From cb070d1eff4af9d90abe2002c8b96ad4e6619c01 Mon Sep 17 00:00:00 2001 From: Brian Furner Date: Wed, 11 Sep 2024 16:23:48 -0500 Subject: [PATCH] including new Specimen entities derived from CRDC-H work --- src/bdchm/schema/bdchm.yaml | 1494 ++++++++++++++++++++++++++++++++++- 1 file changed, 1492 insertions(+), 2 deletions(-) diff --git a/src/bdchm/schema/bdchm.yaml b/src/bdchm/schema/bdchm.yaml index b9d4eea..287fff9 100644 --- a/src/bdchm/schema/bdchm.yaml +++ b/src/bdchm/schema/bdchm.yaml @@ -84,7 +84,6 @@ classes: - identity - associated_participant - Participant: is_a: Entity description: >- @@ -415,7 +414,1022 @@ classes: range: Visit slots: - identity - + + DimensionalObservation: + name: DimensionalObservation + description: A structured object that describes a single data item about the physical + dimensions of an entity (e.g. length width, area), as generated through a point-in-time + observation or measurement. + comments: + - At the core of an Observation is a flexible key-value pair (or a structured + collection of key-value pairs), where a 'key' field defines the type of observation + made, and the 'value' field describes the value or outcome of the observation. + The fact that the type of observation captured is defined in the data allow + Observation to convey a broad range of observation data. + is_a: Entity + attributes: + category: + name: category + description: The general category of observation described + comments: + - Use only if we don't define named subtypes of Observation for specific categories. + values_from: crdch:enum_CRDCH_DimensionalObservation_category + multivalued: false + range: string + required: false + observation_type: + name: observation_type + description: The specific type of observation made - i.e. the feature or characteristic + that was observed, measured, estimated, etc. + comments: + - This field holds the 'key' in the core key-value pair comprised of the observation_type + field and the relevant value(s) field. + values_from: crdch:enum_CRDCH_DimensionalObservation_observation_type + multivalued: false + range: string + required: true + method_type: + name: method_type + description: A type of method used in generating the Observation result. + comments: + - This may be a type of observational, measurement, experimental, or computational + method specifying how to generate data (e.g. 'manual counting', 'bright + field microscopy',). Or a Guideline or SOP specifying how to interpret data + and/or encode the result of an Observation (e.g. a Cancer Staging system + such as that defined by the AJCC, or variant interpretation guideline such + as that provided by the ACMG). + values_from: crdch:enum_CRDCH_DimensionalObservation_method_type + multivalued: true + range: string + required: false + value_quantity: + name: value_quantity + description: The result of the observation, encoded as a free-text Quantity. + multivalued: false + range: Quantity + required: true + + DimensionalObservationSet: + name: DimensionalObservationSet + description: A set of one or more discrete observations about the physical dimensions + of an object (e.g. length, width, area). + is_a: Entity + attributes: + category: + name: category + description: The general category of observation set described + comments: + - FHIR naming conventions are followed here, where 'id' is used for logical + identifiers which are unique only within a given system, and 'identifier' + for business identifiers, which are used to connect entities or share content + across systems. The complex 'Identifier' data type is used to capture + the identifier itself, along with metadata about its source. + values_from: crdch:enum_CRDCH_DimensionalObservationSet_category + multivalued: false + range: string + required: false + method_type: + name: method_type + description: A type of method used in generating each of the Observations + bundled in the set. + comments: + - This may be a type of observational, measurement, experimental, or computational + method specifying how to generate data (e.g. 'manual counting', 'bright + field microscopy'). Or a Guideline or SOP specifying how to interpret data + and/or encode the result of an Observation (e.g. a Cancer Staging system + such as that defined by the AJCC, or variant interpretation guideline such + as that provided by the ACMG). + values_from: crdch:enum_CRDCH_DimensionalObservationSet_method_type + multivalued: true + range: string + required: false + observations: + name: observations + description: A set of one or more more atomic observations that are conceptually + or logically related - e.g. two components of some compound measurement + (e.g. the systolic and diastolic components of a blood pressure measurement), + or a panel of related measurements run and interpreted together on the same + subject/specimen (e.g. a blood panel, or separate dimensional measurements + of a specimen). + multivalued: true + inlined_as_list: true + range: DimensionalObservation + required: false + + Document: + name: Document + description: A collection of information intented to be understood together as + a whole, and codified in human-readable form. + is_a: Entity + attributes: + document_type: + name: document_type + description: The high-level type of the document (e.g. 'publication', 'pathology + report') + values_from: crdch:enum_CRDCH_Document_document_type + multivalued: false + range: string + required: false + description: + name: description + description: A free text description or summary of the report. + multivalued: false + range: string + required: false + focus: + name: focus + description: The entity that the report is primarily about + multivalued: false + range: Entity + required: false + url: + name: url + description: A URL/web address where the document can be accessed. + multivalued: true + inlined_as_list: true + range: string + required: false + slots: + - identity + + Specimen: + name: Specimen + description: Any material taken as a sample from a biological entity (living or + dead), or from a physical object or the environment. Specimens are usually collected + as an example of their kind, often for use in some investigation. + is_a: Entity + attributes: + description: + name: description + description: A free text field to capture additional information or explanation + about the specimen. + multivalued: false + range: string + required: false + specimen_type: + name: specimen_type + description: The high-level type of the specimen, based on its derivation + provenance (i.e. how far removed it is from the original sample extracted + from a source). + examples: + - value: Fresh Specimen + - value: Portion + - value: Aliquot + - value: Analyte + - value: Slide + values_from: crdch:enum_CRDCH_Specimen_specimen_type + multivalued: false + range: SpecimenTypeEnum + required: false + analyte_type: + name: analyte_type + description: For specimens of type 'analyte' (or an 'aliquot' derived from + an analyte), this is the category of chemcial the analyte of interest represents + (e.g. DNA, RNA) + examples: + - value: DNA + - value: FFPE DNA + - value: GenomePlex (Rubicon) Amplified DNA + - value: Repli-G (Qiagen) DNA + - value: RNA + - value: FFPE RNA + values_from: crdch:enum_CRDCH_Specimen_analyte_type + multivalued: false + range: AnalyteTypeEnum + required: false + source_material_type: + name: source_material_type + description: The general kind of material from which the specimen was derived. + comments: + - Values captured here may describe the type of molecular mixture, cell, tissue, + organ, body fluid, embryo, excretory substance, or experimental system from + which a specimen was derived. + examples: + - value: Tissue + - value: Blood + - value: Tumor Aspirate + - value: Cell Line + - value: Expanded Next Generation Cancer Model + - value: Pleural Effusion + - value: Xenograft Tissue + multivalued: false + range: SourceMaterialTypeEnum + required: false + parent_specimen: + name: parent_specimen + description: An existing specimen from which the specimen of interest was + directly derived (i.e its immediate parent specimen). + comments: + - This property indicates only the direct parent specimen(s). Cardinality + is 0..m to account for specimens derived from pooling of multiple specimens. + multivalued: true + inlined_as_list: true + range: Specimen + required: false + source_participant: + name: source_participant + description: A specific Subject from which the specimen was directly or indirectly + derived. + multivalued: false + range: Participant + required: false + creation_activity: + name: creation_activity + description: The activity through which a specimen was created, by removing + material from an biological subject, or deriving material from an existing + specimen. + comments: + - Note that a given specimen is the result of only one and only one SpecimenCreationActivity, + but may be subject to many processing events that subsequently modify or + derive new specimens from it. + multivalued: false + range: SpecimenCreationActivity + required: false + processing_activity: + name: processing_activity + description: An activity that modifies the physical structure, composition, + or state of a specimen. + comments: + - Note that a given specimen may undergo more than one distinct processing + activity, through application of different methodologies that modify its + physical state. However, if an activity generates a new specimen (e.g. via + portioning, slicing) it is considered a SpeciemnCreationActivity. + multivalued: true + range: SpecimenProcessingActivity + required: false + storage_activity: + name: storage_activity + description: An activity that results in the storage or maintenance of a specimen + in a particular location, container, or state. + comments: + - 'The 0..m cardinality of this attribute reflects the fact that a given specimen + may undergo many separate periods of storage, in different locations and/or + under different conditions ' + multivalued: true + range: SpecimenStorageActivity + required: false + transport_activity: + name: transport_activity + description: An activity through which the specimen is transported between + locations. + comments: + - The 0..m cardinality of this attribute reflects the fact that a given specimen + may undergo many separate transport processes at different periods of time. + multivalued: true + range: SpecimenTransportActivity + required: false + contained_in: + name: contained_in + description: A physical container in which a specimen is presently held or + attached - as storage for future use, a substrate for growth (e.g. a cell + culture dish), or a vessel to enable analysis (e.g. a microscope slide or + 96-well plate) + comments: + - 'The 0..1 cardinality on this attribute means that you cannot directly references + multiple nested containers holding a sample. To capture this scenario, use + the ''parent_container'' attribute of the Container entity. ' + multivalued: false + range: SpecimenContainer + required: false + dimensional_measures: + name: dimensional_measures + description: Observations about the current physical dimensions of an object + (e.g. length, width, area). + comments: + - Observations are flexible containers for capturing a specific type of observation/measurement + data about an object, along with metadata about how it was generated. The + specific type of observation made is captured as data in the Observation + object. + multivalued: false + range: DimensionalObservationSet + required: false + quantity_measure: + name: quantity_measure + description: An observation related to the present quantity of a specimen + - e.g. its weight, volume, or analyte concentration. + comments: + - Observations are flexible containers for capturing a specific type of observation/measurement + data about an object, along with metadata about how it was generated. The + specific type of observation made is captured as data in the Observation + object. + multivalued: true + range: SpecimenQuantityObservation + required: false + quality_measure: + name: quality_measure + description: An observation about characteristics of a specimen that are indicative + of its quality or suitability for use. + comments: + - Observations are flexible containers for capturing a specific type of observation/measurement + data about an object, along with metadata about how it was generated. The + specific type of observation made is captured as data in the Observation + object. + multivalued: true + range: SpecimenQualityObservation + required: false + cellular_composition_type: + name: cellular_composition_type + description: A term describing the type of cell or cellular material comprising + a specimen. + examples: + - value: 2D Classical Conditionally Reprogrammed Cells + - value: Adherent Cell Line + - value: Bone Marrow Components + - value: Buccal Cells + - value: Buffy Coat + - value: Derived Cell Line + - value: Granulocytes + - value: Pleural Effusion + - value: Human Original Cells + - value: Liquid Suspension Cell Line + values_from: crdch:enum_CRDCH_Specimen_cellular_composition_type + multivalued: false + range: string + required: false + related_document: + name: related_document + description: A reference to an external document that is about or related + to the specimen (e.g. a publication related to the study it is a part of, + pathology report containing additional details about it, protocol describing + how it was collected) + multivalued: true + range: Document + required: false + section_location: + name: section_location + description: The location in a parent specimen from which a section/portion + was excised (e.g. top, middle, bottom) + comments: + - This attribute applies only to Specimens that are of type 'portion' or 'slide'. + examples: + - value: Top + - value: Bottom + - value: Unknown + values_from: crdch:enum_CRDCH_Specimen_section_location + multivalued: false + range: SectionLocationEnum + required: false + derived_product: + name: derived_product + description: A 'living' biologically active product that was derived from + the specimen (e.g. a cell culture, tissue culture, or organoid) + multivalued: true + inlined_as_list: true + range: BiologicProduct + required: false + slots: + - identity + + SpecimenContainer: + name: SpecimenContainer + description: A vessel in which a specimen is held or to which it is attached - + for storage or as a substrate for growth (e.g. a cell culture dish) or analysis + (e.g. a microscope slide or 96-well plate) + is_a: Entity + attributes: + container_type: + name: container_type + description: The kind of the container. + examples: + - value: Capillary blood collection tube + - value: Sputum specimen container + - value: Cell culture flask + - value: Glass slide + values_from: crdch:enum_CRDCH_SpecimenContainer_container_type + multivalued: false + range: string + required: false + container_number: + name: container_number + description: Informal number by which the container is referenced or identified + (e.g. a slide number, or a well number in a plate) + multivalued: false + range: string + required: false + additive: + name: additive + description: A material substance added to the container (typically to support + the primary contained object - e.g. culture media to support cell growth) + examples: + - value: DMEM + - value: DMEM+Serum + - value: RPMI + - value: RPMI+Serum + multivalued: true + range: Substance + required: false + parent_container: + name: parent_container + description: A larger container of which this container is a part (e.g. the + complete 96-well plate of which a single well is a part) + multivalued: false + range: SpecimenContainer + required: false + + SpecimenCreationActivity: + name: SpecimenCreationActivity + description: The process of creating a specimen. This may occur through observing + and/or collecting material from an biological source or natural setting, or + through derivation from an existing specimen (e.g. via portioning or aliquoting). + comments: + - A creation' activity represents the entire process up to the point where the + specimen is physically modified, stored, or transported. + is_a: Entity + attributes: + activity_type: + name: activity_type + description: The high-level type of creation activity. + comments: + - At present our model collapses two types of processes through which specimens + are created (initial collection from source, and derivation from an existing + specimen). The 'category' is a flag to indicate which applies to a given + instance, so that more specific recommendations about data entry in certain + fields can be specified. + examples: + - value: Collection from Source + - value: Derivation from Specimen + multivalued: false + range: SpecimenCreationActivityTypeEnum + required: false + date_started: + name: date_started + description: The date when the activity began (in this case, a specimen creation + event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + date_ended: + name: date_ended + description: The date when the activity ended (in this case, a specimen creation + event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + performed_by: + name: performed_by + description: The organization or group that performed the activity. + multivalued: false + range: Organization + required: false + collection_method_type: + name: collection_method_type + description: The type of method applied in collecting a sample from its original + source. + comments: + - This attribute applies only when the Specimen.category = 'original'. + examples: + - value: Anterior Resection of Rectum + - value: Ascites Drainage + - value: Excisional Biopsy + - value: Specimen Pooling + multivalued: false + range: SpecimenCollectionMethodType + required: false + derivation_method_type: + name: derivation_method_type + description: The type of method applied to derive a new specimen from an existing + one. + comments: + - This attribute applies only when Specimen.category = 'portion', 'aliquot', + 'analyte', or 'slide'. + examples: + - value: Vibratome + - value: Cryosectioning + - value: Tissuemolds + - value: Slidingmicrotome + - value: Sectioning + - value: Other + - value: Unknown + - value: NotReported + values_from: crdch:enum_CRDCH_SpecimenCreationActivity_derivation_method_type + multivalued: false + range: string + required: false + additive: + name: additive + description: A type of material or reagent used applied as input when creating + a specimen. + multivalued: true + range: Substance + required: false + collection_site: + name: collection_site + description: The anatomic site from which a specimen was collected. + comments: + - This attribute is used when SpecimenCreationActivity.activity_type = 'Collection + from Source'. + examples: + - value: Abdomen + - value: Abdominal Wall + - value: Acetabulum + multivalued: false + range: BodySite + required: false + quantity_collected: + name: quantity_collected + description: The quantity of material in the specimen as originally collected + from its original source material (prior to downstream portioning or processing) + comments: + - This attribute applies only when Specimen.category='initial sample'. + multivalued: false + range: Quantity + required: false + specimen_order: + name: specimen_order + description: A numeric value that represents the sequential order of this + creation activity relative to those producing other specimens from the same + source material or parent specimen. + multivalued: false + range: integer + required: false + + SpecimenQualityObservation: + name: SpecimenQualityObservation + description: A structured object that describes a characteristic of a specimen + indicative of its quality or suitability for use, as generated through a point-in-time + observation or measurement. + is_a: Entity + attributes: + observation_type: + name: observation_type + description: The specific type of observation made - i.e. the feature or characteristic + that was observed, measured, estimated, etc.. + comments: + - This field holds the 'key' in the core key-value pair comprised of the observation_type + field and the relevant value(s) field. + multivalued: false + range: SpecimenQualityObservationTypeEnum + required: true + method_type: + name: method_type + description: A type of method used in generating the Observation result. + comments: + - This may be a type of observational, measurement, experimental, or computational + method specifying how to generate data (e.g. 'manual counting', 'bright + field microscopy',). Or a Guideline or SOP specifying how to interpret data + and/or encode the result of an Observation (e.g. a Cancer Staging system + such as that defined by the AJCC, or variant interpretation guideline such + as that provided by the ACMG). + multivalued: true + range: SpecimenQualityObservationMethodEnum + required: false + focus: + name: focus + description: The entity or entities directly observed/measured in generating + an observation result. + comments: + - 'The ''focus'', ''subject'', and ''specimen'' fields are useful when data + creators want an Observation object to stand on its own, so it can point + back to the entities it is about. These fields are not needed when an Observation + is embedded in a Specimen or other entity, where focus, subject, and specimen + can be determined from context. ' + multivalued: true + range: Specimen + required: false + value_quantity: + name: value_quantity + description: The result of the observation, encoded as a free-text Quantity. + comments: + - One and only one of the value(x) fields must be populated. + multivalued: false + range: Quantity + required: true + + SpecimenQuantityObservation: + name: SpecimenQuantityObservation + description: A structured object that describes a single data item about the quantity + of an entity, as generated through a point-in-time observation or measurement. + comments: + - At the core of an Observation is a flexible key-value pair (or a structured + collection of key-value pairs), where a 'key' field defines the type of observation + made, and the 'value' field describes the value or outcome of the observation. + The fact that the type of observation captured is defined in the data allow + Observation to convey a broad range of observation data. + is_a: Entity + attributes: + observation_type: + name: observation_type + description: The specific type of observation made - i.e. the feature or characteristic + that was observed, measured, estimated, etc.. + comments: + - This field holds the 'key' in the core key-value pair comprised of the observation_type + field and the relevant value(s) field. + multivalued: false + range: SpecimenQuantityObservationTypeEnum + required: true + method_type: + name: method_type + description: A type of method used in generating the Observation result. + comments: + - This may be a type of observational, measurement, experimental, or computational + method specifying how to generate data (e.g. 'manual counting', 'bright + field microscopy',). Or a Guideline or SOP specifying how to interpret data + and/or encode the result of an Observation (e.g. a Cancer Staging system + such as that defined by the AJCC, or variant interpretation guideline such + as that provided by the ACMG). + values_from: crdch:enum_CRDCH_SpecimenQuantityObservation_method_type + multivalued: true + range: string + required: false + focus: + name: focus + description: The entity or entities directly observed/measured in generating + an observation result. + comments: + - 'The ''focus'', ''subject'', and ''specimen'' fields are useful when data + creators want an Observation object to stand on its own, so it can point + back to the entities it is about. These fields are not needed when an Observation + is embedded in a Specimen or other entity, where focus, subject, and specimen + can be determined from context. ' + multivalued: true + inlined_as_list: true + range: Specimen + required: false + value_quantity: + name: value_quantity + description: The result of the observation, encoded as a free-text Quantity. + comments: + - One and only one of the value(x) fields must be populated. + multivalued: false + range: Quantity + required: true + + SpecimenProcessingActivity: + name: SpecimenProcessingActivity + description: An activity that modifies the physical structure, composition, or + state of a specimen. Unlike SpecimenCreation, SpecimenProcessing activities + do not result in the generation of new entities - they take a single specimen + as input, and output that same specimen. + comments: + - '"Processing" as defined here alters the physical nature of a specimen, such + that storage or transport activities do not qualify as processing activities. + When instantiating this class, create a separate instances for each type/method + of processing performed (e.g. each method of fixation, freezing, labeling, etc. + that is applied).' + is_a: Entity + attributes: + activity_type: + name: activity_type + description: The high-level type of processing activity + examples: + - value: Fixation + - value: Freezing + - value: Mounting + - value: Preservation + multivalued: false + range: SpecimenProcessingActivityTypeEnum + required: false + date_started: + name: date_started + description: The date when the activity began (in this case, a specimen processing + event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + date_ended: + name: date_ended + description: The date when the activity began (in this case, a specimen processing + event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + duration: + name: duration + description: The length of time over which the activity was performed. + multivalued: true + inlined_as_list: true + range: Quantity + required: false + method_type: + name: method_type + description: A specific type of method or procedure performed to process the + specimen + examples: + - value: Snap Freezing + - value: Cryopreservation in liquid nitrogen (dead tissue) + - value: Cryopreservation in dry ice (dead tissue) + - value: Formalin fixed paraffin embedded (FFPE) + - value: Formalin fixed-unbuffered + - value: Formalin fixed-buffered + - value: OCT + values_from: crdch:enum_CRDCH_SpecimenProcessingActivity_method_type + multivalued: false + range: string + required: false + additive: + name: additive + description: A type of material or reagent used as input when processing the + specimen + examples: + - value: Formalin + multivalued: true + inlined_as_list: true + range: Substance + required: false + + SpecimenStorageActivity: + name: SpecimenStorageActivity + description: "An activity in which a specimen is stored or maintained in a particular\ + \ location, container, or state. Unlike 'processing' activities, storage does\ + \ not alter the \nintrinsic physical nature of a specimen." + comments: + - Think of the StorageActivity as being one of many possible periods when the + specimen was stored at some location and in some state or condition. We may + want to capture storage dates and conditions for each. + is_a: Entity + attributes: + date_started: + name: date_started + description: The date when the activity began (in this case, a storage event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + date_ended: + name: date_ended + description: The date when the activity ended (in this case, a storage event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + duration: + name: duration + description: The length of time over which the activity was performed. + comments: + - 'Quantity.unit MUST be a unit of time. ' + multivalued: false + range: Quantity + required: false + method_type: + name: method_type + description: A specific type of method or procedure performed to store the + specimen + examples: + - value: ambient temperature + - value: cut slide + - value: fresh + - value: frozen at -70C + - value: frozen at -150C + - value: frozen in liquid nitrogen + - value: frozen in vapor phase + - value: paraffin block + - value: RNAlater at 4C + values_from: crdch:enum_CRDCH_SpecimenStorageActivity_method_type + multivalued: false + range: string + required: false + container: + name: container + description: A container in which the specimen is held or affixed during its + storage. + multivalued: true + inlined_as_list: true + range: SpecimenContainer + required: false + + SpecimenTransportActivity: + name: SpecimenTransportActivity + description: An activity through which a specimen is transported between locations + or organizations. + comments: + - Think of the TransportActivity as being one of many possible occasions when + the specimen was moved from one location to another, in some state or condition. We + may want to capture dates and conditions for each. + is_a: Entity + attributes: + date_started: + name: date_started + description: The date when the activity began (in this case, a transport event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + date_ended: + name: date_ended + description: The date when the activity ended (in this case, a transport event). + comments: + - To allow for more precise specification of dates when an activity was performed, + we provide date_started and date_ended attributes. If source data only + provides a single date, it SHOULD be entered as both the date_started and + date_ended. + multivalued: false + range: TimePoint + required: false + duration: + name: duration + description: The length of time over which the activity was performed. + multivalued: true + inlined_as_list: true + range: string + required: false + transport_origin: + name: transport_origin + description: An organization (facility, site, lab, etc) from which the specimen + was transported as a result of the activity. + multivalued: false + range: Organization + required: false + transport_destination: + name: transport_destination + description: An organization (facility, site, lab, etc) to which the specimen + is delivered as a result of the activity. + multivalued: false + range: Organization + required: false + + BiologicProduct: + name: BiologicProduct + description: A living organism, or a metabolically active biological system such + as a cell culture, tissue culture, or organoid that is maintained or propagated + in vitro. + is_a: Entity + attributes: + description: + name: description + description: A free text field to capture additional info/explanation about + the model system + multivalued: false + range: string + required: false + product_type: + name: product_type + description: The high level type of model system (e.g. cell line, cell culture, + tissue culture, organoid) + examples: + - value: cell line + - value: cell culture + - value: tissue culture + - value: organoid + values_from: crdch:enum_CRDCH_BiologicProduct_product_type + multivalued: false + range: string + required: false + passage_number: + name: passage_number + description: When the specimen an actively growing model system, such as a + cell or tissue culture, this property captures its passage number. + multivalued: true + range: integer + required: false + growth_rate: + name: growth_rate + description: When the specimen an actively growing model system, such as a + cell or tissue culture, this property captures its rate of growth. + multivalued: true + range: string + required: false + slots: + - identity + + Substance: + name: Substance + description: A type of material substance, or instance thereof, as used in a + particular application. May include information about the role the substance + played in a particular application. + is_a: Entity + attributes: + substance_type: + name: substance_type + description: The specific type of the substance - at as granular a level as + possible. May be a specific chemical compound, or the name of a formulation/preparation + made up of many compounds. + examples: + - value: toluene + - value: formalin + - value: DMEM + values_from: crdch:enum_CRDCH_Substance_substance_type + multivalued: false + range: string + required: false + role: + name: role + description: A role played by the substance in a particular application (e.g. + the role of a lysis buffer when applied in a specimen creation activity, + or the role of fixative when applied in specimen processing) + examples: + - value: lysis buffer + - value: fixative + - value: mounting medium + - value: collection media + values_from: crdch:enum_CRDCH_Substance_role + multivalued: true + range: string + required: false + substance_quantity: + name: substance_quantity + description: The quantity of substance this instance stands for. + multivalued: false + range: Quantity + required: false + + Quantity: + name: Quantity + description: A structured object to represent an amount of something (e.g., weight, + mass, length, duration of time) - including a value and unit. + comments: + - QuantityMeasure' may be implemented as an Observation-like object that will + let us capture any type of measure of the amount of some substance (e.g. weight, + volume, maybe even concentration?), with distinct timestamps and methods associated. It + could be implemented as a "simple" observation (one measurement per instance, + where the 'code' fields is bound to a value set describing the different types + of quantity measures allowed - e.g. 'weight', 'volume', 'concentration'), or + as "composite" observation (multiple measurements possible in a single instance, + each captured as a component defined to hold a specific type of quantity measure + - e.g. 'weight', 'volume', 'concentration'). The number of different quantity + measures we anticipate needed to support, and the potential for data sparseness, + are factors that determine whether a simple or composite Observation would be + most appropriate. + is_a: Entity + attributes: + value_decimal: + name: value_decimal + description: An amount, in the given units (if specified) + multivalued: false + range: decimal + required: false + value_concept: + name: value_concept + description: A coded value representing a quantity (e.g. "Adjacent (< or = + 2cm)") + values_from: crdch:enum_CRDCH_Quantity_value_codeable_concept + multivalued: false + range: string + required: false + unit: + name: unit + description: A coded or free text (in the .text field) representation of the + unit. + values_from: crdch:enum_CRDCH_Quantity_unit + multivalued: false + range: string + required: false + + BodySite: + name: BodySite + description: A site in the body of an organism, typically described in terms of + an anatomical concept and optional qualifiers (e.g. left/right, upper/lower). + But body sites as defined here may include non-canonical sites, such as an implanted + medical device. + is_a: Entity + attributes: + site: + name: site + description: A term describing any site in the body. + examples: + - value: Adenoid + - value: Adipose + - value: Adrenal + values_from: crdch:enum_CRDCH_BodySite_site + multivalued: false + range: string + required: true + qualifier: + name: qualifier + description: A qualifier that further refines or specifies the location of + the body site - e.g. to indicate laterality, upper v. lower, containment + in some other anatomical structure (e.g. 'blood' contained in the 'hepatic + vein') + examples: + - value: left + - value: right + - value: bilateral + values_from: crdch:enum_CRDCH_BodySite_qualifier + multivalued: true + range: string + required: false + slots: id: identifier: true @@ -893,3 +1907,479 @@ enums: description: The condition is/was absent in the patient. UNKNOWN: description: The condition is/was of unknown status in the patient. + + SpecimenTypeEnum: + name: SpecimenTypeEnum + description: A high-level type of specimen, based on its derivation provenance + (i.e. how far removed it is from the original sample extracted from a source). + permissible_values: + ALIQUOT: + text: ALIQUOT + description: A specimen that results from the division of some parent specimen + into equal amounts for downstream analysis. + ANALYTE: + text: ANALYTE + description: A specimen generated through the extraction of a specified class + of substance/chemical (e.g. DNA, RNA, protein) from a parent specimen, which + is stored in solution as an analyte. + FRESH_SPECIMEN: + text: FRESH_SPECIMEN + description: A specimen representing the material that was directly collected + from a subject (i.e. not generated through portioning, aliquoting, or analyte + extraction from an existing specimen). + PORTION: + text: PORTION + description: A physical sub-part taken from an existing specimen. + SLIDE: + text: SLIDE + description: A specimen that is mounted on a slide or coverslip for microscopic + analysis. + + AnalyteTypeEnum: + name: AnalyteTypeEnum + permissible_values: + FFPE DNA: + text: FFPE DNA + description: Formalin-Fixed Paraffin-Embedded DNA + Repli-G (Qiagen) DNA: + text: Repli-G (Qiagen) DNA + description: Repli-G (Qiagen) DNA + GenomePlex (Rubicon) Amplified DNA: + text: GenomePlex (Rubicon) Amplified DNA + Total RNA: + text: Total RNA + description: Total Ribonucleic Acid + Repli-G X (Qiagen) DNA: + text: Repli-G X (Qiagen) DNA + description: Repli-G X (Qiagen) DNA + RNA: + text: RNA + description: Ribonucleic Acid + Repli-G Pooled (Qiagen) DNA: + text: Repli-G Pooled (Qiagen) DNA + description: REPLI-g Pooled DNA + DNA: + text: DNA + description: DNA + EBV Immortalized Normal: + text: EBV Immortalized Normal + description: Normal Epstein-Barr Virus Immortalization + FFPE RNA: + text: FFPE RNA + description: Formalin-Fixed Paraffin-Embedded RNA + Protein: + text: Protein + description: Protein + Nuclei RNA: + text: Nuclei RNA + cfDNA: + text: cfDNA + + SourceMaterialTypeEnum: + name: SourceMaterialTypeEnum + permissible_values: + ADDITIONAL_METASTATIC: + text: ADDITIONAL_METASTATIC + ADDITIONAL_NEW_PRIMARY: + text: ADDITIONAL_NEW_PRIMARY + BENIGN_NEOPLASMS: + text: BENIGN_NEOPLASMS + BLOOD_DERIVED_CANCER_BONE_MARROW: + text: BLOOD_DERIVED_CANCER_BONE_MARROW + BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT: + text: BLOOD_DERIVED_CANCER_BONE_MARROW_POST_TREATMENT + BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: + text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD + BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT: + text: BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD_POST_TREATMENT + BLOOD_DERIVED_LIQUID_BIOPSY: + text: BLOOD_DERIVED_LIQUID_BIOPSY + BLOOD_DERIVED_NORMAL: + text: BLOOD_DERIVED_NORMAL + BONE_MARROW_NORMAL: + text: BONE_MARROW_NORMAL + BUCCAL_CELL_NORMAL: + text: BUCCAL_CELL_NORMAL + CELL_LINE_DERIVED_XENOGRAFT_TISSUE: + text: CELL_LINE_DERIVED_XENOGRAFT_TISSUE + CELL_LINES: + text: CELL_LINES + CONTROL_ANALYTE: + text: CONTROL_ANALYTE + DNA: + text: DNA + EBV_IMMORTALIZED_NORMAL: + text: EBV_IMMORTALIZED_NORMAL + EXPANDED_NEXT_GENERATION_CANCER_MODEL: + text: EXPANDED_NEXT_GENERATION_CANCER_MODEL + FFPE_RECURRENT: + text: FFPE_RECURRENT + FFPE_SCROLLS: + text: FFPE_SCROLLS + FIBROBLASTS_FROM_BONE_MARROW_NORMAL: + text: FIBROBLASTS_FROM_BONE_MARROW_NORMAL + GRANULOCYTES: + text: GRANULOCYTES + HUMAN_TUMOR_ORIGINAL_CELLS: + text: HUMAN_TUMOR_ORIGINAL_CELLS + IN_SITU_NEOPLASMS: + text: IN_SITU_NEOPLASMS + LYMPHOID_NORMAL: + text: LYMPHOID_NORMAL + METASTATIC: + text: METASTATIC + MIXED_ADHERENT_SUSPENSION: + text: MIXED_ADHERENT_SUSPENSION + MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL: + text: MONONUCLEAR_CELLS_FROM_BONE_MARROW_NORMAL + NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR: + text: NEOPLASMS_OF_UNCERTAIN_AND_UNKNOWN_BEHAVIOR + NEXT_GENERATION_CANCER_MODEL: + text: NEXT_GENERATION_CANCER_MODEL + NORMAL_ADJACENT_TISSUE: + text: NORMAL_ADJACENT_TISSUE + PLEURAL_EFFUSION: + text: PLEURAL_EFFUSION + POST_NEOADJUVANT_THERAPY: + text: POST_NEOADJUVANT_THERAPY + PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW: + text: PRIMARY_BLOOD_DERIVED_CANCER_BONE_MARROW + PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: + text: PRIMARY_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD + PRIMARY_TUMOR: + text: PRIMARY_TUMOR + PRIMARY_XENOGRAFT_TISSUE: + text: PRIMARY_XENOGRAFT_TISSUE + RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW: + text: RECURRENT_BLOOD_DERIVED_CANCER_BONE_MARROW + RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD: + text: RECURRENT_BLOOD_DERIVED_CANCER_PERIPHERAL_BLOOD + RECURRENT_TUMOR: + text: RECURRENT_TUMOR + RNA: + text: RNA + SALIVA: + text: SALIVA + SLIDES: + text: SLIDES + SOLID_TISSUE_NORMAL: + text: SOLID_TISSUE_NORMAL + TOTAL_RNA: + text: TOTAL_RNA + TUMOR: + text: TUMOR + TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY: + text: TUMOR_ADJACENT_NORMAL_POST_NEOADJUVANT_THERAPY + XENOGRAFT_TISSUE: + text: XENOGRAFT_TISSUE + NOT_ALLOWED_TO_COLLECT: + text: NOT_ALLOWED_TO_COLLECT + NOT_REPORTED: + text: NOT_REPORTED + UNKNOWN: + text: UNKNOWN + + SectionLocationEnum: + name: SectionLocationEnum + description: The location in a parent specimen from which a section/portion was + excised. + permissible_values: + BOTTOM: + text: BOTTOM + description: The part of a specimen designated as its 'bottom' based on specified + orientation criteria. + TOP: + text: TOP + description: The part of a specimen designated as its 'top' based on specified + orientation criteria. + UNKNOWN: + text: UNKNOWN + description: An unknown location on a specimen. + + SpecimenCreationActivityTypeEnum: + name: SpecimenCreationActivityTypeEnum + description: The high-level type of activity through which the specimen was generated + (i.e. via collection from the original source, or via derivation from an existing + specimen) + permissible_values: + COLLECTION_FROM_SOURCE: + text: COLLECTION_FROM_SOURCE + description: An activity that collects an initial sample directly from a subject + / source. + DERIVATION_FROM_SPECIMEN: + text: DERIVATION_FROM_SPECIMEN + description: An activity that derives a new specimen from an existing one. + + SpecimenCollectionMethodType: + name: SpecimenCollectionMethodType + permissible_values: + ORCHIECTOMY: + text: ORCHIECTOMY + METASTASECTOMY: + text: METASTASECTOMY + AUTOPSY: + text: AUTOPSY + UNKNOWN: + text: UNKNOWN + ASPIRATE: + text: ASPIRATE + RIGHT_HEMICOLECTOMY: + text: RIGHT_HEMICOLECTOMY + INCISIONAL_BIOPSY: + text: INCISIONAL_BIOPSY + BLOOD_DRAW: + text: BLOOD_DRAW + PERITONEAL_LAVAGE: + text: PERITONEAL_LAVAGE + OPEN_RADICAL_PROSTATECTOMY: + text: OPEN_RADICAL_PROSTATECTOMY + ABDOMINO_PERINEAL_RESECTION_OF_RECTUM: + text: ABDOMINO_PERINEAL_RESECTION_OF_RECTUM + SALPINGECTOMY: + text: SALPINGECTOMY + ENDO_RECTAL_TUMOR_RESECTION: + text: ENDO_RECTAL_TUMOR_RESECTION + BIOPSY: + text: BIOPSY + SALPINGO_OOPHORECTOMY: + text: SALPINGO_OOPHORECTOMY + NOT_ALLOWED_TO_COLLECT: + text: NOT_ALLOWED_TO_COLLECT + WHIPPLE_PROCEDURE: + text: WHIPPLE_PROCEDURE + ENUCLEATION: + text: ENUCLEATION + MODIFIED_RADICAL_MASTECTOMY: + text: MODIFIED_RADICAL_MASTECTOMY + PARACENTESIS: + text: PARACENTESIS + OPEN_CRANIOTOMY: + text: OPEN_CRANIOTOMY + WEDGE_RESECTION: + text: WEDGE_RESECTION + LAPAROSCOPIC_RADICAL_NEPHRECTOMY: + text: LAPAROSCOPIC_RADICAL_NEPHRECTOMY + OPEN_PARTIAL_NEPHRECTOMY: + text: OPEN_PARTIAL_NEPHRECTOMY + TRANSURETHRAL_RESECTION: + text: TRANSURETHRAL_RESECTION + SIGMOID_COLECTOMY: + text: SIGMOID_COLECTOMY + OOPHORECTOMY: + text: OOPHORECTOMY + TOTAL_HEPATECTOMY: + text: TOTAL_HEPATECTOMY + INDETERMINANT: + text: INDETERMINANT + SUBTOTAL_RESECTION: + text: SUBTOTAL_RESECTION + LEFT_HEMICOLECTOMY: + text: LEFT_HEMICOLECTOMY + NEEDLE_BIOPSY: + text: NEEDLE_BIOPSY + OTHER: + text: OTHER + PANCREATECTOMY: + text: PANCREATECTOMY + THORACOSCOPIC_BIOPSY: + text: THORACOSCOPIC_BIOPSY + TOTAL_MASTECTOMY: + text: TOTAL_MASTECTOMY + EXCISIONAL_BIOPSY: + text: EXCISIONAL_BIOPSY + BONE_MARROW_ASPIRATE: + text: BONE_MARROW_ASPIRATE + LOCAL_RESECTION: + text: LOCAL_RESECTION + LOBECTOMY: + text: LOBECTOMY + FINE_NEEDLE_ASPIRATION: + text: FINE_NEEDLE_ASPIRATION + OMENTECTOMY: + text: OMENTECTOMY + TUMOR_RESECTION: + text: TUMOR_RESECTION + CYSTECTOMY: + text: CYSTECTOMY + GROSS_TOTAL_RESECTION: + text: GROSS_TOTAL_RESECTION + THORACENTESIS: + text: THORACENTESIS + ANTERIOR_RESECTION_OF_RECTUM: + text: ANTERIOR_RESECTION_OF_RECTUM + TRANSPLANT: + text: TRANSPLANT + LAPAROSCOPIC_PARTIAL_NEPHRECTOMY: + text: LAPAROSCOPIC_PARTIAL_NEPHRECTOMY + LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS: + text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITH_ROBOTICS + PNEUMONECTOMY: + text: PNEUMONECTOMY + PAN_PROCTO_COLECTOMY: + text: PAN_PROCTO_COLECTOMY + HYSTERECTOMY_NOS: + text: HYSTERECTOMY_NOS + CORE_BIOPSY: + text: CORE_BIOPSY + SIMPLE_MASTECTOMY: + text: SIMPLE_MASTECTOMY + LUMPECTOMY: + text: LUMPECTOMY + ENDOSCOPIC_BIOPSY: + text: ENDOSCOPIC_BIOPSY + SIMPLE_HYSTERECTOMY: + text: SIMPLE_HYSTERECTOMY + LYMPHADENECTOMY: + text: LYMPHADENECTOMY + LAPAROSCOPIC_BIOPSY: + text: LAPAROSCOPIC_BIOPSY + TUMOR_DEBULKING: + text: TUMOR_DEBULKING + ASCITES_DRAINAGE: + text: ASCITES_DRAINAGE + ENDOSCOPIC_MUCOSAL_RESECTION: + text: ENDOSCOPIC_MUCOSAL_RESECTION + LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS: + text: LAPAROSCOPIC_RADICAL_PROSTATECTOMY_WITHOUT_ROBOTICS + TOTAL_COLECTOMY: + text: TOTAL_COLECTOMY + LIQUID_BIOPSY: + text: LIQUID_BIOPSY + RADICAL_HYSTERECTOMY: + text: RADICAL_HYSTERECTOMY + SURGICAL_RESECTION: + text: SURGICAL_RESECTION + OPEN_RADICAL_NEPHRECTOMY: + text: OPEN_RADICAL_NEPHRECTOMY + TRANSVERSE_COLECTOMY: + text: TRANSVERSE_COLECTOMY + HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY: + text: HAND_ASSISTED_LAPAROSCOPIC_RADICAL_NEPHRECTOMY + PUNCH_BIOPSY: + text: PUNCH_BIOPSY + PARTIAL_HEPATECTOMY: + text: PARTIAL_HEPATECTOMY + SUPRACERVICAL_HYSTERECTOMY: + text: SUPRACERVICAL_HYSTERECTOMY + OTHER_SURGICAL_RESECTION: + text: OTHER_SURGICAL_RESECTION + NOT_REPORTED: + text: NOT_REPORTED + FULL_HYSTERECTOMY: + text: FULL_HYSTERECTOMY + TONSILLECTOMY: + text: TONSILLECTOMY + SUPRAGLOTTIC_LARYNGECTOMY: + text: SUPRAGLOTTIC_LARYNGECTOMY + SUPERFICIAL_PAROTIDECTOMY: + text: SUPERFICIAL_PAROTIDECTOMY + LARYNGOPHARYNGECTOMY: + text: LARYNGOPHARYNGECTOMY + MAXILLECTOMY: + text: MAXILLECTOMY + PARTIAL_NEPHRECTOMY: + text: PARTIAL_NEPHRECTOMY + MANDIBULECTOMY: + text: MANDIBULECTOMY + BUCCAL_MUCOSAL_RESECTION: + text: BUCCAL_MUCOSAL_RESECTION + VERTICAL_HEMILARYNGECTOMY: + text: VERTICAL_HEMILARYNGECTOMY + TOTAL_NEPHRECTOMY: + text: TOTAL_NEPHRECTOMY + TOTAL_LARYNGECTOMY: + text: TOTAL_LARYNGECTOMY + TRANSORAL_LASER_EXCISION: + text: TRANSORAL_LASER_EXCISION + PAROTIDECTOMY_NOS: + text: PAROTIDECTOMY_NOS + RADICAL_MAXILLECTOMY: + text: RADICAL_MAXILLECTOMY + ENDOLARYNGEAL_EXCISION: + text: ENDOLARYNGEAL_EXCISION + PALATECTOMY: + text: PALATECTOMY + GLOSSECTOMY: + text: GLOSSECTOMY + PARTIAL_LARYNGECTOMY: + text: PARTIAL_LARYNGECTOMY + LYMPH_NODE_DISSECTION: + text: LYMPH_NODE_DISSECTION + RADICAL_PROSTATECTOMY: + text: RADICAL_PROSTATECTOMY + DEEP_PAROTIDECTOMY: + text: DEEP_PAROTIDECTOMY + SUBTOTAL_PROSTATECTOMY: + text: SUBTOTAL_PROSTATECTOMY + RADICAL_NEPHRECTOMY: + text: RADICAL_NEPHRECTOMY + SUPRACRICOID_LARYNGECTOMY: + text: SUPRACRICOID_LARYNGECTOMY + PARTIAL_MAXILLECTOMY: + text: PARTIAL_MAXILLECTOMY + + SpecimenQualityObservationTypeEnum: + name: SpecimenQualityObservationTypeEnum + description: Types of measurements that reflect the quality of a specimen or its + suitability for use. + permissible_values: + A260_A280_RATIO: + text: A260_A280_RATIO + description: Ratio of absorbance measured at a wavelength of 260 over that + at a wavelength of 280. + RIBOSOMAL_RNA_28S_16S_RATIO: + text: RIBOSOMAL_RNA_28S_16S_RATIO + description: Ratio of quantity of 28s RNA over that of 16s RNA. + + SpecimenQualityObservationMethodEnum: + name: SpecimenQualityObservationMethodEnum + description: A type of method used in determining the quantity of a specimen. + permissible_values: + UV_SPEC: + text: UV_SPEC + description: A technique used to measure light absorbance across the ultraviolet + and visible ranges of the electromagnetic spectrum. + PICO_GREEN: + text: PICO_GREEN + description: A technique applying the Pico488 fluorescent sensor dye that + is used for quantifying the amount of double-stranded DNA (dsDNA) present + in a given sample. + + SpecimenQuantityObservationTypeEnum: + name: SpecimenQuantityObservationTypeEnum + description: Measures related to the quantity of a specimen or analyte it currently + contains - e.g. its weight, volume, or concentration. + permissible_values: + WEIGHT: + text: WEIGHT + description: The current weight of the specimen, at the time of recording + (as opposed to an initial weight before its processing or portioning). + VOLUME: + text: VOLUME + description: The current total volume of the specimen, at the time of recording. + CONCENTRATION: + text: CONCENTRATION + description: The concentration of an extracted analyte that is present in + a specimen (specifically, in a specimen of type 'analyte', or an 'aliquot' + derived from an analyte). For example, the concentration of DNA in a specimen + created through extracting DNA from a blood sample. + + SpecimenProcessingActivityTypeEnum: + name: SpecimenProcessingActivityTypeEnum + description: The high-level type of processing activity performed. + permissible_values: + FIXATION: + text: FIXATION + description: A processing activity that applies chemicals to preserve biological + tissues from decay due to autolysis or putrefaction + FREEZING: + text: FREEZING + description: A processing activity that aims to freeze a specimen. + MOUNTING: + text: MOUNTING + description: A processing activity that aims to secure a specimen or slide + in place in preparation for further examination (usually via microscopy) + PRESERVATION: + text: PRESERVATION + description: A processing activity that aims to preserve a specimen. +