openapi: 3.0.3 info: version: 2.1.7 title: BridgeDb Webservices description: |- These are the [BridgeDb Webservices](https://github.com/bridgedb/BridgeDbWebservice) for identifier to identifier mapping. license: name: Apache 2.0 url: http://www.apache.org/licenses/LICENSE-2.0.html servers: - url: https://webservice.bridgedb.org/ tags: - name: mappings description: Identifier mapping services for gene products (e.g. genes, RNA, proteins), metabolites, nutrients, hormones, vitamins, drugs, peptides, and chemical compounds from the exposome - name: organism description: Services to find details for the organism identifier mappings - name: search description: Services to find identifiers - name: attributes description: Services to get and search attributes paths: /{organism}/xrefs/{systemCode}/{identifier}: get: tags: - mappings summary: Returns a list of xrefs description: Returns a list of xrefs that map to a given identifier, data source, and organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: systemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' - name: identifier in: path required: true description: source identifier schema: type: string responses: 200: description: Returns a tab-delimited list of xrefs that map to a given identifier content: text/plain: schema: type: string application/json: schema: type: object /{organism}/xrefsBatch: post: tags: - mappings description: Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' requestBody: content: text/plain: schema: $ref: '#/components/schemas/XrefBatchInput' responses: 200: description: Returns a tab-delimited list of xrefs that map to a given identifier content: text/plain: schema: type: string application/json: schema: type: object /{organism}/xrefsBatch/{systemCode}: post: tags: - mappings description: Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: systemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' requestBody: content: text/plain: schema: $ref: '#/components/schemas/XrefBatchInput' responses: 200: description: Returns a tab-delimited list of xrefs that map to a given identifier content: text/plain: schema: type: string application/json: schema: type: object /{organism}/xrefExists/{systemCode}/{identifier}: get: tags: - search description: Returns a list of xrefs, that maps to a given list of identifiers to a given data source and organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: systemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' - name: identifier in: path required: true description: source identifier schema: type: string responses: 200: description: Returns a tab-delimited list of xrefs that map to a given identifier content: text/plain: schema: type: string application/json: schema: type: object /{organism}/search/{query}: get: tags: - search description: Returns a list of xrefs with identifiers that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: query in: path required: true example: 1234 description: identifier query schema: type: string responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: string application/json: schema: type: object /{organism}/attributeSearch/{query}: get: tags: - attributes description: Returns a list of xrefs and associated attributes that contain the query string for a given organism. Results are not restricted to exact matches. Optionally limit results to a specified number per data source, or by the type of attribute. See possible attribute types via /{organism}/attributeSet. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: query in: path required: true example: 1234 description: identifier query schema: type: string responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: string application/json: schema: type: object /{organism}/properties: get: tags: - organism description: Returns the list of properties available for a given organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: string application/json: schema: type: object /{organism}/sourceDataSources: get: tags: - organism description: Returns a list of data sources available as xref sources for a given organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: string application/json: schema: type: object /{organism}/targetDataSources: get: tags: - organism description: Returns a list of data sources available as xref sources for a given organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: string application/json: schema: type: object /{organism}/isFreeSearchSupported: get: tags: - organism description: Returns true or false based on whether or not /{organism}/search/{query} is supported for a given organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: boolean application/json: schema: type: object /{organism}/isMappingSupported/{sourceSystemCode}/{targetSystemCode}: get: tags: - organism description: Returns true or false based on whether or not /{organism}/search/{query} is supported for a given organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: sourceSystemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' - name: targetSystemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' responses: 200: description: Returns true or false based on whether or not /{organism}/xrefs/{systemCode}/{identifier} would possibly return a {targetSystemCode} result given a {sourceSystemCode} query. This function basically combines the results of /{organism}/sourceDataSources and /{organism}/targetDataSources into a single boolean result. content: text/plain: schema: type: boolean application/json: schema: type: object /{organism}/attributeSet: get: tags: - organism description: Returns the supported attributes to the given Organism. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' responses: 200: description: Returns a tab-delimited list of xrefs that match to a given query content: text/plain: schema: type: boolean application/json: schema: type: object /{organism}/attributes/{systemCode}/{identifier}: get: tags: - attributes description: Returns the attributes for a given identifier, data source, organism. Optionally display only a specified attribute. parameters: - name: organism in: path required: true description: Organism (Latin name or short name). schema: $ref: '#/components/schemas/Organism' - name: systemCode in: path required: true description: system code for the source database schema: $ref: '#/components/schemas/SystemCode' - name: identifier in: path required: true description: source identifier schema: type: string responses: 200: description: Returns a tab-delimited list with the attributes and their content content: text/plain: schema: type: boolean application/json: schema: type: object components: schemas: SystemCode: type: string description: System code as used by BridgeDb, see [this list](https://www.bridgedb.org/pages/system-codes.html). default: En enum: - En - Cs - X - E - Rh - Ck - Eco - Cg - Ch - Il - Uc - Rf - Pd - U - Ma - Lm - Wd - Wi - Cpc - Mb - Rk - Ce - S - L - Wg - Om - T - Mc - Ik - H - Re - Ag - Q - Ca - Up - Cks Organism: type: string default: Human enum: - Human - Homo sapiens - Tuberculosis - Mycobacterium tuberculosis - Mosquito - Anopheles gambiae - Zebra fish - Danio rerio - Arabidopsis thaliana - Rice - Oryza sativa - Sea Squirt - Ciona intestinalis - Barley - Hordeum vulgare - Frog - Xenopus tropicalis - Soybean - Glycine max - Fruit fly - Drosophila melanogaster - Horse - Equus caballus - Rhesus Monkey - Macaca mulatta - Wine Grape - Vitis vinifera - Yeast - Saccharomyces cerevisiae - Tomato - Solanum lycopersicum - Rat - Rattus norvegicus - Cow - Bos taurus - Western Balsam Poplar - Populus trichocarpa - Chimpanzee - Pan troglodytes - Indian Rice - Oryza indica - Dog - Canis familiaris - Maize - Zea mays - Pig - Sus scrofa - Worm - Caenorhabditis elegans - Platypus - Ornithorhynchus anatinus - Chicken - Gallus gallus - Fusarium graminearum - Gibberella zeae - Bacillus subtilis - Escherichia coli - Black mold - Aspergillus niger - Mouse - Mus musculus XrefBatchInput: type: string description: TAB separated values with one identifier/system code combination per line example: |- Q90038963 Wd P0DTD1-PRO_0000449625 S ENSMUSG00000032462 En