Open documentation ↗Overview
The RGD REST API provides programmatic access to information and annotation stored in the Rat Genome Database
Rat Genome Database REST API is an open data API from mcw.edu. It needs no API key. It is served over plain HTTP. Its OpenAPI description documents 100 endpoints.
At a glance
- Authentication
- No auth
- HTTPS
- No
- CORS
- Unknown
- Category
- Open Data
- Version
- 1.1
- Endpoints
- 100
- OpenAPI
- Specification ↗
- Spec updated
- 2021-06-21
Endpoints
| Method | Path | What it does |
|---|---|---|
| GET | /agr/affectedGenomicModels/{taxonId} | Get affected genomic models (rat strains with gene alleles) submitted by RGD to AGR by taxonId |
| GET | /agr/alleles/{taxonId} | Get gene allele records submitted by RGD to AGR by taxonId |
| GET | /agr/expression/{taxonId} | Get expression annotations submitted by RGD to AGR by taxonId |
| GET | /agr/phenotypes/{taxonId} | Get phenotype annotations submitted by RGD to AGR by taxonId |
| GET | /agr/variants/{taxonId} | Get basic variant records submitted by RGD to AGR by taxonId |
| GET | /agr/{taxonId} | Get gene records submitted by RGD to AGR by taxonId |
| POST | /annotations/ | Return a list of genes annotated to an ontology term |
| GET | /annotations/accId/{rgdId} | Returns a list ontology term accession IDs annotated to an rgd object |
| GET | /annotations/count/{accId}/{includeChildren} | Returns annotation count for ontology accession ID |
| GET | /annotations/count/{accId}/{speciesTypeKey}/{includeChildren} | Returns annotation count for ontology accession ID and speicies |
| GET | /annotations/count/{accId}/{speciesTypeKey}/{includeChildren}/{objectType} | Returns annotation count for ontology accession ID and object type |
| GET | /annotations/reference/{refRgdId} | Returns a list of annotations for a reference |
| GET | /annotations/rgdId/{rgdId} | Returns a list of annotations by RGD ID |
| GET | /annotations/rgdId/{rgdId}/{ontologyPrefix} | Returns a list of annotations by RGD ID and ontology prefix |
| GET | /annotations/{accId}/{rgdId} | Returns a list of annotations by RGD ID and ontology term accession ID |
| GET | /annotations/{accId}/{speciesTypeKey}/{includeChildren} | Returns a list annotations for an ontology term or a term and it's children |
| POST | /enrichment/annotatedGenes | 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 |
| POST | /enrichment/data | 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 |
| GET | /genes/affyId/{affyId}/{speciesTypeKey} | Return a list of genes for an affymetrix ID |
| GET | /genes/alias/{aliasSymbol}/{speciesTypeKey} | Return a list of genes for an alias and species |
| GET | /genes/allele/{rgdId} | Return a list of gene alleles |
| POST | /genes/annotation | Return a list of genes annotated to an ontology term |
| GET | /genes/annotation/{accId} | Return a list of genes annotated to an ontology term |
| GET | /genes/annotation/{accId}/{speciesTypeKey} | Return a list of genes annotated to an ontology term |
| GET | /genes/keyword/{keyword}/{speciesTypeKey} | Return a list of genes by keyword and species type key |
| GET | /genes/map/{mapKey} | Return a list of all genes with position information for an assembly |
| GET | /genes/mapped/{chr}/{start}/{stop}/{mapKey} | Return a list of genes position and map key |
| POST | /genes/orthologs | Return a list of gene orthologs |
| GET | /genes/orthologs/{rgdId} | Return a list of gene orthologs |
| GET | /genes/region/{chr}/{start}/{stop}/{mapKey} | Return a list of genes in region |
| GET | /genes/species/{speciesTypeKey} | Return a list of all genes for a species in RGD |
| GET | /genes/{chr}/{start}/{stop}/{mapKey} | Return a list of genes position and map key |
| GET | /genes/{rgdId} | Get a gene record by RGD ID |
| GET | /genes/{symbol}/{speciesTypeKey} | Get a gene record by symbol and species type key |
| GET | /lookup/geneTypes | Returns a list of gene types avialable in RGD |
| POST | /lookup/id/map/EnsemblGene | Translate RGD IDs to Ensembl Gene IDs |
| GET | /lookup/id/map/EnsemblGene/{rgdId} | Translate an RGD ID to an Ensembl Gene ID |
| POST | /lookup/id/map/EnsemblProtein | Translate RGD IDs to Ensembl Protein IDs |
| GET | /lookup/id/map/EnsemblProtein/{rgdId} | Translate an RGD ID to an Ensembl Protein ID |
| POST | /lookup/id/map/EnsemblTranscript | Translate RGD IDs to Ensembl Transcript IDs |
| GET | /lookup/id/map/EnsemblTranscript/{rgdId} | Translate an RGD ID to an Ensembl Transcript ID |
| POST | /lookup/id/map/GTEx | Translate RGD IDs to GTEx IDs |
| GET | /lookup/id/map/GTEx/{rgdId} | Translate an RGD ID to an GTEx ID |
| POST | /lookup/id/map/GenBankNucleotide | Translate RGD IDs to GenBank Nucleotide IDs |
| GET | /lookup/id/map/GenBankNucleotide/{rgdId} | Translate an RGD ID to a GenBank Nucleotide ID |
| POST | /lookup/id/map/GenBankProtein | Translate RGD IDs to GenBank Protein IDs |
| GET | /lookup/id/map/GenBankProtein/{rgdId} | Translate an RGD ID to a GenBank Protein ID |
| POST | /lookup/id/map/HGNC | Translate RGD IDs to HGNC IDs |
| GET | /lookup/id/map/HGNC/{rgdId} | Translate an RGD ID to an HGNC ID |
| POST | /lookup/id/map/MGI | Translate RGD IDs to MGI IDs |
| GET | /lookup/id/map/MGI/{rgdId} | Translate an RGD ID to an MGI ID |
| POST | /lookup/id/map/NCBIGene | Translate RGD IDs to NCBI Gene IDs |
| GET | /lookup/id/map/NCBIGene/{rgdId} | Translate an RGD ID to an NCBI Gene ID |
| POST | /lookup/id/map/UniProt | Translate RGD IDs to UniProt IDs |
| GET | /lookup/id/map/UniProt/{rgdId} | Translate an RGD ID to a UniProt ID |
| GET | /lookup/maps/{speciesTypeKey} | Return a list assembly maps for a species |
| GET | /lookup/speciesTypeKeys | Return a Map of species type keys available in RGD |
| GET | /lookup/standardUnit/{accId} | Return a standardUnit for an ontology if it exists |
| GET | /maps/chr/{chromosome}/{mapKey} | Return a list of chromosomes |
| GET | /maps/chr/{mapKey} | Return a list of chromosomes |
| GET | /maps/{speciesTypeKey} | Return a list of assemblies |
| GET | /ontology/ont/{accId} | Returns child and parent terms for Accession ID |
| GET | /ontology/term/{accId1}/{accId2} | Returns true or false for terms |
| GET | /ontology/term/{accId} | Returns term for Accession ID |
| GET | /pathways/diagrams/search/{searchString} | Return a list of pathways based on search term |
| GET | /pathways/diagramsForCategory/{category} | Return a list of pathways based on category provided |
| GET | /phenotype/phenominer/chart/{speciesTypeKey}/{refRgdId}/{termString} | Return a list of quantitative phenotypes values based on a combination of Clinical Measurement, Experimental Condition, Rat Strain, and/or Measurement Method on |
| GET | /phenotype/phenominer/chart/{speciesTypeKey}/{termString} | Return a list of quantitative phenotypes values based on a combination of Clinical Measurement, Experimental Condition, Rat Strain, and/or Measurement Method on |
| GET | /qtls/mapped/{chr}/{start}/{stop}/{mapKey} | Returns a list QTL for given position and assembly map |
| GET | /qtls/{chr}/{start}/{stop}/{mapKey} | Returns a list QTL for given position and assembly map |
| GET | /qtls/{rgdId} | Return a QTL for provided RGD ID |
| GET | /sslps/mapped/{chr}/{start}/{stop}/{mapKey} | Returns a list SSLP for given position and assembly map |
| GET | /stats/count/activeObject/{speciesTypeKey}/{dateYYYYMMDD} | Count of active objects by type, for specified species and date |
| GET | /stats/count/geneType/{speciesTypeKey}/{dateYYYYMMDD} | Count of gene types, for specified species and date |
| GET | /stats/count/objectStatus/{speciesTypeKey}/{dateYYYYMMDD} | Count of objects with given status, for specified species and date |
| GET | /stats/count/objectWithRefSeq/{speciesTypeKey}/{dateYYYYMMDD} | Count of objects with reference sequence(s), by object type, for specified species and date |
| GET | /stats/count/objectWithReference/{speciesTypeKey}/{dateYYYYMMDD} | Count of objects with reference, by object type, for specified species and date |
| GET | /stats/count/objectWithXdb/{speciesTypeKey}/{objectKey}/{dateYYYYMMDD} | Count of objects with external database ids, by database id, for specified species, object type and date |
| GET | /stats/count/proteinInteraction/{speciesTypeKey}/{dateYYYYMMDD} | Count of protein interactions, for specified species and date |
| GET | /stats/count/qtlInheritanceType/{speciesTypeKey}/{dateYYYYMMDD} | Count of strains, by qtl inheritance type, for specified species and date |
| GET | /stats/count/retiredObject/{speciesTypeKey}/{dateYYYYMMDD} | Count of retired objects by type, for specified species and date |
| GET | /stats/count/strainType/{speciesTypeKey}/{dateYYYYMMDD} | Count of strain types, for specified species and date |
| GET | /stats/count/withdrawnObject/{speciesTypeKey}/{dateYYYYMMDD} | Count of withdrawn objects by type, for specified species and date |
| GET | /stats/count/xdb/{speciesTypeKey}/{dateYYYYMMDD} | Count of external database ids, for specied species and date |
| GET | /stats/diff/activeObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of active objects, by type, for specified species and date range |
| GET | /stats/diff/geneType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of gene types, for specified species and date range |
| GET | /stats/diff/objectStatus/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of objects with given status, for specified species and date range |
| GET | /stats/diff/objectWithRefSeq/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of objects with reference sequence(s), by object type, for specified species and date range |
| GET | /stats/diff/objectWithReference/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of objects with reference, by object type, for specified species and date range |
| GET | /stats/diff/objectWithXdb/{speciesTypeKey}/{objectKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of objects with external database ids, by database id, for specified species, object type and date range |
| GET | /stats/diff/proteinInteraction/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of protein interactions, for specified species and date range |
| GET | /stats/diff/qtlInheritanceType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of strains, by qtl inheritance type, for specified species and date range |
| GET | /stats/diff/retiredObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of retired objects, by type, for specified species and date range |
| GET | /stats/diff/strainType/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of strain types, for specified species and date range |
| GET | /stats/diff/withdrawnObject/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of withdrawn objects, by type, for specified species and date range |
| GET | /stats/diff/xdb/{speciesTypeKey}/{dateFromYYYYMMDD}/{dateToYYYYMMDD} | Count difference of external database ids, for specified species and date range |
| GET | /stats/term/{accId}/{filterAccId} | getTermStats |
| GET | /strains/all | Return all active strains in RGD |
| GET | /strains/{chr}/{start}/{stop}/{mapKey} | Return all active strains by position |
| GET | /strains/{rgdId} | Return a strain by RGD ID |
Questions
Does the Rat Genome Database REST API API need an API key?
No. The Rat Genome Database REST API API can be called without an API key or sign-up, which makes it handy for prototypes and front-end demos.
Does the Rat Genome Database REST API API support HTTPS?
The Rat Genome Database REST API API is listed as HTTP only, so avoid sending secrets to it.
How many endpoints does the Rat Genome Database REST API API have?
Its OpenAPI description lists 100 endpoints in version 1.1. All of them are shown on this page.
What are alternatives to the Rat Genome Database REST API API?
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