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added README of JSON structures in service/database
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| # Collections | ||
| These rapresent the structures of the database collections. This "database" folder package retrieve all data from database. | ||
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| Base collections: | ||
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| - `nucleotide_data` contains the data obtainable by searching in the Nucleotide NCBI database. | ||
| - `taxonomy_data` contains the data obtainable by searching in the Taxonomy NCBI database. | ||
| - `protein_data` contains the data obtainable by searching in the Nucleotide Protein database. | ||
| - `sra` contains the data obtainable by searching in the SRA NCBI database. | ||
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| Collections made for performance reason: | ||
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| - `taxonomy_tree` contains the childrens for every taxonomy term, used in Vulgaris Platform's Taxonomy View. | ||
| - `table_basic` contains a lightweight version of the data, used in Vulgaris Platform's Search view. | ||
| - `table_complete` contains a more complete version of the data, used in Vulgaris Platform's Organism View. | ||
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| ## `taxonomy_data` | ||
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| Example of an element from taxonomy_data: | ||
| ```json | ||
| { | ||
| "TaxID" : "string", | ||
| "ScientificName" : "string", | ||
| "ParentTaxID" : "string", | ||
| "Rank" : "string", | ||
| "Divisio" : "string", | ||
| "GeneticCode":{ | ||
| "GCID" : "string", | ||
| "GCName" : "string" | ||
| }, | ||
| "MitoGeneticCode":{ | ||
| "MGCID" : "string", | ||
| "MGCName" : "string" | ||
| }, | ||
| "Lineage" : "string", | ||
| "LineageEx": [ | ||
| { | ||
| "TaxID" : "string", | ||
| "ScientificName" : "string", | ||
| "Rank" : "string", | ||
| }, | ||
| ] | ||
| "CreateDate" : "string", | ||
| "UpdateDate" : "string", | ||
| "PubDate" : "string" | ||
| } | ||
| ``` | ||
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| ## `nucleotide_data` | ||
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| Example of an element from nucleotide_data: | ||
| ```json | ||
| { | ||
| "GBSeqAccessionVersion": "string", | ||
| "GBSeqComment" : "string", | ||
| "GBSeqCreateDate" : "string", | ||
| "GBSeqDefinition" : "string", | ||
| "GBSeqDivision" : "string", | ||
| "GBSeqFeatureTable" : [ | ||
| { | ||
| "GBFeatureIntervals": { | ||
| "GBIntervalAccession": "string", | ||
| "GBIntervalFrom" : "string", | ||
| "GBIntervalTo" : "string" | ||
| }, | ||
| "GBFeatureKey" : "string", | ||
| "GBFeatureLocation": "string", | ||
| "GBFeatureQuals": [ | ||
| { | ||
| "GBQualifierName" : "string", | ||
| "GBQualifierValue": "string" | ||
| } | ||
| ], | ||
| "GBFeaturePartial3": "string", | ||
| "GBFeaturePartial5": "string" | ||
| } | ||
| ], | ||
| "GBSeqLength" : "string", | ||
| "GBSeqLocus" : "string", | ||
| "GBSeqMoltype" : "string", | ||
| "GBSeqOrganism" : "string", | ||
| "GBSeqOtherSeqids" : ["string"], | ||
| "GBSeqPrimaryAccession": "string", | ||
| "GBSeqReferences" : [ | ||
| { | ||
| "GBReferenceAuthors" : ["string"], | ||
| "GBReferenceJournal" : "string", | ||
| "GBReferencePosition" : "string", | ||
| "GBReferenceReference": "string", | ||
| "GBReferenceTitle" : "string" | ||
| } | ||
| ], | ||
| "GBSeqSource" : "string", | ||
| "GBSeqStrandedness": "string", | ||
| "GBSeqTaxonomy" : "string", | ||
| "GBSeqTopology" : "string", | ||
| "GBSeqUpdateDate" : "string" | ||
| } | ||
| ``` | ||
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| ## `protein_data` | ||
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| Example of an element from protein_data: | ||
| ```json | ||
| { | ||
| "GBSeqAccessionVersion" : "string", | ||
| "GBSeqComment" : "string", | ||
| "GBSeqCreateDate" : "string", | ||
| "GBSeqDefinition" : "string", | ||
| "GBSeqDivision" : "string", | ||
| "GBSeqFeatureTable" : [ | ||
| { | ||
| "GBFeatureIntervals": { | ||
| "GBIntervalAccession" : "string", | ||
| "GBIntervalFrom" : "string", | ||
| "GBIntervalTo" : "string" | ||
| }, | ||
| "GBFeatureKey" : "string", | ||
| "GBFeatureLocation" : "string", | ||
| "GBFeatureQuals" : [ | ||
| { | ||
| "GBQualifierName" : "string", | ||
| "GBQualifierValue" : "string" | ||
| } | ||
| ], | ||
| "GBFeaturePartial3" : "string", | ||
| "GBFeaturePartial5" : "string" | ||
| } | ||
| ], | ||
| "GBSeqLength" : "string", | ||
| "GBSeqLocus" : "string", | ||
| "GBSeqMoltype" : "string", | ||
| "GBSeqOrganism" : "string", | ||
| "GBSeqOtherSeqids" : "string", | ||
| "GBSeqPrimaryAccession" : "string", | ||
| "GBSeqReferences" : [ | ||
| { | ||
| "GBReferenceAuthors" : ["string"], | ||
| "GBReferenceJournal" : "string", | ||
| "GBReferencePosition" : "string", | ||
| "GBReferenceReference" : "string", | ||
| "GBReferenceTitle" : "string" | ||
| } | ||
| ], | ||
| "GBSeqSource" : "string", | ||
| "GBSeqStrandedness" : "string", | ||
| "GBSeqTaxonomy" : "string", | ||
| "GBSeqTopology" : "string", | ||
| "GBSeqUpdateDate" : "string" | ||
| } | ||
| ``` | ||
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| ## `table_basic` | ||
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| Example of an element from table_basic: | ||
| ``db.table_basic.findOne({ScientificName:"Chlorella vulgaris"})`` | ||
| ```json | ||
| { | ||
| "ScientificName" : "string", | ||
| "TaxId" : "string", | ||
| "Nucleotides": [ | ||
| { | ||
| "GBSeq_locus" : "string" | ||
| } | ||
| ], | ||
| "Proteins" : [ | ||
| { | ||
| "GBSeq_locus" : "string" | ||
| } | ||
| ], | ||
| "Products" : [ | ||
| { | ||
| "ProductName" : "string", | ||
| "QtyProduct" : "string" | ||
| } | ||
| ], | ||
| "Country" : [ | ||
| { | ||
| "CountryName" : "string" | ||
| } | ||
| ] | ||
| } | ||
| ``` | ||
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| ## `table_complete` | ||
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| Example of an element from table_complete: | ||
| ``db.table_complete.findOne({ScientificName:"Chlorella vulgaris"})`` | ||
| ```json | ||
| { | ||
| "ScientificName" : "string", | ||
| "TaxId" : "string", | ||
| "Nucleotides" : [ | ||
| { | ||
| "SameAs" : "nucleotide_data" | ||
| } | ||
| ], | ||
| "Proteins" : [ | ||
| { | ||
| "SameAs" : "protein_data" | ||
| } | ||
| ], | ||
| "Products" : [ | ||
| { | ||
| "ProductName" : "string", | ||
| "QtyProduct" : "string" | ||
| } | ||
| ], | ||
| "Country" : [ | ||
| { | ||
| "CountryName" : "string" | ||
| } | ||
| ] | ||
| } | ||
| ``` | ||
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| Note: Nucleotides and Proteins have type structure of, respectively, nucleotide_data e protein_data. | ||
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| ## `taxonomy_tree` | ||
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| Example of an element from taxonomy_tree: | ||
| ``db.taxonomy_tree.findOne({TaxId:"3077"})`` | ||
| ```json | ||
| { | ||
| "TaxId" : "string", | ||
| "Rank" : "string", | ||
| "ScientificName" : "string", | ||
| "SubClasses" : [ | ||
| { | ||
| "TaxId" : "string", | ||
| "Rank" : "string", | ||
| "ScientificName" : "string" | ||
| } | ||
| ] | ||
| } | ||
| ``` |