + "pedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + } + }, + "required" : [ "abbreviation", "breedingMethodDbId", "breedingMethodName", "description" ] + }, + "Call" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSetDbId" : { + "type" : "string" + }, + "callSetName" : { + "type" : "string" + }, + "genotypeMetadata" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GenotypeMetadata" + } + }, + "genotypeValue" : { + "type" : "string" + }, + "phaseSet" : { + "type" : "string" + }, + "variantDbId" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "required" : [ "callSetDbId", "variantDbId", "variantSetDbId" ] + }, + "CallSearchRequest" : { + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "CallSet" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSetDbId" : { + "type" : "string" + }, + "callSetName" : { + "type" : "string" + }, + "calls" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Call" + } + }, + "created" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "sampleDbId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "updated" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "callSetDbId" ] + }, + "CallSetSearchRequest" : { + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "callSetNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Contact" : { + "type" : "object", + "properties" : { + "contactDbId" : { + "type" : "string" + }, + "email" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "orcid" : { + "type" : "string" + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "contactDbId" ] + }, + "ContentMixture" : { + "type" : "object", + "properties" : { + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "mixturePercentage" : { + "type" : "integer", + "format" : "int32" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + } + } + }, + "ContentTypes" : { + "type" : "string", + "enum" : [ "application/json", "text/csv", "text/tsv", "application/flapjack" ] + }, + "Context" : { + "type" : "array", + "description" : "The JSON-LD Context is used to provide JSON-LD definitions to each field in a JSON object. By providing an array of context file urls, a BrAPI response object becomes JSON-LD compatible. \n\nFor more information, see https://w3c.github.io/json-ld-syntax/#the-context", + "example" : [ "https://brapi.org/jsonld/context/metadata.jsonld" ], + "items" : { + "type" : "string", + "format" : "uri" + }, + "title" : "context" + }, + "Cross" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "crossAttributes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossAttribute" + } + }, + "crossName" : { + "type" : "string" + }, + "crossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ "BIPARENTAL", "SELF", "OPEN_POLLINATED", "BULK", "BULK_SELFED", "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ] + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "parent1" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "parent2" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + }, + "pollinationEvents" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PollinationEvent" + } + } + }, + "required" : [ "crossDbId" ] + }, + "CrossAttribute" : { + "type" : "object", + "properties" : { + "crossAttributeName" : { + "type" : "string" + }, + "crossAttributeValue" : { + "type" : "string" + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + } + } + }, + "CrossNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "crossAttributes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossAttribute" + } + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "crossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ "BIPARENTAL", "SELF", "OPEN_POLLINATED", "BULK", "BULK_SELFED", "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ] + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "parent1" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "parent2" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + }, + "pollinationEvents" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PollinationEvent" + } + } + }, + "required" : [ "crossDbId", "crossDbId" ] + }, + "CrossParent" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "CrossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ "BIPARENTAL", "SELF", "OPEN_POLLINATED", "BULK", "BULK_SELFED", "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ] + }, + "CrossingProject" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "crosses" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Cross" + } + }, + "crossingProjectDescription" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "pedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "plannedCrosses" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PlannedCross" + } + }, + "potentialParents" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossParent" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + } + }, + "required" : [ "crossingProjectDbId", "crossingProjectName" ] + }, + "CrossingProjectNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "crosses" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Cross" + } + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectDescription" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "pedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "plannedCrosses" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PlannedCross" + } + }, + "potentialParents" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossParent" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + } + }, + "required" : [ "crossingProjectDbId", "crossingProjectDbId", "crossingProjectName" ] + }, + "CrossingProjectSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossingProjectDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossingProjectNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "includePotentialParents" : { + "type" : "boolean" + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "DataLink" : { + "type" : "object", + "properties" : { + "dataFormat" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "fileFormat" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "provenance" : { + "type" : "string" + }, + "scientificType" : { + "type" : "string" + }, + "url" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + } + }, + "DataMatrix" : { + "type" : "object", + "properties" : { + "alleleMatrix" : { + "type" : "object", + "properties" : { + "callSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataMatrices" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DataMatrix" + } + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "pagination" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Pagination" + } + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "callSetDbIds", "variantSetDbIds" ] + }, + "dataMatrix" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "dataMatrixAbbreviation" : { + "type" : "string" + }, + "dataMatrixName" : { + "type" : "string" + }, + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this data matrix. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ] + } + } + }, + "DatasetAuthorships" : { + "type" : "object", + "properties" : { + "datasetPUI" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "publicReleaseDate" : { + "type" : "string" + }, + "submissionDate" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + } + }, + "DocumentationLink" : { + "type" : "object", + "properties" : { + "URL" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "type" : { + "type" : "string", + "enum" : [ "OBO", "RDF", "WEBPAGE" ] + } + } + }, + "Donor" : { + "type" : "object", + "properties" : { + "donorAccessionNumber" : { + "type" : "string" + }, + "donorInstituteCode" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "EnvironmentParameters" : { + "type" : "object", + "properties" : { + "description" : { + "type" : "string" + }, + "environmentParametersDbId" : { + "type" : "string" + }, + "parameterName" : { + "type" : "string" + }, + "parameterPUI" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "unit" : { + "type" : "string" + }, + "unitPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + }, + "valuePUI" : { + "type" : "string" + } + }, + "required" : [ "description", "environmentParametersDbId", "parameterName" ] + }, + "Event" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "eventDateRange" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/EventDateRange" + } + }, + "eventDbId" : { + "type" : "string" + }, + "eventDescription" : { + "type" : "string" + }, + "eventParameters" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/EventParameter" + } + }, + "eventType" : { + "type" : "string" + }, + "eventTypeDbId" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + }, + "required" : [ "eventDbId", "eventType" ] + }, + "EventDateRange" : { + "type" : "object", + "properties" : { + "discreteDates" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "endDate" : { + "type" : "string" + }, + "eventDbId" : { + "type" : "string" + }, + "startDate" : { + "type" : "string" + } + } + }, + "EventParameter" : { + "type" : "object", + "properties" : { + "code" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "eventDbId" : { + "type" : "string" + }, + "name" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "value" : { + "type" : "string" + }, + "valueDescription" : { + "type" : "string" + }, + "valuesByDate" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "EventSearchRequest" : { + "type" : "object", + "properties" : { + "dateRangeEnd" : { + "type" : "string" + }, + "dateRangeStart" : { + "type" : "string" + }, + "eventDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "eventTypes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "ExperimentalDesign" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "ExternalReference" : { + "type" : "object", + "properties" : { + "referenceId" : { + "type" : "string" + }, + "referenceSource" : { + "type" : "string" + } + } + }, + "GenomeMap" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "comments" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "linkageGroupCount" : { + "type" : "integer", + "format" : "int32" + }, + "mapDbId" : { + "type" : "string" + }, + "mapName" : { + "type" : "string" + }, + "mapPUI" : { + "type" : "string" + }, + "markerCount" : { + "type" : "integer", + "format" : "int32" + }, + "markerPositions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/MarkerPosition" + } + }, + "publishedDate" : { + "type" : "string" + }, + "scientificName" : { + "type" : "string" + }, + "type" : { + "type" : "string" + }, + "unit" : { + "type" : "string" + } + }, + "required" : [ "commonCropName", "mapDbId", "type" ] + }, + "GenomeMapSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "mapDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "mapPUI" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scientificName" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "types" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "GenotypeMetadata" : { + "type" : "object", + "properties" : { + "call" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSetDbId" : { + "type" : "string" + }, + "callSetName" : { + "type" : "string" + }, + "genotypeMetadata" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GenotypeMetadata" + } + }, + "genotypeValue" : { + "type" : "string" + }, + "phaseSet" : { + "type" : "string" + }, + "variantDbId" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + }, + "required" : [ "callSetDbId", "variantDbId", "variantSetDbId" ] + }, + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ] + }, + "fieldAbbreviation" : { + "type" : "string" + }, + "fieldName" : { + "type" : "string" + }, + "fieldValue" : { + "type" : "string" + } + } + }, + "GeoJSON" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "GeoJSONGeometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "Germplasm" : { + "type" : "object", + "properties" : { + "accessionNumber" : { + "type" : "string" + }, + "acquisitionDate" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeValues" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum" : [ "100", "110", "120", "130", "200", "300", "400", "410", "411", "412", "413", "414", "415", "416", "420", "421", "422", "423", "500", "600", "999" ] + }, + "biologicalStatusOfAccessionDescription" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "collection" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "countryOfOriginCode" : { + "type" : "string" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "donors" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Donor" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "genus" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmOrigin" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmOrigin" + } + }, + "germplasmPUI" : { + "type" : "string" + }, + "germplasmPreprocessing" : { + "type" : "string" + }, + "instituteCode" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "parentPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "pedigree" : { + "type" : "string" + }, + "progenyPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedSource" : { + "type" : "string" + }, + "seedSourceDescription" : { + "type" : "string" + }, + "siblingPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "species" : { + "type" : "string" + }, + "speciesAuthority" : { + "type" : "string" + }, + "storageTypes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/StorageType" + } + }, + "subtaxa" : { + "type" : "string" + }, + "subtaxaAuthority" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Synonym" + } + }, + "taxonIds" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/TaxonId" + } + } + }, + "required" : [ "commonCropName", "germplasmDbId", "germplasmName", "germplasmPUI" ] + }, + "GermplasmAttribute" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValues" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "attributeDbId", "attributeName", "methodName", "scaleDbId", "scaleName", "traitName" ] + }, + "GermplasmAttributeNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeCategory" : { + "type" : "string" + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeDescription" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValues" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "attributeDbId", "attributeName", "methodName", "scaleDbId", "scaleName", "traitName" ] + }, + "GermplasmAttributeSearchRequest" : { + "type" : "object", + "properties" : { + "attributeCategories" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attributeDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attributeNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attributePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "GermplasmAttributeValue" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "determinedDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "required" : [ "attributeName", "attributeValueDbId" ] + }, + "GermplasmAttributeValueNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeDbId" : { + "type" : "string" + }, + "attributeName" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "attributeValueDbId" : { + "type" : "string" + }, + "determinedDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "required" : [ "attributeName", "attributeValueDbId" ] + }, + "GermplasmAttributeValueSearchRequest" : { + "type" : "object", + "properties" : { + "attributeDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attributeNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attributeValueDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "GermplasmChild" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI", "parentType" ] + }, + "GermplasmNewRequest" : { + "type" : "object", + "properties" : { + "accessionNumber" : { + "type" : "string" + }, + "acquisitionDate" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "attributeValues" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "biologicalStatusOfAccessionCode" : { + "type" : "string", + "description" : "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)", + "enum" : [ "100", "110", "120", "130", "200", "300", "400", "410", "411", "412", "413", "414", "415", "416", "420", "421", "422", "423", "500", "600", "999" ] + }, + "biologicalStatusOfAccessionDescription" : { + "type" : "string" + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "collection" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "countryOfOriginCode" : { + "type" : "string" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "donors" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Donor" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "genus" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmOrigin" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmOrigin" + } + }, + "germplasmPUI" : { + "type" : "string" + }, + "germplasmPreprocessing" : { + "type" : "string" + }, + "instituteCode" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "parentPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "pedigree" : { + "type" : "string" + }, + "progenyPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedSource" : { + "type" : "string" + }, + "seedSourceDescription" : { + "type" : "string" + }, + "siblingPedigreeNodes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "species" : { + "type" : "string" + }, + "speciesAuthority" : { + "type" : "string" + }, + "storageTypes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/StorageType" + } + }, + "subtaxa" : { + "type" : "string" + }, + "subtaxaAuthority" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Synonym" + } + }, + "taxonIds" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/TaxonId" + } + } + }, + "required" : [ "commonCropName", "germplasmDbId", "germplasmDbId", "germplasmName", "germplasmPUI" ] + }, + "GermplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "GermplasmParent" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + }, + "pedigreeNodeDbId" : { + "type" : "string" + } + }, + "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI", "parentType" ] + }, + "GermplasmSearchRequest" : { + "type" : "object", + "properties" : { + "accessionNumbers" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "binomialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "collections" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "familyCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "genus" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "instituteCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "parentDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "progenyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "species" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "GrowthFacility" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "Image" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "imageFileName" : { + "type" : "string" + }, + "imageFileSize" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeight" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "imageName" : { + "type" : "string" + }, + "imageTimeStamp" : { + "type" : "string" + }, + "imageURL" : { + "type" : "string" + }, + "imageWidth" : { + "type" : "integer", + "format" : "int32" + }, + "mimeType" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "imageDbId" ] + }, + "ImageNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageFileName" : { + "type" : "string" + }, + "imageFileSize" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeight" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "imageName" : { + "type" : "string" + }, + "imageTimeStamp" : { + "type" : "string" + }, + "imageURL" : { + "type" : "string" + }, + "imageWidth" : { + "type" : "integer", + "format" : "int32" + }, + "mimeType" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "imageDbId", "imageDbId" ] + }, + "ImageSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "descriptiveOntologyTerms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "imageDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "imageFileNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "imageFileSizeMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageFileSizeMin" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeightMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageHeightMin" : { + "type" : "integer", + "format" : "int32" + }, + "imageLocation" : { + "type" : "object", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "imageNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "imageTimeStampRangeEnd" : { + "type" : "string" + }, + "imageTimeStampRangeStart" : { + "type" : "string" + }, + "imageWidthMax" : { + "type" : "integer", + "format" : "int32" + }, + "imageWidthMin" : { + "type" : "integer", + "format" : "int32" + }, + "mimeTypes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "LastUpdate" : { + "type" : "object", + "properties" : { + "lastUpdateDbId" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "timestamp" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "required" : [ "lastUpdateDbId" ] + }, + "List" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "data" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dateCreated" : { + "type" : "string" + }, + "dateModified" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "listDescription" : { + "type" : "string" + }, + "listName" : { + "type" : "string" + }, + "listOwnerName" : { + "type" : "string" + }, + "listSize" : { + "type" : "integer", + "format" : "int32" + }, + "listSource" : { + "type" : "string" + }, + "listType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ "germplasm", "markers", "variants", "programs", "trials", "studies", "observationUnits", "observations", "observationVariables", "samples" ] + }, + "personDbId" : { + "type" : "string" + } + }, + "required" : [ "listDbId", "listName", "listType" ] + }, + "ListNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "data" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dateCreated" : { + "type" : "string" + }, + "dateModified" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "listDbId" : { + "type" : "string" + }, + "listDescription" : { + "type" : "string" + }, + "listName" : { + "type" : "string" + }, + "listOwnerName" : { + "type" : "string" + }, + "listSize" : { + "type" : "integer", + "format" : "int32" + }, + "listSource" : { + "type" : "string" + }, + "listType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ "germplasm", "markers", "variants", "programs", "trials", "studies", "observationUnits", "observations", "observationVariables", "samples" ] + }, + "personDbId" : { + "type" : "string" + } + }, + "required" : [ "listDbId", "listDbId", "listName", "listType" ] + }, + "ListSearchRequest" : { + "type" : "object", + "properties" : { + "dateCreatedRangeEnd" : { + "type" : "string" + }, + "dateCreatedRangeStart" : { + "type" : "string" + }, + "dateModifiedRangeEnd" : { + "type" : "string" + }, + "dateModifiedRangeStart" : { + "type" : "string" + }, + "listDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "listNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "listOwnerNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "listOwnerPersonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "listSources" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "listType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ "germplasm", "markers", "variants", "programs", "trials", "studies", "observationUnits", "observations", "observationVariables", "samples" ] + } + } + }, + "ListType" : { + "type" : "string", + "description" : "The type of objects that are referenced in a List", + "enum" : [ "germplasm", "markers", "variants", "programs", "trials", "studies", "observationUnits", "observations", "observationVariables", "samples" ] + }, + "Location" : { + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "childLocations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Location" + } + }, + "coordinateDescription" : { + "type" : "string" + }, + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "countryCode" : { + "type" : "string" + }, + "countryName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "environmentType" : { + "type" : "string" + }, + "exposure" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "instituteAddress" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "locationType" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "seedLots" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + }, + "siteStatus" : { + "type" : "string" + }, + "slope" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + }, + "topography" : { + "type" : "string" + } + }, + "required" : [ "locationDbId", "locationName" ] + }, + "LocationNewRequest" : { + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "childLocations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Location" + } + }, + "coordinateDescription" : { + "type" : "string" + }, + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "countryCode" : { + "type" : "string" + }, + "countryName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "environmentType" : { + "type" : "string" + }, + "exposure" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "instituteAddress" : { + "type" : "string" + }, + "instituteName" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "locationType" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "seedLots" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + }, + "siteStatus" : { + "type" : "string" + }, + "slope" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + }, + "topography" : { + "type" : "string" + } + }, + "required" : [ "locationDbId", "locationDbId", "locationName" ] + }, + "LocationSearchRequest" : { + "type" : "object", + "properties" : { + "abbreviations" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "altitudeMax" : { + "type" : "number" + }, + "altitudeMin" : { + "type" : "number" + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "coordinates" : { + "type" : "object", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "countryCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "countryNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "instituteAddresses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "instituteNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationTypes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "parentLocationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "parentLocationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "MarkerPosition" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "linkageGroupName" : { + "type" : "string" + }, + "map" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "comments" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "linkageGroupCount" : { + "type" : "integer", + "format" : "int32" + }, + "mapDbId" : { + "type" : "string" + }, + "mapName" : { + "type" : "string" + }, + "mapPUI" : { + "type" : "string" + }, + "markerCount" : { + "type" : "integer", + "format" : "int32" + }, + "markerPositions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/MarkerPosition" + } + }, + "publishedDate" : { + "type" : "string" + }, + "scientificName" : { + "type" : "string" + }, + "type" : { + "type" : "string" + }, + "unit" : { + "type" : "string" + } + }, + "required" : [ "commonCropName", "mapDbId", "type" ] + }, + "position" : { + "type" : "integer", + "format" : "int32" + }, + "variantDbId" : { + "type" : "string" + } + } + }, + "MarkerPositionSearchRequest" : { + "type" : "object", + "properties" : { + "linkageGroupNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "mapDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "maxPosition" : { + "type" : "integer", + "format" : "int32" + }, + "minPosition" : { + "type" : "integer", + "format" : "int32" + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "MetadataField" : { + "type" : "object", + "properties" : { + "dataType" : { + "type" : "string", + "description" : "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON.", + "enum" : [ "string", "integer", "float", "boolean" ] + }, + "fieldAbbreviation" : { + "type" : "string" + }, + "fieldName" : { + "type" : "string" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + } + } + }, + "Method" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "bibliographicalReference" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "formula" : { + "type" : "string" + }, + "methodClass" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + } + }, + "required" : [ "methodDbId", "methodName" ] + }, + "MethodNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "bibliographicalReference" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "formula" : { + "type" : "string" + }, + "methodClass" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + } + }, + "required" : [ "methodDbId", "methodName" ] + }, + "Observation" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "collector" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "geoCoordinates" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "images" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationTimeStamp" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "uploadedBy" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "required" : [ "observationDbId" ] + }, + "ObservationNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "collector" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "geoCoordinates" : { + "type" : "object", + "description" : "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "geometry" : { + "type" : "object", + "oneOf" : [ { + "type" : "object", + "description" : "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "number" + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + }, { + "type" : "object", + "description" : "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element.", + "properties" : { + "coordinates" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "array", + "items" : { + "type" : "number" + } + } + } + }, + "type" : { + "type" : "string" + } + }, + "required" : [ "type" ] + } ] + }, + "germplasmOrigin" : { + "type" : "object", + "properties" : { + "coordinateUncertainty" : { + "type" : "string" + }, + "coordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "imageDbId" : { + "type" : "string" + }, + "imageName" : { + "type" : "string" + }, + "observationDbId" : { + "type" : "string" + }, + "observationUnit" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "type" : { + "type" : "string" + } + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "images" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationDbId" : { + "type" : "string" + }, + "observationTimeStamp" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "uploadedBy" : { + "type" : "string" + }, + "value" : { + "type" : "string" + } + }, + "required" : [ "observationDbId", "observationDbId" ] + }, + "ObservationSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationTimeStampRangeEnd" : { + "type" : "string" + }, + "observationTimeStampRangeStart" : { + "type" : "string" + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationUnit" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "events" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "images" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Image" + } + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationUnitPosition" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitPosition" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "treatments" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Treatment" + } + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "observationUnitDbId" ] + }, + "ObservationUnitHierarchyLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "ObservationUnitLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "ObservationUnitLevelRelationship" : { + "type" : "object", + "description" : "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + } + }, + "ObservationUnitNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "events" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "images" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Image" + } + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "observationUnitPosition" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitPosition" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "treatments" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Treatment" + } + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "observationUnitDbId", "observationUnitDbId" ] + }, + "ObservationUnitPosition" : { + "type" : "object", + "properties" : { + "entryType" : { + "type" : "string", + "description" : "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\"", + "enum" : [ "CHECK", "TEST", "FILLER" ] + }, + "geoCoordinates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GeoJSON" + } + }, + "observationLevel" : { + "type" : "object", + "description" : "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" ", + "properties" : { + "levelCode" : { + "type" : "string" + }, + "levelName" : { + "type" : "string" + }, + "levelOrder" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "positionCoordinateX" : { + "type" : "string" + }, + "positionCoordinateXType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + }, + "positionCoordinateY" : { + "type" : "string" + }, + "positionCoordinateYType" : { + "type" : "string", + "description" : "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column ", + "enum" : [ "LONGITUDE", "LATITUDE", "PLANTED_ROW", "PLANTED_INDIVIDUAL", "GRID_ROW", "GRID_COL", "MEASURED_ROW", "MEASURED_COL" ] + } + } + }, + "ObservationUnitSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "includeObservations" : { + "type" : "boolean" + }, + "locationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationLevelRelationships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevelRelationship" + } + }, + "observationLevels" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitLevel" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "ObservationVariable" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "methodName", "observationVariableDbId", "observationVariableName", "scaleDbId", "scaleName", "traitName" ] + }, + "ObservationVariableNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "observationVariableDbId" : { + "type" : "string" + }, + "observationVariableName" : { + "type" : "string" + }, + "observationVariablePUI" : { + "type" : "string" + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "methodName", "observationVariableDbId", "observationVariableDbId", "observationVariableName", "scaleDbId", "scaleName", "traitName" ] + }, + "ObservationVariableSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataTypes" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/TraitDataType" + } + }, + "methodDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "methodPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "ontologyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scaleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scaleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "scalePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbId" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitAttributePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitAttributes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitClasses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitEntities" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitEntityPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Ontology" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "authors" : { + "type" : "string" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "licence" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "required" : [ "ontologyDbId", "ontologyName" ] + }, + "OntologyNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "authors" : { + "type" : "string" + }, + "copyright" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "licence" : { + "type" : "string" + }, + "ontologyDbId" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "required" : [ "ontologyDbId", "ontologyDbId", "ontologyName" ] + }, + "OntologyReference" : { + "type" : "object", + "properties" : { + "documentationLinks" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DocumentationLink" + } + }, + "ontologyDbId" : { + "type" : "string" + }, + "ontologyName" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "version" : { + "type" : "string" + } + }, + "required" : [ "ontologyDbId", "ontologyName" ] + }, + "OntologyTerm" : { + "type" : "object", + "properties" : { + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "term" : { + "type" : "string" + }, + "termURI" : { + "type" : "string" + } + } + }, + "Pagination" : { + "type" : "object", + "properties" : { + "alleleMatrix" : { + "type" : "object", + "properties" : { + "callSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "dataMatrices" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DataMatrix" + } + }, + "expandHomozygotes" : { + "type" : "boolean" + }, + "pagination" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Pagination" + } + }, + "sepPhased" : { + "type" : "string" + }, + "sepUnphased" : { + "type" : "string" + }, + "unknownString" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + }, + "required" : [ "callSetDbIds", "variantSetDbIds" ] + }, + "dimension" : { + "type" : "string", + "description" : "The dimension of the matrix being paginated", + "enum" : [ "CALLSETS", "VARIANTS" ] + }, + "page" : { + "type" : "integer", + "format" : "int32" + }, + "pageSize" : { + "type" : "integer", + "format" : "int32" + }, + "totalCount" : { + "type" : "integer", + "format" : "int32" + }, + "totalPages" : { + "type" : "integer", + "format" : "int32" + } + } + }, + "ParentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + }, + "PedigreeNode" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "breedingMethodDbId" : { + "type" : "string" + }, + "breedingMethodName" : { + "type" : "string" + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "crossingYear" : { + "type" : "integer", + "format" : "int32" + }, + "defaultDisplayName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "familyCode" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "parents" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmParent" + } + }, + "pedigreeNodeDbId" : { + "type" : "string" + }, + "pedigreeString" : { + "type" : "string" + }, + "progeny" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmChild" + } + }, + "siblings" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + } + }, + "required" : [ "germplasmDbId", "germplasmName", "germplasmPUI" ] + }, + "PedigreeNodeSearchRequest" : { + "type" : "object", + "properties" : { + "accessionNumbers" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "binomialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "collections" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "familyCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "genus" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "includeFullTree" : { + "type" : "boolean" + }, + "includeParents" : { + "type" : "boolean" + }, + "includeProgeny" : { + "type" : "boolean" + }, + "includeSiblings" : { + "type" : "boolean" + }, + "instituteCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "pedigreeDepth" : { + "type" : "integer", + "format" : "int32" + }, + "progenyDepth" : { + "type" : "integer", + "format" : "int32" + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "species" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Person" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "description" : { + "type" : "string" + }, + "emailAddress" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "firstName" : { + "type" : "string" + }, + "lastName" : { + "type" : "string" + }, + "lists" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/List" + } + }, + "mailingAddress" : { + "type" : "string" + }, + "middleName" : { + "type" : "string" + }, + "phoneNumber" : { + "type" : "string" + }, + "programs" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Program" + } + }, + "userID" : { + "type" : "string" + } + }, + "required" : [ "personDbId" ] + }, + "PersonNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "description" : { + "type" : "string" + }, + "emailAddress" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "firstName" : { + "type" : "string" + }, + "lastName" : { + "type" : "string" + }, + "lists" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/List" + } + }, + "mailingAddress" : { + "type" : "string" + }, + "middleName" : { + "type" : "string" + }, + "personDbId" : { + "type" : "string" + }, + "phoneNumber" : { + "type" : "string" + }, + "programs" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Program" + } + }, + "userID" : { + "type" : "string" + } + }, + "required" : [ "personDbId", "personDbId" ] + }, + "PersonSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "emailAddresses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "firstNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "lastNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "mailingAddresses" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "middleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "personDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "phoneNumbers" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "userIDs" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "PlannedCross" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "crossType" : { + "type" : "string", + "description" : "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'.", + "enum" : [ "BIPARENTAL", "SELF", "OPEN_POLLINATED", "BULK", "BULK_SELFED", "BULK_OPEN_POLLINATED", "DOUBLE_HAPLOID" ] + }, + "crosses" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Cross" + } + }, + "crossingProjectDbId" : { + "type" : "string" + }, + "crossingProjectName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "parent1" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "parent2" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "parentType" : { + "type" : "string", + "description" : "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. ", + "enum" : [ "MALE", "FEMALE", "SELF", "POPULATION", "CLONAL" ] + } + } + }, + "plannedCrossDbId" : { + "type" : "string" + }, + "plannedCrossName" : { + "type" : "string" + }, + "status" : { + "type" : "string", + "description" : "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED').", + "enum" : [ "TODO", "DONE", "SKIPPED" ] + } + }, + "required" : [ "plannedCrossDbId" ] + }, + "PlannedCrossSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossingProjectDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossingProjectNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plannedCrossDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plannedCrossNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "statuses" : { + "type" : "array", + "items" : { + "type" : "string", + "enum" : [ "TODO", "DONE", "SKIPPED" ] + } + } + } + }, + "Plate" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "plateBarcode" : { + "type" : "string" + }, + "plateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ "PLATE_96", "TUBES" ] + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "enum" : [ "DNA", "RNA", "TISSUE", "MIXED" ] + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "plateDbId", "plateName" ] + }, + "PlateNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "plateBarcode" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateFormat" : { + "type" : "string", + "description" : "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format", + "enum" : [ "PLATE_96", "TUBES" ] + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string", + "description" : "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc", + "enum" : [ "DNA", "RNA", "TISSUE", "MIXED" ] + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "plateDbId", "plateName" ] + }, + "PlateSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plateBarcodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plateDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plateNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleGroupDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "PollinationEvent" : { + "type" : "object", + "properties" : { + "crossDbId" : { + "type" : "string" + }, + "crossName" : { + "type" : "string" + }, + "pollinationNumber" : { + "type" : "string" + }, + "pollinationSuccessful" : { + "type" : "boolean" + }, + "pollinationTimeStamp" : { + "type" : "string" + } + } + }, + "Program" : { + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "crossingProjects" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossingProject" + } + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "fundingInformation" : { + "type" : "string" + }, + "objective" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "personDbId" : { + "type" : "string" + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "programName" : { + "type" : "string" + }, + "programType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "enum" : [ "STANDARD", "PROJECT" ] + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedLots" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + }, + "trials" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Trial" + } + } + }, + "required" : [ "programDbId", "programName" ] + }, + "ProgramNewRequest" : { + "type" : "object", + "properties" : { + "abbreviation" : { + "type" : "string" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "crossingProjects" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossingProject" + } + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "fundingInformation" : { + "type" : "string" + }, + "objective" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "personDbId" : { + "type" : "string" + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "programType" : { + "type" : "string", + "description" : "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding ", + "enum" : [ "STANDARD", "PROJECT" ] + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seedLots" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + }, + "trials" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Trial" + } + } + }, + "required" : [ "programDbId", "programDbId", "programName" ] + }, + "ProgramSearchRequest" : { + "type" : "object", + "properties" : { + "abbreviations" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "leadPersonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "leadPersonNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "objectives" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programTypes" : { + "type" : "array", + "items" : { + "type" : "string", + "enum" : [ "STANDARD", "PROJECT" ] + } + } + } + }, + "Publication" : { + "type" : "object", + "properties" : { + "publicationPUI" : { + "type" : "string" + }, + "publicationReference" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + } + }, + "Reference" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "isDerived" : { + "type" : "boolean" + }, + "length" : { + "type" : "integer", + "format" : "int32" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceAccessions" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceDivergence" : { + "type" : "number" + }, + "sourceGermplasm" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "type" : "object", + "properties" : { + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "term" : { + "type" : "string" + }, + "termURI" : { + "type" : "string" + } + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + } + }, + "required" : [ "referenceDbId", "referenceName" ] + }, + "ReferenceSearchRequest" : { + "type" : "object", + "properties" : { + "accessions" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "isDerived" : { + "type" : "boolean" + }, + "maxLength" : { + "type" : "integer", + "format" : "int32" + }, + "md5checksums" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "minLength" : { + "type" : "integer", + "format" : "int32" + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "ReferenceSet" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "assemblyPUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "isDerived" : { + "type" : "boolean" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceAccessions" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceGermplasm" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "type" : "object", + "properties" : { + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "term" : { + "type" : "string" + }, + "termURI" : { + "type" : "string" + } + } + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + } + }, + "required" : [ "referenceSetDbId", "referenceSetName" ] + }, + "ReferenceSetNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "assemblyPUI" : { + "type" : "string" + }, + "commonCropName" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "isDerived" : { + "type" : "boolean" + }, + "md5checksum" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "sourceAccessions" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sourceGermplasm" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + }, + "sourceURI" : { + "type" : "string" + }, + "species" : { + "type" : "object", + "properties" : { + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "term" : { + "type" : "string" + }, + "termURI" : { + "type" : "string" + } + } + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + } + }, + "required" : [ "referenceSetDbId", "referenceSetDbId", "referenceSetName" ] + }, + "ReferenceSetSearchRequest" : { + "type" : "object", + "properties" : { + "accessions" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "assemblyPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "md5checksums" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Sample" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + }, + "column" : { + "type" : "integer", + "format" : "int32" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "row" : { + "type" : "string" + }, + "sampleBarcode" : { + "type" : "string" + }, + "sampleDescription" : { + "type" : "string" + }, + "sampleGroupId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "sampleTimestamp" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "takenBy" : { + "type" : "string" + }, + "tissueType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "well" : { + "type" : "string" + } + }, + "required" : [ "sampleDbId", "sampleName" ] + }, + "SampleNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + }, + "column" : { + "type" : "integer", + "format" : "int32" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + }, + "plateDbId" : { + "type" : "string" + }, + "plateName" : { + "type" : "string" + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "row" : { + "type" : "string" + }, + "sampleBarcode" : { + "type" : "string" + }, + "sampleDbId" : { + "type" : "string" + }, + "sampleDescription" : { + "type" : "string" + }, + "sampleGroupId" : { + "type" : "string" + }, + "sampleName" : { + "type" : "string" + }, + "samplePUI" : { + "type" : "string" + }, + "sampleTimestamp" : { + "type" : "string" + }, + "sampleType" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "takenBy" : { + "type" : "string" + }, + "tissueType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "well" : { + "type" : "string" + } + }, + "required" : [ "sampleDbId", "sampleName" ] + }, + "SampleSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationUnitDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plateDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "plateNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleGroupDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "sampleNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Scale" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "dataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] + }, + "decimalPlaces" : { + "type" : "integer", + "format" : "int32" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "validValues" : { + "type" : "object", + "properties" : { + "categories" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ValidValuesCategory" + } + }, + "maximumValue" : { + "type" : "string" + }, + "minimumValue" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + } + } + } + }, + "required" : [ "scaleDbId", "scaleName" ] + }, + "ScaleNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "dataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] + }, + "decimalPlaces" : { + "type" : "integer", + "format" : "int32" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "units" : { + "type" : "string" + }, + "validValues" : { + "type" : "object", + "properties" : { + "categories" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ValidValuesCategory" + } + }, + "maximumValue" : { + "type" : "string" + }, + "minimumValue" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + } + } + } + }, + "required" : [ "scaleDbId", "scaleDbId", "scaleName" ] + }, + "Season" : { + "type" : "object", + "properties" : { + "seasonDbId" : { + "type" : "string" + }, + "seasonName" : { + "type" : "string" + }, + "year" : { + "type" : "integer", + "format" : "int32" + } + }, + "required" : [ "seasonDbId" ] + }, + "SeasonSearchRequest" : { + "type" : "object", + "properties" : { + "seasonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seasonNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seasons" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "years" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "SeedLot" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "amount" : { + "type" : "number" + }, + "contentMixture" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ContentMixture" + } + }, + "createdDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "fromSeedLotTransactions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLotTransaction" + } + }, + "lastUpdated" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDescription" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "sourceCollection" : { + "type" : "string" + }, + "storageLocation" : { + "type" : "string" + }, + "toSeedLotTransactions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLotTransaction" + } + }, + "units" : { + "type" : "string" + } + }, + "required" : [ "seedLotDbId", "seedLotName" ] + }, + "SeedLotNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "amount" : { + "type" : "number" + }, + "contentMixture" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ContentMixture" + } + }, + "createdDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "fromSeedLotTransactions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLotTransaction" + } + }, + "lastUpdated" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotDescription" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "sourceCollection" : { + "type" : "string" + }, + "storageLocation" : { + "type" : "string" + }, + "toSeedLotTransactions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLotTransaction" + } + }, + "units" : { + "type" : "string" + } + }, + "required" : [ "seedLotDbId", "seedLotDbId", "seedLotName" ] + }, + "SeedLotSearchRequest" : { + "type" : "object", + "properties" : { + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "crossNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seedLotDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "SeedLotTransaction" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "amount" : { + "type" : "number" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "seedLotDbId" : { + "type" : "string" + }, + "seedLotName" : { + "type" : "string" + }, + "transactionDbId" : { + "type" : "string" + }, + "transactionDescription" : { + "type" : "string" + }, + "transactionTimestamp" : { + "type" : "string" + }, + "units" : { + "type" : "string" + } + }, + "required" : [ "transactionDbId" ] + }, + "StorageType" : { + "type" : "object", + "properties" : { + "code" : { + "type" : "string", + "description" : "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)", + "enum" : [ "10", "11", "12", "13", "20", "30", "40", "50", "99" ] + }, + "description" : { + "type" : "string" + }, + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + } + } + }, + "Study" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "culturalPractices" : { + "type" : "string" + }, + "dataLinks" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DataLink" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "environmentParameters" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/EnvironmentParameters" + } + }, + "events" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "experimentalDesign" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthFacility" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "lastUpdateDbId" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationLevels" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "observationUnitsDescription" : { + "type" : "string" + }, + "observationVariables" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seasons" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "startDate" : { + "type" : "string" + }, + "studyCode" : { + "type" : "string" + }, + "studyDescription" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "studyType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + } + }, + "required" : [ "studyDbId", "studyName" ] + }, + "StudyNewRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "callSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "culturalPractices" : { + "type" : "string" + }, + "dataLinks" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DataLink" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "environmentParameters" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/EnvironmentParameters" + } + }, + "events" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "experimentalDesign" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthFacility" : { + "type" : "object", + "properties" : { + "PUI" : { + "type" : "string" + }, + "description" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + } + } + }, + "lastUpdateDbId" : { + "type" : "string" + }, + "license" : { + "type" : "string" + }, + "locationDbId" : { + "type" : "string" + }, + "locationName" : { + "type" : "string" + }, + "observationLevels" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnitHierarchyLevel" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "observationUnitsDescription" : { + "type" : "string" + }, + "observationVariables" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observations" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "seasons" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "startDate" : { + "type" : "string" + }, + "studyCode" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyDescription" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "studyType" : { + "type" : "string" + }, + "trialDbId" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + }, + "variantSets" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + } + }, + "required" : [ "studyDbId", "studyDbId", "studyName" ] + }, + "StudySearchRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "germplasmNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "seasonDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyCodes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyTypes" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "Synonym" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "synonym" : { + "type" : "string" + }, + "type" : { + "type" : "string" + } + } + }, + "TaxonId" : { + "type" : "object", + "properties" : { + "germplasmDbId" : { + "type" : "string" + }, + "germplasmName" : { + "type" : "string" + }, + "germplasmPUI" : { + "type" : "string" + }, + "sourceName" : { + "type" : "string" + }, + "taxonId" : { + "type" : "string" + } + }, + "required" : [ "sourceName", "taxonId" ] + }, + "Trait" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "alternativeAbbreviations" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attribute" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "entity" : { + "type" : "string" + }, + "entityPUI" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "mainAbbreviation" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitClass" : { + "type" : "string" + }, + "traitDescription" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "traitDbId", "traitName" ] + }, + "TraitDataType" : { + "type" : "string", + "description" : "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

", + "enum" : [ "Code", "Date", "Duration", "Nominal", "Numerical", "Ordinal", "Text" ] + }, + "TraitNewRequest" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "alternativeAbbreviations" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "attribute" : { + "type" : "string" + }, + "attributePUI" : { + "type" : "string" + }, + "entity" : { + "type" : "string" + }, + "entityPUI" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "mainAbbreviation" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitClass" : { + "type" : "string" + }, + "traitDbId" : { + "type" : "string" + }, + "traitDescription" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "traitDbId", "traitName" ] + }, + "Treatment" : { + "type" : "object", + "properties" : { + "factor" : { + "type" : "string" + }, + "modality" : { + "type" : "string" + }, + "observationUnitDbId" : { + "type" : "string" + }, + "observationUnitName" : { + "type" : "string" + }, + "observationUnitPUI" : { + "type" : "string" + } + } + }, + "Trial" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "datasetAuthorships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DatasetAuthorships" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "publications" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Publication" + } + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "startDate" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + }, + "trialDescription" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "trialDbId", "trialName" ] + }, + "TrialNewRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "contacts" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "datasetAuthorships" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/DatasetAuthorships" + } + }, + "documentationURL" : { + "type" : "string" + }, + "endDate" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "observationUnits" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "plates" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "programDbId" : { + "type" : "string" + }, + "programName" : { + "type" : "string" + }, + "publications" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Publication" + } + }, + "samples" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "startDate" : { + "type" : "string" + }, + "studies" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + }, + "trialDbId" : { + "type" : "string" + }, + "trialDescription" : { + "type" : "string" + }, + "trialName" : { + "type" : "string" + }, + "trialPUI" : { + "type" : "string" + } + }, + "required" : [ "trialDbId", "trialDbId", "trialName" ] + }, + "TrialSearchRequest" : { + "type" : "object", + "properties" : { + "active" : { + "type" : "boolean" + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "contactDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "locationNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariableNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "observationVariablePUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "searchDateRangeEnd" : { + "type" : "string" + }, + "searchDateRangeStart" : { + "type" : "string" + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialPUIs" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "ValidValues" : { + "type" : "object", + "properties" : { + "categories" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ValidValuesCategory" + } + }, + "maximumValue" : { + "type" : "string" + }, + "minimumValue" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + } + } + }, + "ValidValuesCategory" : { + "type" : "object", + "properties" : { + "label" : { + "type" : "string" + }, + "validValues" : { + "type" : "object", + "properties" : { + "categories" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ValidValuesCategory" + } + }, + "maximumValue" : { + "type" : "string" + }, + "minimumValue" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + } + } + }, + "value" : { + "type" : "string" + } + } + }, + "Variable" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "commonCropName" : { + "type" : "string" + }, + "contextOfUse" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "defaultValue" : { + "type" : "string" + }, + "documentationURL" : { + "type" : "string" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "growthStage" : { + "type" : "string" + }, + "institution" : { + "type" : "string" + }, + "language" : { + "type" : "string" + }, + "methodDbId" : { + "type" : "string" + }, + "methodName" : { + "type" : "string" + }, + "methodPUI" : { + "type" : "string" + }, + "ontologyReferenceDbId" : { + "type" : "string" + }, + "scaleDbId" : { + "type" : "string" + }, + "scaleName" : { + "type" : "string" + }, + "scalePUI" : { + "type" : "string" + }, + "scientist" : { + "type" : "string" + }, + "status" : { + "type" : "string" + }, + "submissionTimestamp" : { + "type" : "string" + }, + "synonyms" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "traitDbId" : { + "type" : "string" + }, + "traitName" : { + "type" : "string" + }, + "traitPUI" : { + "type" : "string" + } + }, + "required" : [ "methodName", "scaleDbId", "scaleName", "traitName" ] + }, + "Variant" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "analysis" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "calls" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Call" + } + }, + "ciend" : { + "type" : "array", + "items" : { + "type" : "integer", + "format" : "int32" + } + }, + "cipos" : { + "type" : "array", + "items" : { + "type" : "integer", + "format" : "int32" + } + }, + "created" : { + "type" : "string" + }, + "end" : { + "type" : "integer", + "format" : "int32" + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "filtersApplied" : { + "type" : "boolean" + }, + "filtersFailed" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "filtersPassed" : { + "type" : "boolean" + }, + "markerPositions" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/MarkerPosition" + } + }, + "referenceBases" : { + "type" : "string" + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceName" : { + "type" : "string" + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "start" : { + "type" : "integer", + "format" : "int32" + }, + "svlen" : { + "type" : "integer", + "format" : "int32" + }, + "updated" : { + "type" : "string" + }, + "variantDbId" : { + "type" : "string" + }, + "variantNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + }, + "variantType" : { + "type" : "string" + } + }, + "required" : [ "variantDbId" ] + }, + "VariantSearchRequest" : { + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "end" : { + "type" : "integer", + "format" : "int32" + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceDbId" : { + "type" : "string" + }, + "referenceDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "start" : { + "type" : "integer", + "format" : "int32" + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "VariantSet" : { + "type" : "object", + "properties" : { + "additionalInfo" : { + "type" : "object", + "description" : "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification.", + "properties" : { + "additionalProperties" : { + "type" : "string" + } + } + }, + "analysis" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Analysis" + } + }, + "callSetCount" : { + "type" : "integer", + "format" : "int32" + }, + "callSets" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "calls" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Call" + } + }, + "externalReferences" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ExternalReference" + } + }, + "metadataFields" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/MetadataField" + } + }, + "referenceSetDbId" : { + "type" : "string" + }, + "referenceSetName" : { + "type" : "string" + }, + "studyDbId" : { + "type" : "string" + }, + "studyName" : { + "type" : "string" + }, + "studyPUI" : { + "type" : "string" + }, + "variantCount" : { + "type" : "integer", + "format" : "int32" + }, + "variantSetDbId" : { + "type" : "string" + }, + "variantSetName" : { + "type" : "string" + }, + "variants" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + } + }, + "required" : [ "variantSetDbId" ] + }, + "VariantSetSearchRequest" : { + "type" : "object", + "properties" : { + "callSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "commonCropNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "programNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "referenceSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "studyNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "trialNames" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + }, + "variantSetDbIds" : { + "type" : "array", + "items" : { + "type" : "string" + } + } + } + }, + "basePagination" : { + "type" : "object", + "description" : "The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Pages are zero indexed, so the first page will be page 0 (zero).", + "properties" : { + "currentPage" : { + "type" : "integer", + "default" : 0, + "description" : "The index number for the returned page of data. This should always match the requested page number or the default page (0).", + "example" : 0 + }, + "pageSize" : { + "type" : "integer", + "default" : 1000, + "description" : "The number of data elements returned, aka the size of the current page. If the requested page does not have enough elements to fill a page at the requested page size, this field should indicate the actual number of elements returned.", + "example" : 1000 + }, + "totalCount" : { + "type" : "integer", + "description" : "The total number of elements that are available on the server and match the requested query parameters.", + "example" : 10 + }, + "totalPages" : { + "type" : "integer", + "description" : "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)", + "example" : 1 + } + }, + "required" : [ "currentPage", "pageSize" ] + }, + "dataFile" : { + "type" : "object", + "description" : "A dataFile contains a URL and the relevant file metadata to represent a file", + "properties" : { + "fileURL" : { + "type" : "string", + "format" : "uri", + "description" : "The absolute URL where the file is located", + "example" : "https://wiki.brapi.org/examples/datafile.xlsx" + }, + "fileName" : { + "type" : "string", + "description" : "The name of the file", + "example" : "datafile.xlsx" + }, + "fileSize" : { + "type" : "integer", + "description" : "The size of the file in bytes", + "example" : 4398 + }, + "fileDescription" : { + "type" : "string", + "description" : "A human readable description of the file contents", + "example" : "This is an Excel data file" + }, + "fileType" : { + "type" : "string", + "description" : "The type or format of the file. Preferably MIME Type.", + "example" : "application/vnd.ms-excel" + }, + "fileMD5Hash" : { + "type" : "string", + "description" : "The MD5 Hash of the file contents to be used as a check sum", + "example" : "c2365e900c81a89cf74d83dab60df146" + } + }, + "required" : [ "fileURL" ] + }, + "metadata" : { + "allOf" : [ { + "$ref" : "#/components/schemas/metadataBase" + }, { + "type" : "object", + "properties" : { + "pagination" : { + "$ref" : "#/components/schemas/basePagination" + } + } + } ] + }, + "metadataBase" : { + "type" : "object", + "description" : "An object in the BrAPI standard response model that describes some information about the service call being performed. This includes supplementary data, status log messages, and pagination information.", + "properties" : { + "datafiles" : { + "type" : "array", + "description" : "The datafiles contains a list of file URLs and metadata. \nThese files contain additional information related to the returned object and can be retrieved by a subsequent call. \nThis could be a supplementary data file, an informational file, the uploaded file where the data originated from, a generated file representing the whole dataset in a particular format, or any other related file. ", + "example" : [ ], + "items" : { + "$ref" : "#/components/schemas/dataFile" + } + }, + "status" : { + "type" : "array", + "description" : "The status field contains a list of informational status messages from the server. \nIf no status is reported, an empty list should be returned. See Error Reporting for more information.", + "items" : { + "$ref" : "#/components/schemas/status" + } + } + } + }, + "metadataTokenPagination" : { + "allOf" : [ { + "$ref" : "#/components/schemas/metadataBase" + }, { + "type" : "object", + "properties" : { + "pagination" : { + "$ref" : "#/components/schemas/tokenPagination" + } + } + } ] + }, + "status" : { + "type" : "object", + "description" : "An array of status messages to convey technical logging information from the server to the client.", + "properties" : { + "message" : { + "type" : "string", + "description" : "A short message concerning the status of this request/response", + "example" : "Request accepted, response successful" + }, + "messageType" : { + "type" : "string", + "description" : "The logging level for the attached message", + "enum" : [ "DEBUG", "ERROR", "WARNING", "INFO" ], + "example" : "INFO" + } + }, + "required" : [ "message", "messageType" ] + }, + "tokenPagination" : { + "allOf" : [ { + "$ref" : "#/components/schemas/basePagination" + }, { + "type" : "object", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The pagination object is applicable only when the payload contains a \"data\" key. It describes the pagination of the data contained in the \"data\" array, as a way to identify which subset of data is being returned. \n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken to construct an additional query and move to the next or previous page respectively. ", + "example" : { + "currentPage" : 0, + "pageSize" : 1000, + "totalCount" : 10, + "totalPages" : 1 + }, + "properties" : { + "nextPageToken" : { + "type" : "string", + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the next page of data.", + "example" : "cb668f63" + }, + "currentPageToken" : { + "type" : "string", + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the current page of data.", + "example" : "48bc6ac1" + }, + "prevPageToken" : { + "type" : "string", + "deprecated" : true, + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
The string token used to query the previous page of data.", + "example" : "9659857e" + } + }, + "required" : [ "nextPageToken" ] + } ] + } + }, + "responses" : { + "ObservationVariableSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationVariable" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationVariableSingleResponse" + } + } + } + }, + "SeedLotSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "SeedLotSingleResponse" + } + } + } + }, + "VariantSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "VariantSingleResponse" + } + } + } + }, + "202AcceptedSearchResponse" : { + "description" : "Accepted", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "@context" : { + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "properties" : { + "searchResultsDbId" : { + "type" : "string", + "example" : "551ae08c" + } + } + } + }, + "title" : "202AcceptedSearchResponse" + } + } + } + }, + "StudySingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "StudySingleResponse" + } + } + } + }, + "MethodSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Method" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "MethodSingleResponse" + } + } + } + }, + "TrialListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Trial" + } + }, + "required" : [ "metadata", "result" ], + "title" : "TrialListResponse" + } + } + } + }, + "SeedLotListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/SeedLot" + } + }, + "required" : [ "metadata", "result" ], + "title" : "SeedLotListResponse" + } + } + } + }, + "VariantSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + }, + "required" : [ "metadata", "result" ], + "title" : "VariantSetListResponse" + } + } + } + }, + "SampleSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "SampleSingleResponse" + } + } + } + }, + "CallSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "CallSetSingleResponse" + } + } + } + }, + "VariantSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/VariantSet" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "VariantSetSingleResponse" + } + } + } + }, + "CallSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/CallSet" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CallSetListResponse" + } + } + } + }, + "ReferenceSetSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ReferenceSet" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ReferenceSetSingleResponse" + } + } + } + }, + "ObservationVariableListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationVariable" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationVariableListResponse" + } + } + } + }, + "EventSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Event" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "EventSingleResponse" + } + } + } + }, + "ImageSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Image" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ImageSingleResponse" + } + } + } + }, + "PlateListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + }, + "required" : [ "metadata", "result" ], + "title" : "PlateListResponse" + } + } + } + }, + "SeasonListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Season" + } + }, + "required" : [ "metadata", "result" ], + "title" : "SeasonListResponse" + } + } + } + }, + "ObservationUnitListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationUnitListResponse" + } + } + } + }, + "ReferenceListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Reference" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ReferenceListResponse" + } + } + } + }, + "ObservationListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationListResponse" + } + } + } + }, + "GenomeMapSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GenomeMap" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "GenomeMapSingleResponse" + } + } + } + }, + "PersonListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Person" + } + }, + "required" : [ "metadata", "result" ], + "title" : "PersonListResponse" + } + } + } + }, + "PlannedCrossListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/PlannedCross" + } + }, + "required" : [ "metadata", "result" ], + "title" : "PlannedCrossListResponse" + } + } + } + }, + "LocationListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Location" + } + }, + "required" : [ "metadata", "result" ], + "title" : "LocationListResponse" + } + } + } + }, + "403Forbidden" : { + "description" : "Forbidden", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - User does not have permission to perform this action" + } + } + }, + "OntologySingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Ontology" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "OntologySingleResponse" + } + } + } + }, + "CrossSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Cross" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossSingleResponse" + } + } + } + }, + "ProgramListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Program" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ProgramListResponse" + } + } + } + }, + "ObservationUnitSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/ObservationUnit" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationUnitSingleResponse" + } + } + } + }, + "ScaleListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Scale" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ScaleListResponse" + } + } + } + }, + "ListListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/List" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ListListResponse" + } + } + } + }, + "400BadRequest" : { + "description" : "Bad Request", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - Malformed JSON Request Object\n\nERROR - 2018-10-08T18:15:11Z - Invalid query parameter\n\nERROR - 2018-10-08T18:15:11Z - Required parameter is missing" + } + } + }, + "MethodListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Method" + } + }, + "required" : [ "metadata", "result" ], + "title" : "MethodListResponse" + } + } + } + }, + "CrossingProjectListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossingProject" + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossingProjectListResponse" + } + } + } + }, + "GermplasmAttributeSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttribute" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeSingleResponse" + } + } + } + }, + "TraitSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Trait" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "TraitSingleResponse" + } + } + } + }, + "401Unauthorized" : { + "description" : "Unauthorized", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - Missing or expired authorization token" + } + } + }, + "GermplasmAttributeListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttribute" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeListResponse" + } + } + } + }, + "GermplasmListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmListResponse" + } + } + } + }, + "CrossingProjectSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/CrossingProject" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "CrossingProjectSingleResponse" + } + } + } + }, + "TraitListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Trait" + } + }, + "required" : [ "metadata", "result" ], + "title" : "TraitListResponse" + } + } + } + }, + "PedigreeNodeSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "PedigreeNodeSingleResponse" + } + } + } + }, + "SampleListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Sample" + } + }, + "required" : [ "metadata", "result" ], + "title" : "SampleListResponse" + } + } + } + }, + "ReferenceSetListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/ReferenceSet" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ReferenceSetListResponse" + } + } + } + }, + "TrialSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Trial" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "TrialSingleResponse" + } + } + } + }, + "GermplasmSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Germplasm" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmSingleResponse" + } + } + } + }, + "PlannedCrossSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/PlannedCross" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "PlannedCrossSingleResponse" + } + } + } + }, + "ReferenceSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Reference" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ReferenceSingleResponse" + } + } + } + }, + "SeasonSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Season" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "SeasonSingleResponse" + } + } + } + }, + "OntologyListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Ontology" + } + }, + "required" : [ "metadata", "result" ], + "title" : "OntologyListResponse" + } + } + } + }, + "404NotFound" : { + "description" : "Not Found", + "content" : { + "application/json" : { + "schema" : { + "type" : "string" + }, + "example" : "ERROR - 2018-10-08T18:15:11Z - The requested object DbId is not found" + } + } + }, + "StudyListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Study" + } + }, + "required" : [ "metadata", "result" ], + "title" : "StudyListResponse" + } + } + } + }, + "ScaleSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Scale" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ScaleSingleResponse" + } + } + } + }, + "BreedingMethodSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/BreedingMethod" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "BreedingMethodSingleResponse" + } + } + } + }, + "LocationSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Location" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "LocationSingleResponse" + } + } + } + }, + "PersonSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Person" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "PersonSingleResponse" + } + } + } + }, + "MarkerPositionSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/MarkerPosition" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "MarkerPositionSingleResponse" + } + } + } + }, + "ImageListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Image" + } + }, + "required" : [ "metadata", "result" ], + "title" : "ImageListResponse" + } + } + } + }, + "PlateSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Plate" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "PlateSingleResponse" + } + } + } + }, + "VariantListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/Variant" + } + }, + "required" : [ "metadata", "result" ], + "title" : "VariantListResponse" + } + } + } + }, + "GermplasmAttributeValueListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeValueListResponse" + } + } + } + }, + "GermplasmAttributeValueSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/GermplasmAttributeValue" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "GermplasmAttributeValueSingleResponse" + } + } + } + }, + "BreedingMethodListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/BreedingMethod" + } + }, + "required" : [ "metadata", "result" ], + "title" : "BreedingMethodListResponse" + } + } + } + }, + "CallSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Call" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "CallSingleResponse" + } + } + } + }, + "GenomeMapListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/GenomeMap" + } + }, + "required" : [ "metadata", "result" ], + "title" : "GenomeMapListResponse" + } + } + } + }, + "PedigreeNodeListResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/metadata" + }, + "result" : { + "type" : "object", + "$ref" : "#/components/schemas/PedigreeNode" + } + }, + "required" : [ "metadata", "result" ], + "title" : "PedigreeNodeListResponse" + } + } + } + }, + "ObservationSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Observation" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ObservationSingleResponse" + } + } + } + }, + "ListSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/List" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ListSingleResponse" + } + } + } + }, + "ProgramSingleResponse" : { + "description" : "OK", + "content" : { + "application/json" : { + "schema" : { + "type" : "object", + "properties" : { + "'@context'" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "metadata" : { + "type" : "object", + "$ref" : "#/components/schemas/Context" + }, + "result" : { + "type" : "object", + "properties" : { + "data" : { + "type" : "array", + "items" : { + "type" : "object", + "$ref" : "#/components/schemas/Program" + } + } + }, + "required" : [ "data" ] + } + }, + "required" : [ "metadata", "result" ], + "title" : "ProgramSingleResponse" + } + } + } + } + }, + "parameters" : { + "externalReferenceID" : { + "name" : "externalReferenceID", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `externalReferenceId`. Github issue number #460 \n
An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "required" : false, + "deprecated" : true, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "externalReferenceId" : { + "name" : "externalReferenceId", + "in" : "query", + "description" : "An external reference ID. Could be a simple string or a URI. (use with `externalReferenceSource` parameter)", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "externalReferenceSource" : { + "name" : "externalReferenceSource", + "in" : "query", + "description" : "An identifier for the source system or database of an external reference (use with `externalReferenceId` parameter)", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + } + }, + "acceptHeader" : { + "name" : "Accept", + "in" : "header", + "description" : "A standard HTTP request header that is used to request a specific content type (JSON, CSV, etc) which is \"acceptable\" to the client and should be returned by the server", + "required" : true, + "style" : "simple", + "explode" : false, + "schema" : { + "$ref" : "#/components/schemas/ContentTypes" + }, + "example" : "application/json" + }, + "searchResultsDbId" : { + "name" : "searchResultsDbId", + "in" : "path", + "description" : "Unique identifier which references the search results", + "required" : true, + "style" : "simple", + "explode" : false, + "schema" : { + "type" : "string" + } + }, + "pageSize" : { + "name" : "pageSize", + "in" : "query", + "description" : "The size of the pages to be returned. Default is `1000`.", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "integer" + }, + "example" : 1000 + }, + "authorizationHeader" : { + "name" : "Authorization", + "in" : "header", + "description" : "HTTP HEADER - Token used for Authorization \n\n Bearer {token_string} ", + "required" : false, + "style" : "simple", + "explode" : false, + "schema" : { + "type" : "string", + "pattern" : "^Bearer .*$" + }, + "example" : "Bearer XXXX" + }, + "pageToken" : { + "name" : "pageToken", + "in" : "query", + "description" : "**Deprecated in v2.1** Please use `page`. Github issue number #451 \n
Used to request a specific page of data to be returned.\n
Tokenized pages are for large data sets which can not be efficiently broken into indexed pages. Use the nextPageToken and prevPageToken from a prior response to construct a query and move to the next or previous page respectively. ", + "required" : false, + "deprecated" : true, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "string" + }, + "example" : "33c27874" + }, + "page" : { + "name" : "page", + "in" : "query", + "description" : "Used to request a specific page of data to be returned.\n\nThe page indexing starts at 0 (the first page is 'page'= 0). Default is `0`.", + "required" : false, + "style" : "form", + "explode" : true, + "schema" : { + "type" : "integer" + }, + "example" : "0" + } + }, + "securitySchemes" : { + "AuthorizationToken" : { + "type" : "http", + "description" : "OAuth Bearer Token - A valid Bearer token to prove authorization", + "scheme" : "bearer", + "bearerFormat" : "nonce token or JWT" + } + } + } +} \ No newline at end of file diff --git a/Specification/Generated/brapi_v2_1.ttl b/Specification/Generated/brapi_v2_1.ttl new file mode 100644 index 00000000..1889a868 --- /dev/null +++ b/Specification/Generated/brapi_v2_1.ttl @@ -0,0 +1,6111 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX xsd: + + + rdf:type owl:DatatypeProperty; + rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; + rdfs:domain ; + rdfs:label "language"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Specifies a FASTA format file/string."@en; + rdfs:domain ; + rdfs:label "sourceURI"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "GermplasmChild"@en . + + + rdf:type owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of the taxonomy provider"@en; + rdfs:domain ; + rdfs:label "sourceName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the approximate slope (height/distance) of a Location."@en; + rdfs:domain ; + rdfs:label "slope"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelOrder"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unique DbId for the Seed Lot Transaction"@en; + rdfs:domain ; + rdfs:label "transactionDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "a custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "cross"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "fromSeedLotTransactions"@en; + rdfs:domain ; + rdfs:label "fromSeedLotTransactions"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "ValidValues"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Other trait names"@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name of the program"@en; + rdfs:domain ; + rdfs:label "programName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "donoers associated with a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:label "PositionCoordinateYType"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "map"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; + rdfs:domain ; + rdfs:label "analysis"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated seedLot"@en; + rdfs:domain ; + rdfs:label "seedLot"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique DbId of the breeding program this Seed Lot belongs to"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The shortened code name of an event parameter\n
ICASA \"Code_Display\""@en; + rdfs:domain ; + rdfs:label "code"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A short description of a type of Location (ex. Field Station, Breeding Location, Storage Location, etc)"@en; + rdfs:domain ; + rdfs:label "locationType"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description of the material source\n\nMIAPPE V1.1 (DM-56) Material source description - Description of the material source"@en; + rdfs:domain ; + rdfs:label "seedSourceDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "If the event parameter 'unit' field is 'code', then use 'valueDescription' to add a human readable description to the value."@en; + rdfs:domain ; + rdfs:label "valueDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable description of a trial\n\nMIAPPE V1.1 (DM-4) Investigation description - Human-readable text describing the investigation in more detail."@en; + rdfs:domain ; + rdfs:label "trialDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-27) Type of growth facility - Type of growth facility in which the study was carried out, in the form of an accession number from the Crop Ontology."@en; + rdfs:domain ; + rdfs:label "PUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Experimental design associated with a study"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name for a cross"@en; + rdfs:domain ; + rdfs:label "crossName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Method description\n
MIAPPE V1.1 (DM-90) Method description - Textual description of the method, which may extend a method defined in an external reference with specific parameters, e.g. growth stage, inoculation precise organ (leaf number)"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The child germplasm"@en; + rdfs:domain ; + rdfs:label "childGermplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Zero or more filters that failed for this variant. VCF column 7 \"FILTER\" shared across all alleles in the same VCF record."@en; + rdfs:domain ; + rdfs:label "filtersFailed"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "DocumentationLink"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or identifier of the entity which took the `Sample` from the field"@en; + rdfs:domain ; + rdfs:label "takenBy"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A Permanent Unique Identifier for an observation unit\n\nMIAPPE V1.1 (DM-72) External ID - Identifier for the observation unit in a persistent repository, comprises the name of the repository and the identifier of the observation unit therein. The EBI Biosamples repository can be used. URI are recommended when possible."@en; + rdfs:domain ; + rdfs:label "observationUnitPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Publication"@en . + + + rdf:type owl:Class; + rdfs:label "Season"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A general description of this Seed Lot Transaction"@en; + rdfs:domain ; + rdfs:label "transactionDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "links to various ontology documentation"@en; + rdfs:domain ; + rdfs:label "documentationLinks"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of the `Sample`"@en; + rdfs:domain ; + rdfs:label "sampleName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of an Attribute, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "attributePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The total number of elements that are available on the server and match the requested query parameters."@en; + rdfs:domain ; + rdfs:label "totalCount"@en; + rdfs:range xsd:integer . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of the analysis"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "pedigreeNodes"@en; + rdfs:domain ; + rdfs:label "pedigreeNodes"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Geometry associated with an image"@en; + rdfs:domain ; + rdfs:label "germplasmOrigin"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The code representing the family of this germplasm"@en; + rdfs:domain ; + rdfs:label "familyCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of germplasm references that are direct children of this germplasm. These represent edges in the tree, connecting to other nodes.\n
The given germplasm could have a large number of progeny, across a number of different breeding methods. The 'parentType' shows \n the type of parent this germplasm is to each of the child germplasm references.\n
If the parameter 'includeProgeny' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "progeny"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated ontology reference"@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "GermplasmOrigin"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "alleleMatrices"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of the country where a Location is located\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code."@en; + rdfs:domain ; + rdfs:label "countryName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a representation for missing data."@en; + rdfs:domain ; + rdfs:label "unknownString"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a CallSet within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable description of an image."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; + rdfs:label "BiologicalStatusOfAccessionCode"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The 'dataMatrices' are an array of matrix objects that hold the allele data and associated metadata. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; + rdfs:domain ; + rdfs:label "dataMatrices"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A program identifier to search for"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:domain ; + rdfs:label "positionCoordinateYType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of this study\n\nMIAPPE V1.1 (DM-13) Study description - Human-readable text describing the study"@en; + rdfs:domain ; + rdfs:label "studyDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the value of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the unique identifier for a program"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The contacts email address\n\nMIAPPE V1.1 (DM-32) Person email - The electronic mail address of the person."@en; + rdfs:domain ; + rdfs:label "email"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** "@en; + rdfs:domain ; + rdfs:label "observationLevelRelationships"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "CallSet"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Formats associated with a variant set"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "attributeValues"@en; + rdfs:domain ; + rdfs:label "attributeValues"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp for the last update to this Seed Lot (including transactions)"@en; + rdfs:domain ; + rdfs:label "lastUpdated"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The array of DbIds of the BrAPI objects contained in a List"@en; + rdfs:domain ; + rdfs:label "data"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "SeedLotTransaction"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Trait status (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID of the call set this variant call belongs to.\n\nIf this field is not present, the ordering of the call sets from a `SearchCallSetsRequest` over this `VariantSet` is guaranteed to match the ordering of the calls on this `Variant`. The number of results will also be the same."@en; + rdfs:domain ; + rdfs:label "callSet"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The Ontology for this reference"@en; + rdfs:domain ; + rdfs:label "ontology"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "All known corresponding Germplasm"@en; + rdfs:domain ; + rdfs:label "sourceGermplasm"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:Class; + rdfs:label "AlleleMatrix"@en . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "additionalProperties"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "When the data for a VariantSet is retrieved, it can be retrieved in a variety of data formats and file formats. \n
'dataFormat' defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)\n
'fileFormat' defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:domain ; + rdfs:label "availableFormats"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "crosses"@en; + rdfs:domain ; + rdfs:label "crosses"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; + rdfs:domain ; + rdfs:label "programType"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The start position at which this variant occurs (0-based). This corresponds to the first base of the string \nof reference bases. Genomic positions are non-negative integers less than reference length. Variants spanning \nthe join of circular genomes are represented as two variants one on each side of the join (position 0)."@en; + rdfs:domain ; + rdfs:label "start"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) which must include a version number, e.g. `GCF_000001405.26`."@en; + rdfs:domain ; + rdfs:label "sourceAccessions"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The beginning of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; + rdfs:domain ; + rdfs:label "startDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Data matrices associated with an alleleMatrix"@en; + rdfs:domain ; + rdfs:label "alleleMatrix"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the type of cross"@en; + rdfs:domain ; + rdfs:label "crossType"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "variants"@en; + rdfs:domain ; + rdfs:label "variants"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the type of cross"@en; + rdfs:domain ; + rdfs:label "crossType"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The an observation unit\n
If this level has on ObservationUnit associated with it, record the observationUnitDbId here. This is intended to construct a strict hierarchy of observationUnits. \n
If there is no ObservationUnit associated with this level, this field can set to NULL or omitted from the response."@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a trait"@en; + rdfs:domain ; + rdfs:label "traitDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "BreedingMethod"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated pedigreeNode"@en; + rdfs:domain ; + rdfs:label "pedigreeNode"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Observation"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + rdfs:domain ; + rdfs:label "contextOfUse"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProjectName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The reference bases for this variant. They start at the given start position."@en; + rdfs:domain ; + rdfs:label "referenceBases"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The literal string \"Point\""@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of a ReferenceSet"@en; + rdfs:domain ; + rdfs:label "referenceSetName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated valid values"@en; + rdfs:domain ; + rdfs:label "validValues"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An identifier for the source system or database of this reference"@en; + rdfs:domain ; + rdfs:label "referenceSource"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "GermplasmParent"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "publicationReference"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "references"@en; + rdfs:domain ; + rdfs:label "references"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of `Sample` taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; + rdfs:domain ; + rdfs:label "sampleType"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "ObservationUnitPosition"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; + rdfs:domain ; + rdfs:label "expandHomozygotes"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier which represents a germplasm\n\nMIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below.\n\nMIAPPE V1.1 (DM-51) Material source DOI - Digital Object Identifier (DOI) of the material source\n\nMCPD (v2.1) (PUID) 0. Any persistent, unique identifier assigned to the accession so it can be unambiguously referenced at the global level and the information associated with it harvested through automated means. Report one PUID for each accession. The Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture (PGRFA) is facilitating the assignment of a persistent unique identifier (PUID), in the form of a DOI, to PGRFA at the accession level. Genebanks not applying a true PUID to their accessions should use, and request recipients to use, the concatenation of INSTCODE, ACCENUMB, and GENUS as a globally unique identifier similar in most respects to the PUID whenever they exchange information on accessions with third parties."@en; + rdfs:domain ; + rdfs:label "germplasmPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format"@en; + rdfs:domain ; + rdfs:label "plateFormat"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "GermplasmAttributeValue"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; + rdfs:label "DataFormat"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelOrder"@en; + rdfs:range xsd:integer . + + + rdf:type owl:Class; + rdfs:label "Call"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The copyright information of this image. Example 'Copyright 2018 Bob Robertson'"@en; + rdfs:domain ; + rdfs:label "copyright"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Reference"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; + rdfs:domain ; + rdfs:label "submissionTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; + rdfs:label "EntryType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology database unique identifier"@en; + rdfs:domain ; + rdfs:label "ontologyDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of institution submitting the variable"@en; + rdfs:domain ; + rdfs:label "institution"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "toSeedLotTransactions"@en; + rdfs:domain ; + rdfs:label "toSeedLotTransactions"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of an image. Might be the same as 'imageFileName', but could be different."@en; + rdfs:domain ; + rdfs:label "imageName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A shortened version of the human readable name for a Location"@en; + rdfs:domain ; + rdfs:label "abbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of where a List originated from"@en; + rdfs:domain ; + rdfs:label "listSource"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the institute that maintains the material"@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "DatasetAuthorships"@en . + + + rdf:type owl:Class; + rdfs:label "Germplasm"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Persons first name"@en; + rdfs:domain ; + rdfs:label "firstName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "markerPositions"@en; + rdfs:domain ; + rdfs:label "markerPositions"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The institute code for the donor institute\n
MCPD (v2.1) (DONORCODE) 22. FAO WIEWS code of the donor institute. Follows INSTCODE standard."@en; + rdfs:domain ; + rdfs:label "donorInstituteCode"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "PedigreeNode"@en . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology licence"@en; + rdfs:domain ; + rdfs:label "licence"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Y position coordinate for an observation unit. Different systems may use different coordinate systems."@en; + rdfs:domain ; + rdfs:label "positionCoordinateY"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or identifier of the entity which collected the observation"@en; + rdfs:domain ; + rdfs:label "collector"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name or id of the user who uploaded the observation to the database system"@en; + rdfs:domain ; + rdfs:label "uploadedBy"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a `Reference`"@en; + rdfs:domain ; + rdfs:label "referenceDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a ReferenceSet"@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Genotype metadata associated with a call"@en; + rdfs:domain ; + rdfs:label "call"@en; + rdfs:range . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Information for material (orchard, natural sites, ...). Geographic identification of the plants from which seeds or cutting have been taken to produce that germplasm."@en; + rdfs:domain ; + rdfs:label "germplasmOrigin"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en , "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en , "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; + rdfs:label "DataType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Supplemental text description for 'biologicalStatusOfAccessionCode'"@en; + rdfs:domain ; + rdfs:label "biologicalStatusOfAccessionDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Pagination"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a season. For backward compatibility it can be a string like '2012', '1957-2004'"@en; + rdfs:domain ; + rdfs:label "seasonDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Observation Variable, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "observationVariablePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the germplasm of the cross parent"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "email address for this person"@en; + rdfs:domain ; + rdfs:label "emailAddress"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + rdfs:domain ; + rdfs:label "contextOfUse"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated event"@en; + rdfs:domain ; + rdfs:label "event"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date and time when this study was last modified"@en; + rdfs:domain ; + rdfs:label "lastUpdateDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "seedLots"@en; + rdfs:domain ; + rdfs:label "seedLots"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for phased allele calls."@en; + rdfs:domain ; + rdfs:label "sepPhased"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Trait, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "traitPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unique DbId for the Seed Lot"@en; + rdfs:domain ; + rdfs:label "seedLotDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:label "FileFormat"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-5) Submission date - Date of submission of the dataset presently being described to a host repository."@en; + rdfs:domain ; + rdfs:label "submissionDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of entry for this observation unit. ex. \"CHECK\", \"TEST\", \"FILLER\""@en; + rdfs:domain ; + rdfs:label "entryType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Length of the - if labeled as such in variant_type - structural variation. Based on the use in VCF v4.2"@en; + rdfs:domain ; + rdfs:label "svlen"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; + rdfs:domain ; + rdfs:label "submissionTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Pagination for the matrix"@en; + rdfs:domain ; + rdfs:label "pagination"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "variantSets"@en; + rdfs:domain ; + rdfs:label "variantSets"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this attribute"@en; + rdfs:domain ; + rdfs:label "attributeDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date the study ends\n\nMIAPPE V1.1 (DM-15) End date of study - Date and, if relevant, time when the experiment ended"@en; + rdfs:domain ; + rdfs:label "endDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "calls"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The list of IDs for this SPECIES from different sources. If present, NCBI Taxon should be always listed as \"ncbiTaxon\" preferably with a purl. The rank of this ID should be species.\n\nMIAPPE V1.1 (DM-42) Organism - An identifier for the organism at the species level. Use of the NCBI taxon ID is recommended."@en; + rdfs:domain ; + rdfs:label "taxonIds"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Type"@en . + + + rdf:type owl:Class; + rdfs:label "Ontology"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The germplasm using in this content mixture"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The X position coordinate for an observation unit. Different systems may use different coordinate systems."@en; + rdfs:domain ; + rdfs:label "positionCoordinateX"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A systems user ID associated with this person. Different from personDbId because you could have a person who is not a user of the system."@en; + rdfs:domain ; + rdfs:label "userID"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The remaining information is about the source of the sequences Public id of this reference set, such as `GRCH_37`."@en; + rdfs:domain ; + rdfs:label "assemblyPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Analysis"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The complete, absolute URI path to the image file. Images might be stored on a different host or path than the BrAPI web server."@en; + rdfs:domain ; + rdfs:label "imageURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Environmental parameters that were kept constant throughout the study and did not change between observation units.\n\nMIAPPE V1.1 (DM-57) Environment - Environmental parameters that were kept constant throughout the study and did not change between observation units or assays. Environment characteristics that vary over time, i.e. environmental variables, should be recorded as Observed Variables (see below)."@en; + rdfs:domain ; + rdfs:label "environmentParameters"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Variable"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of parent ex. 'MALE', 'FEMALE', 'SELF', 'POPULATION', etc."@en; + rdfs:domain ; + rdfs:label "parentType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:label "AdditionalInfo"@en . + + + rdf:type owl:Class; + rdfs:label "Location"@en . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string representation of the pedigree for this germplasm in PURDY notation"@en; + rdfs:domain ; + rdfs:label "pedigreeString"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of units being transferred between SeedLots. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)."@en; + rdfs:domain ; + rdfs:label "amount"@en; + rdfs:range xsd:double . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the unique identifier for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProject"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The related observation unit identifier, if relevant."@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A list of terms to formally describe the image. Each item could be a simple Tag, an Ontology reference Id, or a full ontology URL."@en; + rdfs:domain ; + rdfs:label "descriptiveOntologyTerms"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Sample"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop associated with this study"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The DOI or other permanent identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:domain ; + rdfs:label "trait"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The file type of the image. Examples 'image/jpeg', 'image/png', 'image/svg', etc"@en; + rdfs:domain ; + rdfs:label "mimeType"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a germplasm within the given database server \n
MIAPPE V1.1 (DM-41) Biological material ID - Code used to identify the biological material in the data file. Should be unique within the Investigation. Can correspond to experimental plant ID, seed lot ID, etc. This material identification is different from a BiosampleID which corresponds to Observation Unit or Samples sections below."@en; + rdfs:domain ; + rdfs:label "germplasmDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "calls"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; + rdfs:domain ; + rdfs:label "parentType"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies an observation variable"@en; + rdfs:domain ; + rdfs:label "observationVariable"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "siblingPedigreeNodes"@en; + rdfs:domain ; + rdfs:label "siblingPedigreeNodes"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "GermplasmAttribute"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; + rdfs:domain ; + rdfs:label "attributeDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Minimum value for numerical, date, and time scales. Typically used for data capture control and QC."@en; + rdfs:domain ; + rdfs:label "minimumValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "events"@en; + rdfs:domain ; + rdfs:label "events"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A supplemental text description of the storage type"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Similar to \"cipos\", but for the variant's end position (which is derived from start + svlen)."@en; + rdfs:domain ; + rdfs:label "ciend"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable unique identifier\n\nMIAPPE V1.1 (DM-83) Variable ID - Code used to identify the variable in the data file. We recommend using a variable definition from the Crop Ontology where possible. Otherwise, the Crop Ontology naming convention is recommended: __). A variable ID must be unique within a given investigation."@en; + rdfs:domain ; + rdfs:label "observationVariableDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for the breeding method used to create this germplasm"@en; + rdfs:domain ; + rdfs:label "breedingMethod"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated observation Unit"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "locationDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "physical address of this person"@en; + rdfs:domain ; + rdfs:label "mailingAddress"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "If this field is populated, this variant call's genotype ordering implies the phase of the bases and \nis consistent with any other variant calls on the same contig which have the same phase set string."@en; + rdfs:domain ; + rdfs:label "phaseSet"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of a trial\n\nMIAPPE V1.1 (DM-3) Investigation title - Human-readable string summarising the investigation."@en; + rdfs:domain ; + rdfs:label "trialName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "MetadataField"@en . + + + rdf:type owl:Class; + rdfs:label "Method"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for an observation unit"@en; + rdfs:domain ; + rdfs:label "observationUnitName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "crosses"@en; + rdfs:domain ; + rdfs:label "crosses"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for unphased allele calls."@en; + rdfs:domain ; + rdfs:label "sepUnphased"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the description for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProjectDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time stamp for when this seed lot was created"@en; + rdfs:domain ; + rdfs:label "createdDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Column identifier for this `Sample` location in the `Plate`"@en; + rdfs:domain ; + rdfs:label "column"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A descriptive classification for this synonym"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this trial ends"@en; + rdfs:domain ; + rdfs:label "endDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology copyright"@en; + rdfs:domain ; + rdfs:label "copyright"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The IDs of the variantSets this callSet has calls in."@en; + rdfs:domain ; + rdfs:label "variantSets"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Analysis associated with a variant set"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID of the reference set that describes the sequences used by the variants in this set."@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The single value of this event parameter. This single value is accurate for all the dates in the date range. If 'value' is populated then 'valuesByDate' should NOT be populated."@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of `VariantSet` IDs this variant belongs to. This also defines the `ReferenceSet` against which the `Variant` is to be interpreted."@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "ObservationVariable"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; + rdfs:domain ; + rdfs:label "language"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "progenyPedigreeNodes"@en; + rdfs:domain ; + rdfs:label "progenyPedigreeNodes"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of elements in a List"@en; + rdfs:domain ; + rdfs:label "listSize"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "True if all filters for this variant passed. VCF column 7 \"FILTER\" value PASS."@en; + rdfs:domain ; + rdfs:label "filtersPassed"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A unique identifier physically attached to the `Sample`"@en; + rdfs:domain ; + rdfs:label "sampleBarcode"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Donor"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The external reference ID. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "referenceId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; + rdfs:label "SampleType"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Reference"@en; + rdfs:domain ; + rdfs:label "reference"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date and time a `Sample` was collected from the field\n
MIAPPE V1.1 (DM-80) Collection date - The date and time when the sample was collected / harvested"@en; + rdfs:domain ; + rdfs:label "sampleTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name associated with a `Variant`"@en; + rdfs:domain ; + rdfs:label "variantNames"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "parentPedigreeNodes"@en; + rdfs:domain ; + rdfs:label "parentPedigreeNodes"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a trial"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for phased allele calls."@en; + rdfs:domain ; + rdfs:label "sepPhased"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name of a List"@en; + rdfs:domain ; + rdfs:label "listName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-7) License - License for the reuse of the data associated with this investigation. The Creative Commons licenses cover most use cases and are recommended."@en; + rdfs:domain ; + rdfs:label "license"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of unique identifiers for the Variants contained in the matrix response. This array should match the ordering for rows in the matrix."@en; + rdfs:domain ; + rdfs:label "variants"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology version (no specific format)"@en; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "GenotypeMetadata"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Uniquely Identifiable name of a `LinkageGroup`\n
This might be a chromosome identifier or the generic linkage group identifier if the chromosome is not applicable."@en; + rdfs:domain ; + rdfs:label "linkageGroupName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description the storage location"@en; + rdfs:domain ; + rdfs:label "storageLocation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Information describing the grant or funding source for this program"@en; + rdfs:domain ; + rdfs:label "fundingInformation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date and time when this observation was made"@en; + rdfs:domain ; + rdfs:label "observationTimeStamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:Class; + rdfs:comment "The type of objects that are referenced in a List"@en; + rdfs:label "ListType"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of an Attribute, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "attributePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "studies"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "[ISO_3166-1_alpha-3](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-3) spec\n
MIAPPE V1.1 (DM-17) Geographic location (country) - The country where the experiment took place, either as a full name or preferably as a 2-letter code.'"@en; + rdfs:domain ; + rdfs:label "countryCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Specific epithet portion of the scientific name in lowercase letters.\n\nMCPD (v2.1) (SPECIES) 6. Specific epithet portion of the scientific name in lowercase letters. Only the following abbreviation is allowed: \"sp.\" \n\nMIAPPE V1.1 (DM-44) Species - Species name (formally: specific epithet) for the organism under study, according to standard scientific nomenclature."@en; + rdfs:domain ; + rdfs:label "species"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-6) Public release date - Date of first public release of the dataset presently being described."@en; + rdfs:domain ; + rdfs:label "publicReleaseDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The identifier for the Seed Lot being transferred out of"@en; + rdfs:domain ; + rdfs:label "fromSeedLot"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "callSets"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "General category for the attribute. very similar to Trait class."@en; + rdfs:domain ; + rdfs:label "attributeCategory"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for the originating Seed Lot"@en; + rdfs:domain ; + rdfs:label "seedLot"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A list of shortened, human readable, names for a Trait. These abbreviations are acceptable alternatives to the mainAbbreviation and do not need to follow any formatting convention."@en; + rdfs:domain ; + rdfs:label "alternativeAbbreviations"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Scale, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "scalePUI"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The mixture of germplasm present in the seed lot.\n
\nIf this seed lot only contains a single germplasm, the response should contain the name \nand DbId of that germplasm with a mixturePercentage value of 100\n
\nIf the seed lot contains a mixture of different germplasm, the response should contain \nthe name and DbId every germplasm present. The mixturePercentage field should contain \nthe ratio of each germplasm in the total mixture. All of the mixturePercentage values \nin this array should sum to equal 100."@en; + rdfs:domain ; + rdfs:label "contentMixture"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The identifier (name, ID, URI) of a particular taxonomy within the source provider"@en; + rdfs:domain ; + rdfs:label "taxonId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the maximum number of elements per page in this dimension of the matrix"@en; + rdfs:domain ; + rdfs:label "pageSize"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An array of linear rings"@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range xsd:double . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies the program"@en; + rdfs:domain ; + rdfs:label "programDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Should homozygotes be expanded (true) or collapsed into a single occurrence (false)"@en; + rdfs:domain ; + rdfs:label "expandHomozygotes"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of treatment/factor. ex. 'fertilizer', 'inoculation', 'irrigation', etc\n\nMIAPPE V1.1 (DM-61) Experimental Factor type - Name/Acronym of the experimental factor."@en; + rdfs:domain ; + rdfs:label "factor"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for the breeding method used to create this germplasm"@en; + rdfs:domain ; + rdfs:label "breedingMethod"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\""@en; + rdfs:domain ; + rdfs:label "entity"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "crossingProjects"@en; + rdfs:domain ; + rdfs:label "crossingProjects"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the unique identifier for a cross"@en; + rdfs:domain ; + rdfs:label "crossDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of the origin or ownership of this linked data. Could be a formal reference to software, method, or workflow."@en; + rdfs:domain ; + rdfs:label "provenance"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The type of cross make. Accepted values for this field are 'BIPARENTAL', 'SELF', 'OPEN_POLLINATED', 'BULK', 'BULK_SELFED', 'BULK_OPEN_POLLINATED' and 'DOUBLE_HAPLOID'."@en; + rdfs:label "CrossType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "True if the pollination was successful"@en; + rdfs:domain ; + rdfs:label "pollinationSuccessful"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for this analysis"@en; + rdfs:domain ; + rdfs:label "analysisName"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name of a cross attribute"@en; + rdfs:domain ; + rdfs:label "crossAttributeName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "An array of Linear Rings. Each Linear Ring is an array of Points. \n\nA Point is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:label "GeoJSONPolygon"@en . + + + rdf:type owl:Class; + rdfs:comment "Copied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:label "GeoJSONPoint"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Persons last name"@en; + rdfs:domain ; + rdfs:label "lastName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Geometry associated with an image"@en; + rdfs:domain ; + rdfs:label "image"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Short description of the facility in which the study was carried out."@en; + rdfs:domain ; + rdfs:label "growthFacility"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable name for a planned cross"@en; + rdfs:domain ; + rdfs:label "plannedCrossName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop which this program is for"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A shortened version of the human readable name for a Breeding Method"@en; + rdfs:domain ; + rdfs:label "abbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:domain ; + rdfs:label "trait"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "PlannedCross"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; + rdfs:domain ; + rdfs:label "attribute"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "calls"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; + rdfs:domain ; + rdfs:label "submissionTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "imageLocation"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the requested page number (zero indexed)"@en; + rdfs:domain ; + rdfs:label "page"@en; + rdfs:range xsd:integer . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The common name of the `Crop`"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A classification to describe the type of trait and the context it should be considered in.\n
examples- \"morphological\", \"phenological\", \"agronomical\", \"physiological\", \"abiotic stress\", \"biotic stress\", \"biochemical\", \"quality traits\", \"fertility\", etc."@en; + rdfs:domain ; + rdfs:label "traitClass"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a ontology reference"@en; + rdfs:domain ; + rdfs:label "ontologyReferenceDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a pedigree node"@en; + rdfs:domain ; + rdfs:label "pedigreeNodeDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "GenomeMap"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "markerPositions"@en; + rdfs:domain ; + rdfs:label "markerPositions"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Scale describes the units and acceptable values for an ObservationVariable. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Scale \"inches\" or \"pixels\"."@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "publicationPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this event parameter. This description is usually associated with the 'name' and 'code' of an event parameter."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time stamp for when the transaction occurred"@en; + rdfs:domain ; + rdfs:label "transactionTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A flag to indicate the type of objects that are referenced in a List"@en; + rdfs:domain ; + rdfs:label "listType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "All known corresponding accession IDs in INSDC (GenBank/ENA/DDBJ) ideally with a version number, e.g. `NC_000001.11`."@en; + rdfs:domain ; + rdfs:label "sourceAccessions"@en; + rdfs:range xsd:string . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Plate` of `Sample`"@en; + rdfs:domain ; + rdfs:label "plate"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Pollination events associated with a cross"@en; + rdfs:domain ; + rdfs:label "cross"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "PollinationEvent"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Environment parameters associated with a study"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "This field is optional and may be ignored if there is no relevant map or reference to be associated with.\n
The end position (exclusive), resulting in [start, end) closed-open interval. This is typically calculated \nby `start + referenceBases.length`."@en; + rdfs:domain ; + rdfs:label "end"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "phone number of this person"@en; + rdfs:domain ; + rdfs:label "phoneNumber"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The usage license associated with the study data"@en; + rdfs:domain ; + rdfs:label "license"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "variants"@en; + rdfs:domain ; + rdfs:label "variants"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An identifier for the source of the biological material\n
MIAPPE V1.1 (DM-50) Material source ID (Holding institute/stock centre, accession) - An identifier for the source of the biological material, in the form of a key-value pair comprising the name/identifier of the repository from which the material was sourced plus the accession number of the repository for that material. Where an accession number has not been assigned, but the material has been derived from the crossing of known accessions, the material can be defined as follows: \"mother_accession X father_accession\", or, if father is unknown, as \"mother_accession X UNKNOWN\". For in situ material, the region of provenance may be used when an accession is not available."@en; + rdfs:domain ; + rdfs:label "seedSource"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "studies"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Person"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name for a VariantSet"@en; + rdfs:domain ; + rdfs:label "variantSetName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "EnvironmentParameters"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "trials"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The code for the institute that maintains the material. \n\nMCPD (v2.1) (INSTCODE) 1. FAO WIEWS code of the institute where the accession is maintained. The codes consist of the 3-letter ISO 3166 country code of the country where the institute is located plus a number (e.g. PER001). The current set of institute codes is available from http://www.fao.org/wiews. For those institutes not yet having an FAO Code, or for those with \"obsolete\" codes, see \"Common formatting rules (v)\"."@en; + rdfs:domain ; + rdfs:label "instituteCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The URI from which the sequence was obtained. Specifies a FASTA format file/string with one name, sequence pair. In most cases, clients should call the `getReferenceBases()` method to obtain sequence bases for a `Reference` instead of attempting to retrieve this URI."@en; + rdfs:domain ; + rdfs:label "sourceURI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Optional free text description of this reference set."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies an observation unit"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for this attribute"@en; + rdfs:domain ; + rdfs:label "attributeName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The \"variant_type\" is used to denote e.g. structural variants.\nExamples:\n DUP : duplication of sequence following \"start\"\n DEL : deletion of sequence following \"start\""@en; + rdfs:domain ; + rdfs:label "variantType"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated observation Unit"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "LastUpdate"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "plates"@en; + rdfs:domain ; + rdfs:label "plates"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name for a study\n\nMIAPPE V1.1 (DM-12) Study title - Human-readable text summarising the study"@en; + rdfs:domain ; + rdfs:label "studyName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of the affected observation units. If this parameter is not given, it is understood that the event affected all units in the study"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of unique identifiers for the CallSets contained in the matrix response. This array should match the ordering for columns in the matrix. A CallSet is a unique combination of a Sample and a sequencing event. CallSets often have a 1-to-1 relationship with Samples, but this is not always the case."@en; + rdfs:domain ; + rdfs:label "callSets"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A general description of this Seed Lot"@en; + rdfs:domain ; + rdfs:label "seedLotDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The primary objective of the program"@en; + rdfs:domain ; + rdfs:label "objective"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The 'metadataField' indicates which types of genotyping data and metadata are available in the VariantSet. \n
When possible, these field names and abbreviations should follow the VCF standard "@en; + rdfs:domain ; + rdfs:label "metadataFields"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of donor institutes"@en; + rdfs:domain ; + rdfs:label "donors"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of samples taken. ex. 'DNA', 'RNA', 'Tissue', etc"@en; + rdfs:domain ; + rdfs:label "sampleType"@en; + rdfs:range . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the topography of the land at a Location. (ex. Plateau, Cirque, Hill, Valley, etc)"@en; + rdfs:domain ; + rdfs:label "topography"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A description of the things being transferred between SeedLots in a transaction (seeds, bulbs, kg, etc)"@en; + rdfs:domain ; + rdfs:label "units"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "timestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The abbreviated code of the field represented in this data matrix. These codes should match the VCF standard when possible and the key word \"GT\" is reserved for the allele matrix. Examples of other metadata matrices include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "dataMatrixAbbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:label "GeoJSON"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "plates"@en; + rdfs:domain ; + rdfs:label "plates"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A reference set may be derived from a source if it contains additional sequences, or some of the sequences within it are derived (see the definition of `isDerived` in `Reference`)."@en; + rdfs:domain ; + rdfs:label "isDerived"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description of a `Sample`\n
MIAPPE V1.1 (DM-79) Sample description - Any information not captured by the other sample fields, including quantification, sample treatments and processing."@en; + rdfs:domain ; + rdfs:label "sampleDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "alleleMatrices"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProjectDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a ReferenceSet"@en; + rdfs:domain ; + rdfs:label "referenceSetDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Pagination associated with an alleleMatrix"@en; + rdfs:domain ; + rdfs:label "alleleMatrix"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description of the accessibility of the location (ex. Public, Private)"@en; + rdfs:domain ; + rdfs:label "siteStatus"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID of the variant this call belongs to."@en; + rdfs:domain ; + rdfs:label "variant"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An array of values corresponding to each timestamp in the 'discreteDates' array of this event. The 'valuesByDate' array should exactly match the size of the 'discreteDates' array. If 'valuesByDate' is populated then 'value' should NOT be populated."@en; + rdfs:domain ; + rdfs:label "valuesByDate"@en; + rdfs:range xsd:string . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Study` within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A sequence X is said to be derived from source sequence Y, if X and Y are of the same length and the per-base sequence divergence at A/C/G/T bases is sufficiently small. Two sequences derived from the same official sequence share the same coordinates and annotations, and can be replaced with the official sequence for certain use cases."@en; + rdfs:domain ; + rdfs:label "isDerived"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:Class; + rdfs:label "TaxonId"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The literal string \"Feature\""@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of unique identifiers for the VariantSets contained in the matrix response. A VariantSet is a data set originating from a sequencing event. Often, users will only be interested in data from a single VariantSet, but in some cases a user might be interested in a matrix with data from multiple VariantSets."@en; + rdfs:domain ; + rdfs:label "variantSets"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A geometry as defined by GeoJSON (RFC 7946). In this context, only Point or Polygon geometry are allowed."@en; + rdfs:domain ; + rdfs:label "geometry"@en; + rdfs:range , . + + + rdf:type owl:Class; + rdfs:comment "The status of this planned cross. Is it waiting to be performed ('TODO'), has it been completed successfully ('DONE'), or has it not been done on purpose ('SKIPPED')."@en; + rdfs:label "PlannedCrossStatus"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Genus name for taxon. Initial uppercase letter required.\n\nMCPD (v2.1) (GENUS) 5. Genus name for taxon. Initial uppercase letter required.\n\nMIAPPE V1.1 (DM-43) Genus - Genus name for the organism under study, according to standard scientific nomenclature."@en; + rdfs:domain ; + rdfs:label "genus"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name for the method\n
MIAPPE V1.1 (DM-88) Method Name of the method of observation"@en; + rdfs:domain ; + rdfs:label "methodName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of institution submitting the variable"@en; + rdfs:domain ; + rdfs:label "institution"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the Variable was added (ISO 8601)"@en; + rdfs:domain ; + rdfs:label "submissionTimestamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "All positional and layout information related to this Observation Unit \n\nMIAPPE V1.1 (DM-73) Spatial distribution - Type and value of a spatial coordinate (georeference or relative) \nor level of observation (plot 45, subblock 7, block 2) provided as a key-value pair of the form type:value. \nLevels of observation must be consistent with those listed in the Study section."@en; + rdfs:domain ; + rdfs:label "observationUnitPosition"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "seedLots"@en; + rdfs:domain ; + rdfs:label "seedLots"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "lists"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Trial` within the given database server"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:domain ; + rdfs:label "observationLevel"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of tissue sampled. ex. 'Leaf', 'Root', etc.\n
MIAPPE V1.1 (DM-78) Plant anatomical entity - A description of the plant part (e.g. leaf) or the plant product (e.g. resin) from which the sample was taken, in the form of an accession number to a suitable controlled vocabulary (Plant Ontology)."@en; + rdfs:domain ; + rdfs:label "tissueType"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "URI pointing to an ontology class for the parameter value"@en; + rdfs:domain ; + rdfs:label "valuePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier of an image"@en; + rdfs:domain ; + rdfs:label "imageDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "human readable description of the breeding method"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "eventType"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The authority organization responsible for tracking and maintaining the species name \n\nMCPD (v2.1) (SPAUTHOR) 7. Provide the authority for the species name."@en; + rdfs:domain ; + rdfs:label "speciesAuthority"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a group of `Samples`"@en; + rdfs:domain ; + rdfs:label "sampleGroupId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated pedigreeNode"@en; + rdfs:domain ; + rdfs:label "pedigreeNode"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "OntologyReference"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; + rdfs:domain ; + rdfs:label "language"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The MD5 checksum uniquely representing this `Reference` as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM)."@en; + rdfs:domain ; + rdfs:label "md5checksum"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The two dimensional array of data, providing the allele matrix or an additional layer of metadata associated with each genotype value. Each matrix should be the same size and orientation, aligned with the \"callSetDbIds\" as columns and the \"variantDbIds\" as rows."@en; + rdfs:domain ; + rdfs:label "dataMatrix"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of the scale\n
MIAPPE V1.1 (DM-92) Scale Name of the scale associated with the variable"@en; + rdfs:domain ; + rdfs:label "scaleName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "List"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp when the pollination took place"@en; + rdfs:domain ; + rdfs:label "pollinationTimeStamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Treatment"@en . + + rdf:type owl:Ontology . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for this pollination event"@en; + rdfs:domain ; + rdfs:label "pollinationNumber"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this record was created, in ISO 8601 format."@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "URI pointing to an ontology class for the parameter"@en; + rdfs:domain ; + rdfs:label "parameterPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "ValidValuesCategory"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of the environment parameter constant within the experiment\n\nMIAPPE V1.1 (DM-58) Environment parameter - Name of the environment parameter constant within the experiment. "@en; + rdfs:domain ; + rdfs:label "parameterName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The cross name and optional selection history.\n\nMCPD (v2.1) (ANCEST) 20. Information about either pedigree or other description of ancestral information (e.g. parent variety in case of mutant or selection). For example a pedigree 'Hanna/7*Atlas//Turk/8*Atlas' or a description 'mutation found in Hanna', 'selection from Irene' or 'cross involving amongst others Hanna and Irene'."@en; + rdfs:domain ; + rdfs:label "pedigree"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a `ReferenceSet`"@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date a material or germplasm was acquired by the genebank \n\nMCPD (v2.1) (ACQDATE) 12. Date on which the accession entered the collection [YYYYMMDD] where YYYY is the year, MM is the month and DD is the day. Missing data (MM or DD) should be indicated with hyphens or \"00\" [double zero]."@en; + rdfs:domain ; + rdfs:label "acquisitionDate"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of institution submitting the variable"@en; + rdfs:domain ; + rdfs:label "institution"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of links to extra data files associated with this study. Extra data could include notes, images, and reference data."@en; + rdfs:domain ; + rdfs:label "dataLinks"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "studies"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "The dimension of the matrix being paginated"@en; + rdfs:label "Dimension"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of custom attributes associated with a cross"@en; + rdfs:domain ; + rdfs:label "crossAttributes"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the human readable identifier for this breeding method"@en; + rdfs:domain ; + rdfs:label "breedingMethodName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology version (no specific format)"@en; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of study being performed. ex. \"Yield Trial\", etc"@en; + rdfs:domain ; + rdfs:label "studyType"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The general type of data. For example- Genotyping, Phenotyping raw data, Phenotyping reduced data, Environmental, etc"@en; + rdfs:domain ; + rdfs:label "scientificType"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "validValues"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The list of pollination events that occurred for this cross"@en; + rdfs:domain ; + rdfs:label "pollinationEvents"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of a trait"@en; + rdfs:domain ; + rdfs:label "traitDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Genotype Metadata are additional layers of metadata associated with each genotype."@en; + rdfs:domain ; + rdfs:label "genotypeMetadata"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MCPD (v2.1) (SAMPSTAT) 19. The coding scheme proposed can be used at 3 different levels of detail: either by using the general codes such as 100, 200, 300, 400, or by using the more specific codes such as 110, 120, etc. \n\n100) Wild \n110) Natural \n120) Semi-natural/wild \n130) Semi-natural/sown \n200) Weedy \n300) Traditional cultivar/landrace \n400) Breeding/research material \n410) Breeders line \n411) Synthetic population \n412) Hybrid \n413) Founder stock/base population \n414) Inbred line (parent of hybrid cultivar) \n415) Segregating population \n416) Clonal selection \n420) Genetic stock \n421) Mutant (e.g. induced/insertion mutants, tilling populations) \n422) Cytogenetic stocks (e.g. chromosome addition/substitution, aneuploids, amphiploids) \n423) Other genetic stocks (e.g. mapping populations) \n500) Advanced or improved cultivar (conventional breeding methods) \n600) GMO (by genetic engineering) \n999) Other (Elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "biologicalStatusOfAccessionCode"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this attribute for a given germplasm"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:label "StorageTypeCode"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology's list of authors (no specific format)"@en; + rdfs:domain ; + rdfs:label "authors"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this call set was created"@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Other variable names"@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range xsd:string . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:domain ; + rdfs:label "positionCoordinateXType"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Plate"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The 4 digit year of the season."@en; + rdfs:domain ; + rdfs:label "year"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown."@en; + rdfs:domain ; + rdfs:label "coordinateUncertainty"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; + rdfs:domain ; + rdfs:label "environmentParametersDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Order-independent MD5 checksum which identifies this `ReferenceSet`.\n\nTo compute this checksum, make a list of `Reference.md5checksum` for all\n`Reference` s in this set. Then sort that list, and take the MD5 hash of\nall the strings concatenated together. Express the hash as a lower-case\nhexadecimal string."@en; + rdfs:domain ; + rdfs:label "md5checksum"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of analysis."@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Study"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Alternative name or ID used to reference this germplasm"@en; + rdfs:domain ; + rdfs:label "synonym"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "URL describing the location of this data file to view or download\n\nMIAPPE V1.1 (DM-37) Data file link - Link to the data file (or digital object) in a public database or in a persistent institutional repository; or identifier of the data file when submitted together with the MIAPPE submission."@en; + rdfs:domain ; + rdfs:label "url"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Species associated with a referenceSet"@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Trial` within the given database server"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human-readable value of the environment parameter (defined above) constant within the experiment"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of this genotype call"@en; + rdfs:domain ; + rdfs:label "genotypeValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "callSets"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of sibling germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Siblings share at least one parent with the given germplasm. \n
If the parameter 'includeSiblings' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "siblings"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated scale"@en; + rdfs:domain ; + rdfs:label "scale"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "ContentMixture"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a location, associated with this study"@en; + rdfs:domain ; + rdfs:label "location"@en; + rdfs:range . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The end of a continuous or regularly repetitive event\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; + rdfs:domain ; + rdfs:label "endDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "CrossParent"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for a `Plate`"@en; + rdfs:domain ; + rdfs:label "plateName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the unique identifier for a crossing project"@en; + rdfs:domain ; + rdfs:label "crossingProject"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the Observation Unit of the cross parent"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a trial"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a List Owner. (usually a user or person)"@en; + rdfs:domain ; + rdfs:label "listOwnerPerson"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "2 letter ISO 639-1 code for the language of submission of the variable."@en; + rdfs:domain ; + rdfs:label "language"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \\n\\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \\n\\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \\nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \\nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\\nIn this way, A could be a male parent to B, but a female parent to C. "@en; + rdfs:label "ParentType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The current balance of the amount of material in a SeedLot. Could be a count (seeds, bulbs, etc) or a weight (kg of seed)."@en; + rdfs:domain ; + rdfs:label "amount"@en; + rdfs:range xsd:double . + + + rdf:type owl:Class; + rdfs:label "Attribute"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the second parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent2"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The structure of the data within a file. For example - VCF, table, image archive, multispectral image archives in EDAM ontology (used in Galaxy)\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; + rdfs:domain ; + rdfs:label "dataFormat"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The list of Observation Variables being used in this study. \n\nThis list is intended to be the wishlist of variables to collect in this study. It may or may not match the set of variables used in the collected observation records. "@en; + rdfs:domain ; + rdfs:label "observationVariables"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Other variable names"@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of contact entities associated with this trial"@en; + rdfs:domain ; + rdfs:label "contacts"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "For numerical, number of decimal places to be reported"@en; + rdfs:domain ; + rdfs:label "decimalPlaces"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\""@en; + rdfs:domain ; + rdfs:label "fieldName"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-22) Description of the experimental design - Short description of the experimental design, possibly including statistical design. In specific cases, e.g. legacy datasets or data computed from several studies, the experimental design can be \"unknown\"/\"NA\", \"aggregated/reduced data\", or simply 'none'."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A shortened version of the human readable name for a Program"@en; + rdfs:domain ; + rdfs:label "abbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the precision and landmarks of the coordinate values used for a Location. (ex. the site, the nearest town, a 10 kilometers radius circle, +/- 20 meters, etc)"@en; + rdfs:domain ; + rdfs:label "coordinateDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The percentage of the given germplasm in the seed lot mixture."@en; + rdfs:domain ; + rdfs:label "mixturePercentage"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A name for this level \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a trial\n\nMIAPPE V1.1 (DM-2) Investigation unique ID - Identifier comprising the unique name of the institution/database hosting the submission of the investigation data, and the accession number of the investigation in that institution."@en; + rdfs:domain ; + rdfs:label "trialDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID of the dataset this variant set belongs to."@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "DataMatrix"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The value of the data collected as an observation"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "plannedCrosses"@en; + rdfs:domain ; + rdfs:label "plannedCrosses"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Other variable names"@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name of a List Owner. (usually a user or person)"@en; + rdfs:domain ; + rdfs:label "listOwnerName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "General category for the attribute. very similar to Trait class."@en; + rdfs:domain ; + rdfs:label "attributeCategory"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "attributeValues"@en; + rdfs:domain ; + rdfs:label "attributeValues"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies an observation unit\n\nMIAPPE V1.1 (DM-70) Observation unit ID - Identifier used to identify the observation unit in data files containing the values observed or measured on that unit. Must be locally unique. "@en; + rdfs:domain ; + rdfs:label "observationUnitDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Germplasm associated with a reference"@en; + rdfs:domain ; + rdfs:label "referenceSet"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "variants"@en; + rdfs:domain ; + rdfs:label "variants"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "List of seasons over which this study was performed."@en; + rdfs:domain ; + rdfs:label "seasons"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Trial"@en . + + + rdf:type owl:Class; + rdfs:label "Image"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Crop name (examples: \"Maize\", \"Wheat\")"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of CallSets included in this VariantSet"@en; + rdfs:domain ; + rdfs:label "callSetCount"@en; + rdfs:range xsd:integer . + + + rdf:type owl:Class; + rdfs:label "Contact"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A description of the way an Observation should be collected. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Method \"estimation\" or \"drone image processing\". "@en; + rdfs:domain ; + rdfs:label "method"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of Variants included in this VariantSet"@en; + rdfs:domain ; + rdfs:label "variantCount"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the first parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent1"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The actual value for a category"@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "SeedLot"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "dataFormat defines the structure of the data within a file (ie DartSeq, VCF, Hapmap, tabular, etc)"@en; + rdfs:domain ; + rdfs:label "dataFormat"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The year the parents were originally crossed"@en; + rdfs:domain ; + rdfs:label "crossingYear"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this attribute value within the given database server"@en; + rdfs:domain ; + rdfs:label "attributeValueDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1 (DM-9) Associated publication - An identifier for a literature publication where the investigation is described. Use of DOIs is recommended."@en; + rdfs:domain ; + rdfs:label "publications"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "URI pointing to an ontology class for the unit"@en; + rdfs:domain ; + rdfs:label "unitPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The MIME type of the file (ie text/csv, application/excel, application/zip).\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; + rdfs:domain ; + rdfs:label "fileFormat"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitLevel"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; + rdfs:domain ; + rdfs:label "attribute"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the unique identifier for a planned cross"@en; + rdfs:domain ; + rdfs:label "plannedCross"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Additional comments about a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "comments"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-25) Observation unit description - General description of the observation units in the study."@en; + rdfs:domain ; + rdfs:label "observationUnitsDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this `GenomeMap` was published"@en; + rdfs:domain ; + rdfs:label "publishedDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a program"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of linkage groups present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "linkageGroupCount"@en; + rdfs:range xsd:integer . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Numerical or categorical value\n\nMIAPPE V1.1 (DM-59) Environment parameter value - Value of the environment parameter (defined above) constant within the experiment."@en; + rdfs:domain ; + rdfs:label "value"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "childLocations"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en; + rdfs:label "TraitDataType"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An ontology term describing an attribute."@en; + rdfs:domain ; + rdfs:label "species"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A unique identifier physically attached to a `Plate`"@en; + rdfs:domain ; + rdfs:label "plateBarcode"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a List"@en; + rdfs:domain ; + rdfs:label "listDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). `levelCode` is an ID code for this level tag. Identify \nthis observation unit by each level of the hierarchy where it exists. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** "@en; + rdfs:label "ObservationUnitLevelRelationship"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Full scientific binomial format name. This includes Genus, Species, and Sub-species"@en; + rdfs:domain ; + rdfs:label "scientificName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Variant` within the given database server\n
A `Variant` can also represent a Marker "@en; + rdfs:domain ; + rdfs:label "variant"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A single position"@en; + rdfs:domain ; + rdfs:label "coordinates"@en; + rdfs:range xsd:double . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this study started\n\nMIAPPE V1.1 (DM-14) Start date of study - Date and, if relevant, time when the experiment started"@en; + rdfs:domain ; + rdfs:label "startDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The literal string \"Polygon\""@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "AvailableFormat"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The accession number assigned by the donor\n\nMCPD (v2.1) (DONORNUMB) 23. Identifier assigned to an accession by the donor. Follows ACCENUMB standard."@en; + rdfs:domain ; + rdfs:label "donorAccessionNumber"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of this contact person\n\nMIAPPE V1.1 (DM-31) Person name - The name of the person (either full name or as used in scientific publications)"@en; + rdfs:domain ; + rdfs:label "name"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-28) Cultural practices - General description of the cultural practices of the study."@en; + rdfs:domain ; + rdfs:label "culturalPractices"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "plates"@en; + rdfs:domain ; + rdfs:label "plates"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated event"@en; + rdfs:domain ; + rdfs:label "event"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "Trait"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A flag to indicate if a Trial is currently active and ongoing"@en; + rdfs:domain ; + rdfs:label "active"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a separator for unphased allele calls."@en; + rdfs:domain ; + rdfs:label "sepUnphased"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "fieldAbbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "ReferenceSet"@en . + + + rdf:type owl:Class; + rdfs:label "Event"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the field represented in this Genotype Field. Examples include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "fieldName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A permanent unique identifier associated with this study data. For example, a URI or DOI"@en; + rdfs:domain ; + rdfs:label "studyPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a `Variant`"@en; + rdfs:domain ; + rdfs:label "variantDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A flag to indicate if a Study is currently active and ongoing"@en; + rdfs:domain ; + rdfs:label "active"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The cross for the germplasm using in this content mixture"@en; + rdfs:domain ; + rdfs:label "cross"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A detailed, human-readable description of this event\n
MIAPPE V1.1 (DM-67) Event description - Description of the event, including details such as amount applied and possibly duration of the event. "@en; + rdfs:domain ; + rdfs:label "eventDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of all the potential parents in the crossing block, available in the crossing project\n
If the parameter 'includePotentialParents' is false, the array 'potentialParents' should be empty, null, or excluded from the response object."@en; + rdfs:domain ; + rdfs:label "potentialParents"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Scale"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "events"@en; + rdfs:domain ; + rdfs:label "events"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The crossing project used to generate this germplasm"@en; + rdfs:domain ; + rdfs:label "crossingProject"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "fileFormat defines the MIME type of the file (ie text/csv, application/excel, application/zip). This should also be reflected in the Accept and ContentType HTTP headers for every relevant request and response."@en; + rdfs:domain ; + rdfs:label "fileFormat"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "`levelOrder` defines where that level exists in the hierarchy of levels. `levelOrder`'s lower numbers \nare at the top of the hierarchy (ie field -> 1) and higher numbers are at the bottom of the hierarchy (ie plant -> 9). \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "levelOrder"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name which identifies a germplasm within the given database server"@en; + rdfs:domain ; + rdfs:label "callSetName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "images"@en; + rdfs:domain ; + rdfs:label "images"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unique identifier for this analysis description"@en; + rdfs:domain ; + rdfs:label "analysisDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Uncertainty associated with the coordinates in meters. Leave the value empty if the uncertainty is unknown."@en; + rdfs:domain ; + rdfs:label "coordinateUncertainty"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The units used to describe the data in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "unit"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The date and time when this study was last modified"@en; + rdfs:domain ; + rdfs:label "lastUpdate"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Method class (examples: \"Measurement\", \"Counting\", \"Estimation\", \"Computation\", etc.)"@en; + rdfs:domain ; + rdfs:label "methodClass"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An object describing when a particular Event has taken place. An Event can occur at one or more discrete time points (`discreteDates`) or an event can happen continuously over a longer period of time (`startDate`, `endDate`)"@en; + rdfs:domain ; + rdfs:label "eventDateRange"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The full name of an event parameter\n
ICASA \"Variable_Name\""@en; + rdfs:domain ; + rdfs:label "name"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of observation Ids this image is associated with, if applicable."@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the second parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent2"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The number of markers present in a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "markerCount"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A short human readable code for a study"@en; + rdfs:domain ; + rdfs:label "studyCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the unique identifier for a planned cross"@en; + rdfs:domain ; + rdfs:label "plannedCrossDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Synonym"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the level of protection/exposure for things like sun light and wind at a particular Location"@en; + rdfs:domain ; + rdfs:label "exposure"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "ExperimentalDesign"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Formats associated with a variant set"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Germplasm associated with a reference"@en; + rdfs:domain ; + rdfs:label "reference"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "GrowthFacility"@en . + + + rdf:type owl:Class; + rdfs:label "OntologyTerm"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The additional metadata value associated with this genotype call"@en; + rdfs:domain ; + rdfs:label "fieldValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Set of Analysis descriptors for this VariantSet"@en; + rdfs:domain ; + rdfs:label "analysis"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Location\n
The Parent Location defines the encompassing Location that a smaller Location belongs to. \nFor example, an Institution might have multiple Field Stations inside it and each Field Station might have multiple Fields."@en; + rdfs:domain ; + rdfs:label "parentLocation"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this variant was last updated."@en; + rdfs:domain ; + rdfs:label "updated"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of a trait\n
MIAPPE V1.1 (DM-86) Trait - Name of the (plant or environmental) trait under observation"@en; + rdfs:domain ; + rdfs:label "traitName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the unique identifier for a cross"@en; + rdfs:domain ; + rdfs:label "cross"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "variantSets"@en; + rdfs:domain ; + rdfs:label "variantSets"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Internal database identifier"@en; + rdfs:domain ; + rdfs:label "eventDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this record was last updated, in ISO 8601 format."@en; + rdfs:domain ; + rdfs:label "updated"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "alleleMatrices"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date and time the image was taken"@en; + rdfs:domain ; + rdfs:label "imageTimeStamp"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Growth facility associated with a study"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier of the program leader"@en; + rdfs:domain ; + rdfs:label "leadPerson"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A text label for a category"@en; + rdfs:domain ; + rdfs:label "label"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A permanent unique identifier for the `Sample` (DOI, URL, UUID, etc)\n
MIAPPE V1.1 (DM-81) External ID - An identifier for the sample in a persistent repository, comprising the name of the repository and the accession number of the observation unit therein. Submission to the EBI Biosamples repository is recommended. URI are recommended when possible. "@en; + rdfs:domain ; + rdfs:label "samplePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:domain ; + rdfs:label "season"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The position of a marker or variant within a `LinkageGroup`"@en; + rdfs:domain ; + rdfs:label "position"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The identifier for the Seed Lot being transferred into"@en; + rdfs:domain ; + rdfs:label "toSeedLot"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of person this contact represents (ex: Coordinator, Scientist, PI, etc.)\n\nMIAPPE V1.1 (DM-34) Person role - Type of contribution of the person to the investigation"@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "The type of program entity this object represents\n
'STANDARD' represents a standard, permanent breeding program\n
'PROJECT' represents a short term project, usually with a set time limit based on funding "@en; + rdfs:label "ProgramType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of institution submitting the variable"@en; + rdfs:domain ; + rdfs:label "institution"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of objects describing additional event parameters. Each of the following accepts a human-readable value or URI"@en; + rdfs:domain ; + rdfs:label "eventParameters"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The 2 digit code representing the type of storage this germplasm is kept in at a genebank. \n\nMCPD (v2.1) (STORAGE) 26. If germplasm is maintained under different types of storage, multiple choices are allowed, separated by a semicolon (e.g. 20;30). (Refer to FAO/IPGRI Genebank Standards 1994 for details on storage type.) \n\n10) Seed collection \n11) Short term \n12) Medium term \n13) Long term \n20) Field collection \n30) In vitro collection \n40) Cryo-preserved collection \n50) DNA collection \n99) Other (elaborate in REMARKS field)"@en; + rdfs:domain ; + rdfs:label "code"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "the first parent used in the cross"@en; + rdfs:domain ; + rdfs:label "parent1"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL to the human readable documentation of an object"@en; + rdfs:domain ; + rdfs:label "documentationURL"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a VariantSet"@en; + rdfs:domain ; + rdfs:label "variantSetDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The experimental and statistical design full description plus a category PUI taken from crop research ontology or agronomy ontology"@en; + rdfs:domain ; + rdfs:label "experimentalDesign"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Maximum value for numerical, date, and time scales. Typically used for data capture control and QC."@en; + rdfs:domain ; + rdfs:label "maximumValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "images"@en; + rdfs:domain ; + rdfs:label "images"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:Class; + rdfs:label "EventDateRange"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies an observation"@en; + rdfs:domain ; + rdfs:label "observationDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "CrossingProject"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of possible values with optional labels"@en; + rdfs:domain ; + rdfs:label "categories"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "ExternalReference"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The time at which this call set was last updated"@en; + rdfs:domain ; + rdfs:label "updated"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "License and citation information for the data in this trial"@en; + rdfs:domain ; + rdfs:label "datasetAuthorships"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Subtaxon can be used to store any additional taxonomic identifier.\n\nMCPD (v2.1) (SUBTAXA) 8. Subtaxon can be used to store any additional taxonomic identifier. The following abbreviations are allowed: \"subsp.\" (for subspecies); \"convar.\" (for convariety); \"var.\" (for variety); \"f.\" (for form); \"Group\" (for \"cultivar group\").\n\nMIAPPE V1.1 (DM-44) Infraspecific name - Name of any subtaxa level, including variety, crossing name, etc. It can be used to store any additional taxonomic identifier. Either free text description or key-value pair list format (the key is the name of the rank and the value is the value of the rank). Ranks can be among the following terms: subspecies, cultivar, variety, subvariety, convariety, group, subgroup, hybrid, line, form, subform. For MCPD compliance, the following abbreviations are allowed: subsp. (subspecies); convar. (convariety); var. (variety); f. (form); Group (cultivar group)."@en; + rdfs:domain ; + rdfs:label "subtaxa"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a material or germplasm within a genebank\n\nMCPD (v2.1) (ACCENUMB) 2. This is the unique identifier for accessions within a genebank, and is assigned when a sample is entered into the genebank collection (e.g. \"PI 113869\")."@en; + rdfs:domain ; + rdfs:label "accessionNumber"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server\n\nMIAPPE V1.1 (DM-11) Study unique ID - Unique identifier comprising the name or identifier for the institution/database hosting the submission of the study data, and the identifier of the study in that institution."@en; + rdfs:domain ; + rdfs:label "studyDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this attribute within the given database server"@en; + rdfs:domain ; + rdfs:label "attributeDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology name"@en; + rdfs:domain ; + rdfs:label "ontologyName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "location"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The type of map this represents, usually \"Genetic\" or \"Physical\""@en; + rdfs:domain ; + rdfs:label "type"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "Enum for plate formats, usually \"PLATE_96\" for a 96 well plate or \"TUBES\" for plateless format"@en; + rdfs:label "PlateFormat"@en . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of alternative names or IDs used to reference this germplasm\n\nMCPD (v2.1) (OTHERNUMB) 24. Any other identifiers known to exist in other collections for this accession. Use the following format: INSTCODE:ACCENUMB;INSTCODE:identifier;INSTCODE and identifier are separated by a colon without space. Pairs of INSTCODE and identifier are separated by a semicolon without space. When the institute is not known, the identifier should be preceded by a colon."@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a `Sample`\n
MIAPPE V1.1 (DM-76) Sample ID - Unique identifier for the sample."@en; + rdfs:domain ; + rdfs:label "sampleDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology term - the label of the ontology term the termId is pointing to."@en; + rdfs:domain ; + rdfs:label "term"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The DOI or other permanent unique identifier for this published dataset"@en; + rdfs:domain ; + rdfs:label "datasetPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Growth stage at which measurement is made (examples: \"flowering\")"@en; + rdfs:domain ; + rdfs:label "growthStage"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies an `ObservationUnit`"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "VariantSet"@en . + + + rdf:type owl:Class; + rdfs:label "Cross"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the entity was last updated"@en; + rdfs:domain ; + rdfs:label "dateModified"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The authority organization responsible for tracking and maintaining the subtaxon information\n\nMCPD (v2.1) (SUBTAUTHOR) 9. Provide the subtaxon authority at the most detailed taxonomic level."@en; + rdfs:domain ; + rdfs:label "subtaxaAuthority"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The version number for this data \n\nMIAPPE V1.1 (DM-39) Data file version - The version of the dataset (the actual data)."@en; + rdfs:domain ; + rdfs:label "version"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "CrossAttribute"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The human readable name of a `Reference` within a `ReferenceSet`."@en; + rdfs:domain ; + rdfs:label "referenceName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The `sourceDivergence` is the fraction of non-indel bases that do not match the `Reference` this message was derived from."@en; + rdfs:domain ; + rdfs:label "sourceDivergence"@en; + rdfs:range xsd:double . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The height of the image in Pixels."@en; + rdfs:domain ; + rdfs:label "imageHeight"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The units or data type of the 'value'. \n
If the 'value' comes from a standardized vocabulary or an encoded list of values, then 'unit' should be 'code'. \n
If the 'value' IS NOT a number, then 'unit' should specify a data type eg. 'text', 'boolean', 'date', etc. \n
If the value IS a number, then 'unit' should specify the units used eg. 'ml', 'cm', etc\n
ICASA \"Unit_or_type\""@en; + rdfs:domain ; + rdfs:label "units"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The treatment/factor description. ex. 'low fertilizer', 'yellow rust inoculation', 'high water', etc\n\nMIAPPE V1.1 (DM-62) Experimental Factor description - Free text description of the experimental factor. This includes all relevant treatments planned and protocol planned for all the plants targeted by a given experimental factor. "@en; + rdfs:domain ; + rdfs:label "modality"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A permanent identifier for a trial. Could be DOI or other URI formatted identifier."@en; + rdfs:domain ; + rdfs:label "trialPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The general description of this data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Method, usually in the form of a URI"@en; + rdfs:domain ; + rdfs:label "methodPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A description of the things being counted in a SeedLot (seeds, bulbs, kg, tree, etc)"@en; + rdfs:domain ; + rdfs:label "units"@en; + rdfs:range xsd:string . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The study in which the event occurred"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of the season. ex. 'Spring', 'Q2', 'Season A', etc."@en; + rdfs:domain ; + rdfs:label "seasonName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "pedigreeNodes"@en; + rdfs:domain ; + rdfs:label "pedigreeNodes"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Ontology term identifier - the CURIE for an ontology term. It differs from the standard GA4GH schema's :ref:`id ` in that it is a CURIE pointing to an information resource outside of the scope of the schema or its resource implementation."@en; + rdfs:domain ; + rdfs:label "termURI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable description of Ontology"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; + rdfs:domain ; + rdfs:label "levelCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Open Researcher and Contributor ID for this contact person (orcid.org)\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; + rdfs:domain ; + rdfs:label "orcid"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Method unique identifier"@en; + rdfs:domain ; + rdfs:label "methodDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observationUnits"@en; + rdfs:domain ; + rdfs:label "observationUnits"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Dataset authorships associated with a trial"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A specific panel/collection/population name this germplasm belongs to."@en; + rdfs:domain ; + rdfs:label "collection"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An identifier for this event type, in the form of an ontology class reference\n
ICASA Management events allow for the following types: planting, fertilizer, irrigation, tillage, organic_material, harvest, bed_prep, inorg_mulch, inorg_mul_rem, chemicals, mowing, observation, weeding, puddling, flood_level, other\n
MIAPPE V1.1 (DM-66) Event accession number - Accession number of the event type in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "eventTypeDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "geoCoordinates"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for this Seed Lot"@en; + rdfs:domain ; + rdfs:label "seedLotName"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:comment "The exact level and level code of an observation unit. \n\nFor more information on Observation Levels, please review the Observation Levels documentation. \n\nMIAPPE V1.1 DM-71 Observation unit type \"Type of observation unit in textual form, usually one of the following: study, block, sub-block, plot, sub-plot, pot, plant. Use of other observation unit types is possible but not recommended. \nThe observation unit type can not be used to indicate sub-plant levels. However, observations can still be made on the sub-plant level, as long as the details are indicated in the associated observed variable (see observed variables). \nAlternatively, it is possible to use samples for more detailed tracing of sub-plant units, attaching the observations to them instead.\" "@en; + rdfs:label "ObservationUnitHierarchyLevel"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "For computational methods i.e., when the method consists in assessing the trait by computing measurements, write the generic formula used for the calculation"@en; + rdfs:domain ; + rdfs:label "formula"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "MIAPPE V1.1\n\n(DM-85) Variable accession number - Accession number of the variable in the Crop Ontology\n\n(DM-87) Trait accession number - Accession number of the trait in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-89) Method accession number - Accession number of the method in a suitable controlled vocabulary (Crop Ontology, Trait Ontology).\n\n(DM-93) Scale accession number - Accession number of the scale in a suitable controlled vocabulary (Crop Ontology)."@en; + rdfs:domain ; + rdfs:label "ontologyReference"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Germplasm`"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop \n\nMCPD (v2.1) (CROPNAME) 10. Common name of the crop. Example: \"malting barley\", \"mas\"."@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unique identifier of the scale. If left blank, the upload system will automatically generate a scale ID."@en; + rdfs:domain ; + rdfs:label "scaleDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + rdfs:domain ; + rdfs:label "contextOfUse"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a `Program` within the given database server"@en; + rdfs:domain ; + rdfs:label "program"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "One geometry as defined by GeoJSON (RFC 7946). All coordinates are decimal values on the WGS84 geographic coordinate reference system.\n\nCopied from RFC 7946 Section 3.1.1\n\nA position is an array of numbers. There MUST be two or more elements. The first two elements are longitude and latitude, or\neasting and northing, precisely in that order and using decimal numbers. Altitude or elevation MAY be included as an optional third element."@en; + rdfs:domain ; + rdfs:label "geoCoordinates"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the institution which this contact is part of\n\nMIAPPE V1.1 (DM-35) Person affiliation - The institution the person belongs to"@en; + rdfs:domain ; + rdfs:label "instituteName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Describes the general type of environment of a Location. (ex. forest, field, nursery, etc)"@en; + rdfs:domain ; + rdfs:label "environmentType"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "associated germplasm"@en; + rdfs:domain ; + rdfs:label "germplasm"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-26) Description of growth facility - Short description of the facility in which the study was carried out."@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "DataLink"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Trait Entity, usually in the form of a URI\n
A Trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the Entity is the part of the plant that the trait refers to e.g., for \"grain colour\", entity = \"grain\" "@en; + rdfs:domain ; + rdfs:label "entityPUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a VariantSet"@en; + rdfs:domain ; + rdfs:label "variantSet"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Observation levels indicate the granularity level at which the measurements are taken. `levelName` \ndefines the level, `levelOrder` defines where that level exists in the hierarchy of levels. \n`levelOrder`s lower numbers are at the top of the hierarchy (ie field > 0) and higher numbers are \nat the bottom of the hierarchy (ie plant > 6). \n\n**Standard Level Names: study, field, entry, rep, block, sub-block, plot, sub-plot, plant, pot, sample** \n\nFor more information on Observation Levels, please review the Observation Levels documentation. "@en; + rdfs:domain ; + rdfs:label "observationLevels"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The width of the image in Pixels."@en; + rdfs:domain ; + rdfs:label "imageWidth"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "This field can be used to describe the units used for this scale. This should be the abbreviated \nform of the units, intended to be displayed with every value using this scale. Usually this only \napplies when `dataType` is Numeric, but could also be included for other dataTypes when applicable."@en; + rdfs:domain ; + rdfs:label "units"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unique ID for a person"@en; + rdfs:domain ; + rdfs:label "personDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Unit of the value for this parameter"@en; + rdfs:domain ; + rdfs:label "unit"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "Variant"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the unique identifier for this breeding method"@en; + rdfs:domain ; + rdfs:label "breedingMethodDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of storage this germplasm is kept in at a genebank."@en; + rdfs:domain ; + rdfs:label "storageTypes"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The description of the source where this material was originally collected (wild, nursery, etc)"@en; + rdfs:domain ; + rdfs:label "sourceCollection"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:domain ; + rdfs:label "URL"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of the germplasm. It can be the preferred name and does not have to be unique.\n\nMCPD (v2.1) (ACCENAME) 11. Either a registered or other designation given to the material received, other than the donors accession number (23) or collecting number (3). First letter uppercase. Multiple names are separated by a semicolon without space."@en; + rdfs:domain ; + rdfs:label "germplasmName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of field represented in this data matrix. This is intended to help parse the data out of JSON."@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A list of parent germplasm references in the pedigree tree for this germplasm. These represent edges in the tree, connecting to other nodes.\n
Typically, this array should only have one parent (clonal or self) or two parents (cross). In some special cases, there may be more parents, usually when the exact parent is not known. \n
If the parameter 'includeParents' is set to false, then this array should be empty, null, or not present in the response."@en; + rdfs:domain ; + rdfs:label "parents"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Indication of how trait is routinely used. (examples: [\"Trial evaluation\", \"Nursery evaluation\"])"@en; + rdfs:domain ; + rdfs:label "contextOfUse"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for this attribute"@en; + rdfs:domain ; + rdfs:label "attributeName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The parent germplasm"@en; + rdfs:domain ; + rdfs:label "parentGermplasm"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "An ID code or number to represent a real thing that may or may not be an an observation unit.\n
For example, if the 'levelName' is 'plot', then the 'levelCode' would be the plot number or plot barcode. If this plot is also considered an ObservationUnit, then the appropriate observationUnitDbId should also be recorded.\n
If the 'levelName' is 'field', then the 'levelCode' might be something like '3' or 'F3' to indicate the third field at a research station. "@en; + rdfs:domain ; + rdfs:label "levelCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description of any process or treatment applied uniformly to the germplasm, prior to the study itself. Can be provided as free text or as an accession number from a suitable controlled vocabulary."@en; + rdfs:domain ; + rdfs:label "germplasmPreprocessing"@en; + rdfs:range xsd:string . + + + rdf:type owl:Class; + rdfs:label "EventParameter"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "In the case of structural variants, start and end of the variant may not\nbe known with an exact base position. \"cipos\" provides an interval with\nhigh confidence for the start position. The interval is provided by 0 or\n2 signed integers which are added to the start position.\nBased on the use in VCF v4.2"@en; + rdfs:domain ; + rdfs:label "cipos"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies this contact\n\nMIAPPE V1.1 (DM-33) Person ID - An identifier for the data submitter. If that submitter is an individual, ORCID identifiers are recommended."@en; + rdfs:domain ; + rdfs:label "contactDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable name (usually a short name)\n\nMIAPPE V1.1 (DM-84) Variable name - Name of the variable."@en; + rdfs:domain ; + rdfs:label "observationVariableName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The software run to generate this analysis."@en; + rdfs:domain ; + rdfs:label "software"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "StorageType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A list of dates when the event occurred\n
MIAPPE V1.1 (DM-68) Event date - Date and time of the event."@en; + rdfs:domain ; + rdfs:label "discreteDates"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Last update associated with a study"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Permanent Unique Identifier of a Trait Attribute, usually in the form of a URI\n
A trait can be decomposed as \"Trait\" = \"Entity\" + \"Attribute\", the attribute is the observed feature (or characteristic) of the entity e.g., for \"grain colour\", attribute = \"colour\""@en; + rdfs:domain ; + rdfs:label "attributePUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Bibliographical reference describing the method.\n
MIAPPE V1.1 (DM-91) Reference associated to the method - URI/DOI of reference describing the method."@en; + rdfs:domain ; + rdfs:label "bibliographicalReference"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "programs"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The total number of pages of elements available on the server. This should be calculated with the following formula. \n
totalPages = CEILING( totalCount / requested_page_size)"@en; + rdfs:domain ; + rdfs:label "totalPages"@en; + rdfs:range xsd:integer . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:comment "The type of positional coordinate used. Must be one of the following values \n\nLONGITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nLATITUDE - ISO 6709 standard, WGS84 geodetic datum. See 'Location Coordinate Encoding' for details \n\nPLANTED_ROW - The physical planted row number \n\nPLANTED_INDIVIDUAL - The physical counted number, could be independent or within a planted row \n\nGRID_ROW - The row index number of a square grid overlay \n\nGRID_COL - The column index number of a square grid overlay \n\nMEASURED_ROW - The distance in meters from a defined 0-th row \n\nMEASURED_COL - The distance in meters from a defined 0-th column "@en; + rdfs:label "PositionCoordinateXType"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Description of a List"@en; + rdfs:domain ; + rdfs:label "listDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Other variable names"@en; + rdfs:domain ; + rdfs:label "synonyms"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable name for a Location\n
MIAPPE V1.1 (DM-18) Experimental site name - The name of the natural site, experimental field, greenhouse, phenotyping facility, etc. where the experiment took place."@en; + rdfs:domain ; + rdfs:label "locationName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:domain ; + rdfs:label "trait"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A URL which indicates the location of the file version of this VariantSet. Could be a static file URL or an API endpoint which generates the file."@en; + rdfs:domain ; + rdfs:label "fileURL"@en; + rdfs:range xsd:string . + + + rdf:type , owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The string used as a representation for missing data."@en; + rdfs:domain ; + rdfs:label "unknownString"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Common name for the crop associated with this trial"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "samples"@en; + rdfs:domain ; + rdfs:label "samples"@en; + rdfs:range . + + + rdf:type owl:Class; + rdfs:label "MarkerPosition"@en . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The unique identifier for a `GenomeMap`"@en; + rdfs:domain ; + rdfs:label "mapDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable default value. (examples: \"red\", \"2.3\", etc.)"@en; + rdfs:domain ; + rdfs:label "defaultValue"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date this trial started"@en; + rdfs:domain ; + rdfs:label "startDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A human readable description of this attribute"@en; + rdfs:domain ; + rdfs:label "attributeDescription"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Human readable name used for display purposes"@en; + rdfs:domain ; + rdfs:label "defaultDisplayName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The ID which uniquely identifies a study within the given database server"@en; + rdfs:domain ; + rdfs:label "study"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The timestamp when this variant was created."@en; + rdfs:domain ; + rdfs:label "created"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The size of the image in Bytes."@en; + rdfs:domain ; + rdfs:label "imageFileSize"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The length of this `Reference` sequence."@en; + rdfs:domain ; + rdfs:label "length"@en; + rdfs:range xsd:integer . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The ID which uniquely identifies a `Plate`"@en; + rdfs:domain ; + rdfs:label "plateDbId"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "

Class of the scale, entries can be

\n

\"Code\" - This scale class is exceptionally used to express complex traits. Code is a nominal scale that combines the expressions of the different traits composing the complex trait. For example a severity trait might be expressed by a 2 digit and 2 character code. The first 2 digits are the percentage of the plant covered by a fungus and the 2 characters refer to the delay in development, e.g. \"75VD\" means \"75 %\" of the plant is infected and the plant is very delayed.

\n

\"Date\" - The date class is for events expressed in a time format, See ISO 8601

\n

\"Duration\" - The Duration class is for time elapsed between two events expressed in a time format, e.g. days, hours, months

\n

\"Nominal\" - Categorical scale that can take one of a limited and fixed number of categories. There is no intrinsic ordering to the categories

\n

\"Numerical\" - Numerical scales express the trait with real numbers. The numerical scale defines the unit e.g. centimeter, ton per hectare, branches

\n

\"Ordinal\" - Ordinal scales are scales composed of ordered categories

\n

\"Text\" - A free text is used to express the trait.

"@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Name of scientist submitting the variable."@en; + rdfs:domain ; + rdfs:label "scientist"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Timestamp when the entity was first created"@en; + rdfs:domain ; + rdfs:label "dateCreated"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the image file. Might be the same as 'imageName', but could be different."@en; + rdfs:domain ; + rdfs:label "imageFileName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of contact entities associated with this study"@en; + rdfs:domain ; + rdfs:label "contacts"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "3-letter ISO 3166-1 code of the country in which the sample was originally collected \n\nMCPD (v2.1) (ORIGCTY) 13. 3-letter ISO 3166-1 code of the country in which the sample was originally collected (e.g. landrace, crop wild relative, farmers variety), bred or selected (breeding lines, GMOs, segregating populations, hybrids, modern cultivars, etc.). Note- Descriptors 14 to 16 below should be completed accordingly only if it was \"collected\"."@en; + rdfs:domain ; + rdfs:label "countryOfOriginCode"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An ontology term describing an attribute."@en; + rdfs:domain ; + rdfs:label "species"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "the common name of a crop (for multi-crop systems)"@en; + rdfs:domain ; + rdfs:label "commonCropName"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the field represented in this data matrix. The key word \"Genotype\" is reserved for the allele matrix. Examples of other metadata matrices include: \"Genotype Quality\", \"Read Depth\", and \"Haplotype Quality\"\n
This maps to a FORMAT field in the VCF file standard."@en; + rdfs:domain ; + rdfs:label "dataMatrixName"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Persons middle name"@en; + rdfs:domain ; + rdfs:label "middleName"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The Biosample entity the call set data was generated from."@en; + rdfs:domain ; + rdfs:label "sample"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Geometry associated with an image"@en; + rdfs:domain ; + rdfs:label "observationUnit"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "Variable status. (examples: \"recommended\", \"obsolete\", \"legacy\", etc.)"@en; + rdfs:domain ; + rdfs:label "status"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "description of this person"@en; + rdfs:domain ; + rdfs:label "description"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "All known corresponding Germplasm"@en; + rdfs:domain ; + rdfs:label "sourceGermplasm"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The date the value of this attribute was determined for a given germplasm"@en; + rdfs:domain ; + rdfs:label "determinedDate"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The dimension of the matrix being paginated"@en; + rdfs:domain ; + rdfs:label "dimension"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of field represented in this Genotype Field. This is intended to help parse the data out of JSON."@en; + rdfs:domain ; + rdfs:label "dataType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The street address of the institute at a particular Location\n
MIAPPE V1.1 (DM-16) Contact institution - Name and address of the institution responsible for the study."@en; + rdfs:domain ; + rdfs:label "instituteAddress"@en; + rdfs:range xsd:string . + + + rdf:type owl:NamedIndividual , . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "True if filters were applied for this variant. VCF column 7 \"FILTER\" any value other than the missing value."@en; + rdfs:domain ; + rdfs:label "filtersApplied"@en; + rdfs:range xsd:boolean . + + + rdf:type owl:Class; + rdfs:label "ObservationUnit"@en . + + + rdf:type owl:Class; + rdfs:label "Program"@en . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Well identifier for this `Sample` location in the `Plate`. Usually a concatenation of Row and Column, or just a number if the `Samples` are not part of an ordered `Plate`."@en; + rdfs:domain ; + rdfs:label "well"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The abbreviated code of the field represented in this Genotype Field. These codes should match the VCF standard when possible. Examples include: \"GQ\", \"RD\", and \"HQ\""@en; + rdfs:domain ; + rdfs:label "fieldAbbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "A shortened version of the human readable name for a Trait"@en; + rdfs:domain ; + rdfs:label "mainAbbreviation"@en; + rdfs:range xsd:string . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "MIAPPE V1.1 (DM-23) Type of experimental design - Type of experimental design of the study, in the form of an accession number from the Crop Ontology."@en; + rdfs:domain ; + rdfs:label "PUI"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "observations"@en; + rdfs:domain ; + rdfs:label "observations"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A free space containing any additional information related to a particular object. A data source may provide any JSON object, unrestricted by the BrAPI specification."@en; + rdfs:domain ; + rdfs:label "additionalInfo"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The unique identifier for a Location"@en; + rdfs:domain ; + rdfs:label "location"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "A Trait describes what property is being observed. \n
For example, an ObservationVariable might be defined with a Trait of \"plant height\", a Scale of \"meters\", and a Method of \"tape measure\". This variable would be distinct from a variable with the Trait \"Leaf length\" or \"Flower height\". "@en; + rdfs:domain ; + rdfs:label "trait"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . + + + rdf:type owl:ObjectProperty; + rdfs:comment "An array of external reference ids. These are references to this piece of data in an external system. Could be a simple string or a URI."@en; + rdfs:domain ; + rdfs:label "externalReferences"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Geometry associated with an image"@en; + rdfs:domain ; + rdfs:label "observation"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Species associated with a reference"@en; + rdfs:domain ; + rdfs:label "reference"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The name of the external data link\n\nMIAPPE V1.1 (DM-38) Data file description - Description of the format of the data file. May be a standard file format name, or a description of organization of the data in a tabular file."@en; + rdfs:domain ; + rdfs:label "name"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "The type of parent used during crossing. Accepted values for this field are 'MALE', 'FEMALE', 'SELF', 'POPULATION', and 'CLONAL'. \n\nIn a pedigree record, the 'parentType' describes each parent of a particular germplasm. \n\nIn a progeny record, the 'parentType' is used to describe how this germplasm was crossed to generate a particular progeny. \nFor example, given a record for germplasm A, having a progeny B and C. The 'parentType' field for progeny B item refers \nto the 'parentType' of A toward B. The 'parentType' field for progeny C item refers to the 'parentType' of A toward C.\nIn this way, A could be a male parent to B, but a female parent to C. "@en; + rdfs:domain ; + rdfs:label "parentType"@en; + rdfs:range . + + + rdf:type owl:DatatypeProperty; + rdfs:comment "The Row identifier for this `Sample` location in the `Plate`"@en; + rdfs:domain ; + rdfs:label "row"@en; + rdfs:range xsd:string . + + + rdf:type owl:ObjectProperty; + rdfs:comment "List of treatments applied to an observation unit.\n\nMIAPPE V1.1 (DM-74) Observation Unit factor value - List of values for each factor applied to the observation unit."@en; + rdfs:domain ; + rdfs:label "treatments"@en; + rdfs:range . + + + rdf:type owl:NamedIndividual , . + + + rdf:type owl:ObjectProperty; + rdfs:comment ""@en; + rdfs:domain ; + rdfs:label "callSets"@en; + rdfs:range . + + + rdf:type owl:ObjectProperty; + rdfs:comment "Publications associated with a trial"@en; + rdfs:domain ; + rdfs:label "trial"@en; + rdfs:range . + +[ rdf:type owl:Class; + owl:oneOf ( ) +] . diff --git a/generator/gradlew b/generator/gradlew old mode 100644 new mode 100755