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@datafire/mcw_edu

Client library for Rat Genome Database REST API

Installation and Usage

npm install --save @datafire/mcw_edu

let mcw_edu = require('@datafire/mcw_edu').create();

.then(data => {
  console.log(data);
});

Description

The RGD REST API provides programmatic access to information and annotation stored in the Rat Genome Database

Actions

getAffectedGenomicModelsUsingGET

Get affected genomic models (rat strains with gene alleles) submitted by RGD to AGR by taxonId

mcw_edu.getAffectedGenomicModelsUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getAllelesForTaxonUsingGET

Get gene allele records submitted by RGD to AGR by taxonId

mcw_edu.getAllelesForTaxonUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getExpressionForTaxonUsingGET

Get expression annotations submitted by RGD to AGR by taxonId

mcw_edu.getExpressionForTaxonUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getPhenotypesForTaxonUsingGET

Get phenotype annotations submitted by RGD to AGR by taxonId

mcw_edu.getPhenotypesForTaxonUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getVariantsForTaxonUsingGET

Get basic variant records submitted by RGD to AGR by taxonId

mcw_edu.getVariantsForTaxonUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getGenesForLatestAssemblyUsingGET

Get gene records submitted by RGD to AGR by taxonId

mcw_edu.getGenesForLatestAssemblyUsingGET({
  "taxonId": ""
}, context)

Input

input object
- taxonId required string: The taxon ID for species

Output

output object

getAnnotationsUsingPOST

Return a list of genes annotated to an ontology term

mcw_edu.getAnnotationsUsingPOST({}, context)

Input

input object
- body AnnotationRequest

Output

output array
- items Annotation

getTermAccIdsUsingGET

Returns a list ontology term accession IDs annotated to an rgd object

mcw_edu.getTermAccIdsUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output array
- items MapPair

getAnnotationCountByAccIdUsingGET

Returns annotation count for ontology accession ID

mcw_edu.getAnnotationCountByAccIdUsingGET({
  "accId": "",
  "includeChildren": true
}, context)

Input

input object
- accId required string: Ontology term accession ID
- includeChildren required boolean: true: return annotations for the term and children, false: return annotations for the term only

Output

output integer

getAnnotationCountByAccIdAndSpeciesUsingGET

Returns annotation count for ontology accession ID and speicies

mcw_edu.getAnnotationCountByAccIdAndSpeciesUsingGET({
  "accId": "",
  "speciesTypeKey": 0,
  "includeChildren": true
}, context)

Input

input object
- accId required string: Ontology term accession ID
- speciesTypeKey required integer: A list of species type keys can be found using the lookup service
- includeChildren required boolean: true: return annotations for the term and children, false: return annotations for the term only

Output

output integer

getAnnotationCountByAccIdAndObjectTypeUsingGET

Returns annotation count for ontology accession ID and object type

mcw_edu.getAnnotationCountByAccIdAndObjectTypeUsingGET({
  "accId": "",
  "speciesTypeKey": 0,
  "includeChildren": true,
  "objectType": 0
}, context)

Input

input object
- accId required string: Ontology term accession ID
- speciesTypeKey required integer: A list of species type keys can be found using the lookup service
- includeChildren required boolean: true: return annotations for the term and children, false: return annotations for the term only
- objectType required integer: A list of object types can be found using the lookup service

Output

output integer

getAnnotsByRefrerenceUsingGET

Returns a list of annotations for a reference

mcw_edu.getAnnotsByRefrerenceUsingGET({
  "refRgdId": 0
}, context)

Input

input object
- refRgdId required integer: Reference RGD ID

Output

output array
- items Annotation

getAnnotationsByRgdIdUsingGET

Returns a list of annotations by RGD ID

mcw_edu.getAnnotationsByRgdIdUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output array
- items Annotation

getAnnotationsByRgdIdAndOntologyUsingGET

Returns a list of annotations by RGD ID and ontology prefix

mcw_edu.getAnnotationsByRgdIdAndOntologyUsingGET({
  "rgdId": 0,
  "ontologyPrefix": ""
}, context)

Input

input object
- rgdId required integer: RGD ID
- ontologyPrefix required string: Ontology Prefix. The prefix can be found left of the semicolon in an ontology term accession ID. As an example, term accession PW:0000034 has the ontology prefix PW

Output

output array
- items Annotation

getAnnotationsByAccIdAndRgdIdUsingGET

Returns a list of annotations by RGD ID and ontology term accession ID

mcw_edu.getAnnotationsByAccIdAndRgdIdUsingGET({
  "accId": "",
  "rgdId": 0
}, context)

Input

input object
- accId required string: Ontology Term Accession ID
- rgdId required integer: RGD ID

Output

output array
- items Annotation

getAnnotationsUsingGET

Returns a list annotations for an ontology term or a term and it's children

mcw_edu.getAnnotationsUsingGET({
  "accId": "",
  "speciesTypeKey": 0,
  "includeChildren": true
}, context)

Input

input object
- accId required string: Ontology term accession ID
- speciesTypeKey required integer: A list of species type keys can be found using the lookup service
- includeChildren required boolean: true: return annotations for the term and children, false: return annotations for the term only

Output

output array
- items Annotation

getEnrichmentDataUsingPOST

Return a list of genes annotated to the term.Genes are rgdids separated by comma.Species type is an integer value.term is the ontology

mcw_edu.getEnrichmentDataUsingPOST({
  "body": {}
}, context)

Input

input object
- body required EnrichmentGeneRequest

Output

output object

getEnrichmentDataUsingPOST_1

Return a chart of ontology terms annotated to the genes.Genes are rgdids separated by comma.Species type is an integer value.Aspect is the Ontology group

mcw_edu.getEnrichmentDataUsingPOST_1({
  "body": {}
}, context)

Input

input object
- body required EnrichmentRequest

Output

output object

getGenesByAffyIdUsingGET

Return a list of genes for an affymetrix ID

mcw_edu.getGenesByAffyIdUsingGET({
  "affyId": "",
  "speciesTypeKey": 0
}, context)

Input

input object
- affyId required string: Affymetrix ID
- speciesTypeKey required integer: A list of RGD species type keys can be found in the lookup service

Output

output array
- items Gene

getGenesByAliasSymbolUsingGET

Return a list of genes for an alias and species

mcw_edu.getGenesByAliasSymbolUsingGET({
  "aliasSymbol": "",
  "speciesTypeKey": 0
}, context)

Input

input object
- aliasSymbol required string: Gene alias symbol
- speciesTypeKey required integer: A list of RGD species type keys can be found in the lookup service

Output

output array
- items Gene

getGeneAllelesUsingGET

Return a list of gene alleles

mcw_edu.getGeneAllelesUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID of gene

Output

output array
- items Gene

getAnnotatedGenesUsingPOST

Return a list of genes annotated to an ontology term

mcw_edu.getAnnotatedGenesUsingPOST({}, context)

Input

input object
- body AnnotatedGeneRequest

Output

output array
- items Gene

getAllAnnotatedGenesUsingGET

Return a list of genes annotated to an ontology term

mcw_edu.getAllAnnotatedGenesUsingGET({
  "accId": ""
}, context)

Input

input object
- accId required string: Accesstion ID

Output

output array
- items Gene

getGenesAnnotatedUsingGET

Return a list of genes annotated to an ontology term

mcw_edu.getGenesAnnotatedUsingGET({
  "accId": "",
  "speciesTypeKey": 0
}, context)

Input

input object
- accId required string: Ontology term accession ID
- speciesTypeKey required integer: Species type key. A list of species type keys can be found in the lookup service

Output

output array
- items Gene

getGenesByKeywordUsingGET

Return a list of genes by keyword and species type key

mcw_edu.getGenesByKeywordUsingGET({
  "keyword": "",
  "speciesTypeKey": 0
}, context)

Input

input object
- keyword required string: Search keyword
- speciesTypeKey required integer: Species type key. A list of species type keys can be found in the lookup service

Output

output array
- items Gene

getGeneByMapKeyUsingGET

Return a list of all genes with position information for an assembly

mcw_edu.getGeneByMapKeyUsingGET({
  "mapKey": 0
}, context)

Input

input object
- mapKey required integer: A list of RGD assembly map keys can be found in the lookup service

Output

output array
- items MappedGene

getMappedGenesByPositionUsingGET

Return a list of genes position and map key

mcw_edu.getMappedGenesByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of RGD assembly map keys can be found in the lookup service

Output

output array
- items MappedGene

getOrthologsByListUsingPOST

Return a list of gene orthologs

mcw_edu.getOrthologsByListUsingPOST({
  "body": {}
}, context)

Input

input object
- body required OrthologRequest

Output

output object

getGeneOrthologsUsingGET

Return a list of gene orthologs

mcw_edu.getGeneOrthologsUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID of a gene

Output

output array
- items Gene

getGenesInRegionUsingGET

Return a list of genes in region

mcw_edu.getGenesInRegionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of RGD assembly map keys can be found in the lookup service

Output

output array
- items MappedGenePosition

getGenesBySpeciesUsingGET

Return a list of all genes for a species in RGD

mcw_edu.getGenesBySpeciesUsingGET({
  "speciesTypeKey": 0
}, context)

Input

input object
- speciesTypeKey required integer: A list of RGD species type keys can be found in the lookup service

Output

output array
- items Gene

getGenesByPositionUsingGET

Return a list of genes position and map key

mcw_edu.getGenesByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of RGD assembly map keys can be found in the lookup service

Output

output array
- items Gene

getGeneByRgdIdUsingGET

Get a gene record by RGD ID

mcw_edu.getGeneByRgdIdUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: The RGD ID of a Gene in RGD

Output

output Gene

getGeneBySymbolUsingGET

Get a gene record by symbol and species type key

mcw_edu.getGeneBySymbolUsingGET({
  "symbol": "",
  "speciesTypeKey": 0
}, context)

Input

input object
- symbol required string: Gene Symbol
- speciesTypeKey required integer: Species type key. A list of species type keys can be found in the lookup service

Output

output Gene

getGeneTypesUsingGET

Returns a list of gene types avialable in RGD

mcw_edu.getGeneTypesUsingGET(null, context)

Input

This action has no parameters

Output

output array
- items string

getEnsemblGeneMappingUsingPOST

Translate RGD IDs to Ensembl Gene IDs

mcw_edu.getEnsemblGeneMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getEnsemblGeneMappingUsingGET

Translate an RGD ID to an Ensembl Gene ID

mcw_edu.getEnsemblGeneMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getEnsemblProteinMappingUsingPOST

Translate RGD IDs to Ensembl Protein IDs

mcw_edu.getEnsemblProteinMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getEnsemblProteinMappingUsingGET

Translate an RGD ID to an Ensembl Protein ID

mcw_edu.getEnsemblProteinMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getEnsemblTranscriptMappingUsingPOST

Translate RGD IDs to Ensembl Transcript IDs

mcw_edu.getEnsemblTranscriptMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getEnsemblTranscriptMappingUsingGET

Translate an RGD ID to an Ensembl Transcript ID

mcw_edu.getEnsemblTranscriptMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getGTEXMappingUsingPOST

Translate RGD IDs to GTEx IDs

mcw_edu.getGTEXMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getGTEXMappingUsingGET

Translate an RGD ID to an GTEx ID

mcw_edu.getGTEXMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getGenBankNucleotideMappingUsingPOST

Translate RGD IDs to GenBank Nucleotide IDs

mcw_edu.getGenBankNucleotideMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getGenBankNucleotideMappingUsingGET

Translate an RGD ID to a GenBank Nucleotide ID

mcw_edu.getGenBankNucleotideMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getGenBankProteinMappingUsingPOST

Translate RGD IDs to GenBank Protein IDs

mcw_edu.getGenBankProteinMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getGenBankProteinMappingUsingGET

Translate an RGD ID to a GenBank Protein ID

mcw_edu.getGenBankProteinMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getHGNCMappingUsingPOST

Translate RGD IDs to HGNC IDs

mcw_edu.getHGNCMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getHGNCMappingUsingGET

Translate an RGD ID to an HGNC ID

mcw_edu.getHGNCMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getMGIMappingUsingPOST

Translate RGD IDs to MGI IDs

mcw_edu.getMGIMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getMGIMappingUsingGET

Translate an RGD ID to an MGI ID

mcw_edu.getMGIMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getNCBIGeneMappingUsingPOST

Translate RGD IDs to NCBI Gene IDs

mcw_edu.getNCBIGeneMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getNCBIGeneMappingUsingGET

Translate an RGD ID to an NCBI Gene ID

mcw_edu.getNCBIGeneMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getUniProtMappingUsingPOST

Translate RGD IDs to UniProt IDs

mcw_edu.getUniProtMappingUsingPOST({}, context)

Input

input object
- body RGDIDListRequest

Output

output object

getUniProtMappingUsingGET

Translate an RGD ID to a UniProt ID

mcw_edu.getUniProtMappingUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output object

getMapsUsingGET

Return a list assembly maps for a species

mcw_edu.getMapsUsingGET({
  "speciesTypeKey": 0
}, context)

Input

input object
- speciesTypeKey required integer: RGD species type key. A full list of keys is available throught the lookup service. 1=human, 2=mouse, 3=rat,ect

Output

output array
- items Map

getSpeciesTypesUsingGET

Return a Map of species type keys available in RGD

mcw_edu.getSpeciesTypesUsingGET(null, context)

Input

This action has no parameters

Output

output object

getMapsUsingGET_1

Return a standardUnit for an ontology if it exists

mcw_edu.getMapsUsingGET_1({
  "accId": ""
}, context)

Input

input object
- accId required string: RGD term acc

Output

output string

getChromosomeByAssemblyUsingGET

Return a list of chromosomes

mcw_edu.getChromosomeByAssemblyUsingGET({
  "chromosome": "",
  "mapKey": 0
}, context)

Input

input object
- chromosome required string: chromosome
- mapKey required integer: mapKey

Output

output Chromosome

getChromosomesByAssemblyUsingGET

Return a list of chromosomes

mcw_edu.getChromosomesByAssemblyUsingGET({
  "mapKey": 0
}, context)

Input

input object
- mapKey required integer: mapKey

Output

output array
- items string

getMapsBySpeciesUsingGET

Return a list of assemblies

mcw_edu.getMapsBySpeciesUsingGET({
  "speciesTypeKey": 0
}, context)

Input

input object
- speciesTypeKey required integer: species Key

Output

output array
- items Map

getOntDagsUsingGET

Returns child and parent terms for Accession ID

mcw_edu.getOntDagsUsingGET({
  "accId": ""
}, context)

Input

input object
- accId required string: Accession ID

Output

output object

isDescendantOfUsingGET

Returns true or false for terms

mcw_edu.isDescendantOfUsingGET({
  "accId1": "",
  "accId2": ""
}, context)

Input

input object
- accId1 required string: Child Term Accession ID
- accId2 required string: Parent Term Accession ID

Output

output boolean

getTermUsingGET

Returns term for Accession ID

mcw_edu.getTermUsingGET({
  "accId": ""
}, context)

Input

input object
- accId required string: Term Accession ID

Output

output Term

searchPathwaysUsingGET

Return a list of pathways based on search term

mcw_edu.searchPathwaysUsingGET({
  "searchString": ""
}, context)

Input

input object
- searchString required string: Free text search string

Output

output array
- items Pathway

getPathwaysWithDiagramsForCategoryUsingGET

Return a list of pathways based on category provided

mcw_edu.getPathwaysWithDiagramsForCategoryUsingGET({
  "category": ""
}, context)

Input

input object
- category required string: Pathway Category

Output

output array
- items Pathway

getChartInfoUsingGET

Return a list of quantitative phenotypes values based on a combination of Clinical Measurement, Experimental Condition, Rat Strain, and/or Measurement Method ontology terms. Results will be all records that match all terms submitted. Ontology ids should be submitted as a comma delimited list (ex. RS:0000029,CMO:0000155,CMO:0000139). Species type is an integer value (3=rat, 4=chinchilla). Reference RGD ID for a study works like a filter.

mcw_edu.getChartInfoUsingGET({
  "speciesTypeKey": 0,
  "refRgdId": 0,
  "termString": ""
}, context)

Input

input object
- speciesTypeKey required integer: Species Type Key - 3=rat 4=chinchilla
- refRgdId required integer: Reference RGD ID for a study
- termString required string: List of term accession IDs

Output

output object

getChartInfoUsingGET_1

mcw_edu.getChartInfoUsingGET_1({
  "speciesTypeKey": 0,
  "termString": ""
}, context)

Input

input object
- speciesTypeKey required integer: Species Type Key - 3=rat 4=chinchilla
- termString required string: List of term accession IDs

Output

output object

getMappedQTLByPositionUsingGET

Returns a list QTL for given position and assembly map

mcw_edu.getMappedQTLByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of assembly map keys can be found using the lookup service

Output

output array
- items MappedQTL

getQtlListByPositionUsingGET

Returns a list QTL for given position and assembly map

mcw_edu.getQtlListByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of assembly map keys can be found using the lookup service

Output

output array
- items QTL

getQTLByRgdIdUsingGET

Return a QTL for provided RGD ID

mcw_edu.getQTLByRgdIdUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID

Output

output QTL

getMappedSSLPByPositionUsingGET

Returns a list SSLP for given position and assembly map

mcw_edu.getMappedSSLPByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: A list of assembly map keys can be found using the lookup service

Output

output array
- items MappedSSLP

getActiveObjectCountUsingGET

Count of active objects by type, for specified species and date

mcw_edu.getActiveObjectCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getGeneTypeCountUsingGET

Count of gene types, for specified species and date

mcw_edu.getGeneTypeCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getObjectStatusCountUsingGET

Count of objects with given status, for specified species and date

mcw_edu.getObjectStatusCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getObjectsWithRefSeqCountUsingGET

Count of objects with reference sequence(s), by object type, for specified species and date

mcw_edu.getObjectsWithRefSeqCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getObjectsWithReferenceCountUsingGET

Count of objects with reference, by object type, for specified species and date

mcw_edu.getObjectsWithReferenceCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getObjectsWithXDBsCountUsingGET

Count of objects with external database ids, by database id, for specified species, object type and date

mcw_edu.getObjectsWithXDBsCountUsingGET({
  "speciesTypeKey": 0,
  "objectKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- objectKey required integer: objectKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getProteinInteractionCountUsingGET

Count of protein interactions, for specified species and date

mcw_edu.getProteinInteractionCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getQtlInheritanceTypeCountUsingGET

Count of strains, by qtl inheritance type, for specified species and date

mcw_edu.getQtlInheritanceTypeCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getRetiredObjectCountUsingGET

Count of retired objects by type, for specified species and date

mcw_edu.getRetiredObjectCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getStrainTypeCountUsingGET

Count of strain types, for specified species and date

mcw_edu.getStrainTypeCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getWithdrawnObjectCountUsingGET

Count of withdrawn objects by type, for specified species and date

mcw_edu.getWithdrawnObjectCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getXdbsCountUsingGET

Count of external database ids, for specied species and date

mcw_edu.getXdbsCountUsingGET({
  "speciesTypeKey": 0,
  "dateYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateYYYYMMDD required string: dateYYYYMMDD

Output

output object

getActiveObjectDiffUsingGET

Count difference of active objects, by type, for specified species and date range

mcw_edu.getActiveObjectDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getGeneTypeDiffUsingGET

Count difference of gene types, for specified species and date range

mcw_edu.getGeneTypeDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getObjectStatusDiffUsingGET

Count difference of objects with given status, for specified species and date range

mcw_edu.getObjectStatusDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getObjectsWithRefSeqDiffUsingGET

Count difference of objects with reference sequence(s), by object type, for specified species and date range

mcw_edu.getObjectsWithRefSeqDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getObjectsWithReferenceDiffUsingGET

Count difference of objects with reference, by object type, for specified species and date range

mcw_edu.getObjectsWithReferenceDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getObjectsWithXDBsDiffUsingGET

Count difference of objects with external database ids, by database id, for specified species, object type and date range

mcw_edu.getObjectsWithXDBsDiffUsingGET({
  "speciesTypeKey": 0,
  "objectKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- objectKey required integer: objectKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getProteinInteractionDiffUsingGET

Count difference of protein interactions, for specified species and date range

mcw_edu.getProteinInteractionDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getQtlInheritanceTypeDiffUsingGET

Count difference of strains, by qtl inheritance type, for specified species and date range

mcw_edu.getQtlInheritanceTypeDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getRetiredObjectDiffUsingGET

Count difference of retired objects, by type, for specified species and date range

mcw_edu.getRetiredObjectDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getStrainTypeDiffUsingGET

Count difference of strain types, for specified species and date range

mcw_edu.getStrainTypeDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getWithdrawnObjectDiffUsingGET

Count difference of withdrawn objects, by type, for specified species and date range

mcw_edu.getWithdrawnObjectDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getXdbsDiffUsingGET

Count difference of external database ids, for specified species and date range

mcw_edu.getXdbsDiffUsingGET({
  "speciesTypeKey": 0,
  "dateFromYYYYMMDD": "",
  "dateToYYYYMMDD": ""
}, context)

Input

input object
- speciesTypeKey required integer: speciesTypeKey
- dateFromYYYYMMDD required string: dateFromYYYYMMDD
- dateToYYYYMMDD required string: dateToYYYYMMDD

Output

output object

getTermStatsUsingGET

getTermStats

mcw_edu.getTermStatsUsingGET({
  "accId": "",
  "filterAccId": ""
}, context)

Input

input object
- accId required string: accId
- filterAccId required string: filterAccId

Output

output object

getAllStrainsUsingGET

Return all active strains in RGD

mcw_edu.getAllStrainsUsingGET(null, context)

Input

This action has no parameters

Output

output array
- items Strain

getStrainsByPositionUsingGET

Return all active strains by position

mcw_edu.getStrainsByPositionUsingGET({
  "chr": "",
  "start": 0,
  "stop": 0,
  "mapKey": 0
}, context)

Input

input object
- chr required string: Chromosome
- start required integer: Start Position
- stop required integer: Stop Position
- mapKey required integer: RGD Map Key (available through lookup service)

Output

output array
- items Strain

getStrainByRgdIdUsingGET

Return a strain by RGD ID

mcw_edu.getStrainByRgdIdUsingGET({
  "rgdId": 0
}, context)

Input

input object
- rgdId required integer: RGD ID of the strain

Output

output Strain

Definitions

AnnotatedGeneRequest

AnnotatedGeneRequest object
- accId string
- evidenceCodes array
  - items string
- speciesTypeKeys array
  - items integer

Annotation

Annotation object
- annotatedObjectRgdId integer
- annotationExtension string
- aspect string
- createdBy integer
- createdDate string
- dataSrc string
- evidence string
- geneProductFormId string
- key integer
- lastModifiedBy integer
- lastModifiedDate string
- notes string
- objectName string
- objectSymbol string
- qualifier string
- refRgdId integer
- relativeTo string
- rgdObjectKey integer
- speciesTypeKey integer
- term string
- termAcc string
- withInfo string
- xrefSource string

AnnotationRequest

AnnotationRequest object
- evidenceCodes array
  - items string
- ids array
  - items string
- speciesTypeKeys array
  - items integer
- termAcc string

Chromosome

Chromosome object
- chromosome string
- contigCount integer
- gapCount integer
- gapLength integer
- genbankId string
- mapKey integer
- ordinalNumber integer
- refseqId string
- seqLength integer

EnrichmentGeneRequest

EnrichmentGeneRequest object
- accId string
- geneSymbols array
  - items string
- species string

EnrichmentRequest

EnrichmentRequest object
- aspect string
- genes array
  - items string
- species string

Gene

Gene object
- agrDescription string
- description string
- ensemblFullName string
- ensemblGeneSymbol string
- ensemblGeneType string
- geneSource string
- key integer
- mergedDescription string
- name string
- ncbiAnnotStatus string
- nomenReviewDate string
- nomenSource string
- notes string
- refSeqStatus string
- rgdId integer
- soAccId string
- speciesTypeKey integer
- symbol string
- type string
- variant boolean

Map

Map object
- dbsnpVersion string
- description string
- key integer
- methodKey integer
- name string
- notes string
- primaryRefAssembly boolean
- rank integer
- refSeqAssemblyAcc string
- refSeqAssemblyName string
- rgdId integer
- source string
- speciesTypeKey integer
- ucscAssemblyId string
- unit string
- version string

MapPair

MapPair object
- keyValue string
- stringValue string

MappedGene

MappedGene object
- chromosome string
- gene Gene
- mapKey integer
- start integer
- stop integer
- strand string

MappedGenePosition

MappedGenePosition object
- chromosome string
- mapKey integer
- rgdId integer
- start integer
- stop integer
- strand string
- symbol string

MappedQTL

MappedQTL object
- chromosome string
- mapKey integer
- qtl QTL
- start integer
- stop integer
- strand string

MappedSSLP

MappedSSLP object
- chromosome string
- mapKey integer
- sslp SSLP
- start integer
- stop integer
- strand string

OrthologRequest

OrthologRequest object
- rgdIds array
  - items integer
- speciesTypeKeys array
  - items integer

Pathway

Pathway object
- description string
- hasAlteredPath string
- id string
- name string
- objectList array
  - items PathwayObject
- pathwayCategories array
  - items string
- referenceList array
  - items Reference

PathwayObject

PathwayObject object
- accId string
- id string
- objDesc string
- objName string
- typeId integer
- typeName string
- url string
- xdb_key integer

QTL

QTL object
- chromosome string
- flank1RgdId integer
- flank2RgdId integer
- inheritanceType string
- key integer
- linkageImage string
- lod number
- lodImage string
- mostSignificantCmoTerm string
- name string
- notes string
- peakOffset integer
- peakRgdId integer
- pvalue number
- rgdId integer
- sourceUrl string
- speciesTypeKey integer
- symbol string
- variance number

RGDIDListRequest

RGDIDListRequest object
- rgdIds array
  - items integer

Reference

Reference object
- citation string
- doi string
- editors string
- issue string
- key integer
- notes string
- pages string
- pubDate string
- pubStatus string
- publication string
- publisher string
- publisherCity string
- refAbstract string
- referenceType string
- rgdId integer
- speciesTypeKey integer
- title string
- urlWebReference string
- volume string

SSLP

SSLP object
- expectedSize integer
- forwardSeq string
- key integer
- name string
- notes string
- reverseSeq string
- rgdId integer
- speciesTypeKey integer
- sslpType string
- templateSeq string

Status

Status object
- cryopreservedEmbryo boolean
- cryopreservedSperm boolean
- cryorecovery boolean
- key integer
- liveAnimals boolean
- statusDate string
- strainRgdId integer

Strain

Strain object
- backgroundStrainRgdId integer
- chrAltered string
- color string
- geneticStatus string
- genetics string
- imageUrl string
- inbredGen string
- key integer
- lastStatus string
- lastStatusObject Status
- modificationMethod string
- name string
- notes string
- origin string
- researchUse string
- rgdId integer
- source string
- speciesTypeKey integer
- statusLog array
  - items Status
- strain string
- strainTypeName string
- substrain string
- symbol string

Term

Term object
- accId string
- comment string
- createdBy string
- creationDate string
- definition string
- modificationDate string
- obsolete integer
- ontologyId string
- term string
- xrefs array
  - items TermXRef

TermXRef

TermXRef object
- key integer
- termAcc string
- xrefDescription string
- xrefValue string

Files

mcw_edu

Directory actions

More options

Directory actions

More options

Latest commit

History

mcw_edu

Folders and files

parent directory

README.md

@datafire/mcw_edu

Installation and Usage

Description

Actions

getAffectedGenomicModelsUsingGET

Input

Output

getAllelesForTaxonUsingGET

Input

Output

getExpressionForTaxonUsingGET

Input

Output

getPhenotypesForTaxonUsingGET

Input

Output

getVariantsForTaxonUsingGET

Input

Output

getGenesForLatestAssemblyUsingGET

Input

Output

getAnnotationsUsingPOST

Input

Output

getTermAccIdsUsingGET

Input

Output

getAnnotationCountByAccIdUsingGET

Input

Output

getAnnotationCountByAccIdAndSpeciesUsingGET

Input

Output

getAnnotationCountByAccIdAndObjectTypeUsingGET

Input

Output

getAnnotsByRefrerenceUsingGET

Input

Output

getAnnotationsByRgdIdUsingGET

Input

Output

getAnnotationsByRgdIdAndOntologyUsingGET

Input

Output

getAnnotationsByAccIdAndRgdIdUsingGET

Input

Output

getAnnotationsUsingGET

Input

Output

getEnrichmentDataUsingPOST

Input

Output

getEnrichmentDataUsingPOST_1

Input

Output

getGenesByAffyIdUsingGET

Input

Output

getGenesByAliasSymbolUsingGET

Input

Output

getGeneAllelesUsingGET

Input

Output

getAnnotatedGenesUsingPOST