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Shima Dastgheib
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mygene spec compatible with openapi+smartAPI schema
mygene.info spec compatible with openapi+smartAPI schema
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‎spec-files/mygene_opanapi.json

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{
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"openapi": "string",
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"info": {
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"version": "3.0.0.2",
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"title": "MyGene.info API",
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"description": "Documentation of the MyGene.info Gene Query web services. Learn more about [MyGene.info](http://mygene.info/)",
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"termsOfService": "http://example.com/terms/",
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"contact": {
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"name": "Chunlei Wu",
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"x-role": "responsible developer",
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"email": "[email protected]",
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"x-id": "http://orcid.org/0000-0002-2629-6124"
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},
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"x-accessRestriction": "none",
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"x-maturity": "production",
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"x-implementationLanguage": "python"
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},
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"externalDocs": {
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"description": "Find more info here",
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"url": "https://example.com"
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},
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"x-externalResource": [
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{
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"x-url": "http://example.org/api/docs",
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"x-type": "api documentation"
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},
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{
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"x-url": "https://doi.org/10.1093/nar/gks1114",
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"x-type": "publication",
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"x-description": "BioGPS and MyGene.info: organizing online, gene-centric information"
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},
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{
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"x-url": "http://twitter.com/mygeneinfo",
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"x-type": "social media"
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}
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],
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"servers": [{
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"url": "http://mygene.info",
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"description": "Development server",
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"x-___location": "California, USA"
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}],
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"tags": [
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{
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"name": "http://purl.bioontology.org/ontology/MESH/D005796",
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"description": "Genes"
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}
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],
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"components": {
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"schemas": {
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"Category": {
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"type": "object",
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"properties": {
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"id": {
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"type": "integer",
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"format": "int64"
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},
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"name": {
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"type": "string"
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}
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}
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},
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"Tag": {
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"type": "object",
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"properties": {
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"id": {
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"type": "integer",
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"format": "int64"
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},
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"name": {
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"type": "string"
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}
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}
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}
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},
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"parameters": {
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"skipParam": {
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"name": "skip",
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"in": "query",
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"description": "number of items to skip",
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"required": true,
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"schema": {
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"type": "integer",
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"format": "int32"
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}
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},
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"limitParam": {
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"name": "limit",
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"in": "query",
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"description": "max records to return",
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"required": true,
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"schema": {
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"type": "integer",
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"format": "int32"
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}
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}
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},
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"responses": {
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"NotFound": {
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"description": "Entity not found."
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},
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"IllegalInput": {
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"description": "Illegal input for operation."
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}
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},
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"securitySchemes": {
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"api_key": {
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"type": "apiKey",
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"name": "api_key",
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"in": "header"
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},
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"petstore_auth": {
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"type": "oauth2",
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"flows": {
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"implicit": {
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"authorizationUrl": "http://example.org/api/oauth/dialog",
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"scopes": {
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"write:pets": "modify genes in your account",
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"read:pets": "read your genes"
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}
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}
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}
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}
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}
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},
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"paths": {
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"/query": {
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"get": {
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"description": "Makes gene query and returns matching gene list.",
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"summary": "Makes gene query and returns matching gene list.",
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"x-accessRestriction": "free",
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"parameters": [
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{
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"name": "q",
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"in": "query",
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"description": "Query string. Examples \"CDK2\", \"NM_052827\", \"204639_at\". The detailed query syntax can be found at http://docs.mygene.info/en/latest/doc/query_service.html",
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"required": true,
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"schema": {
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"type": "string"
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},
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"x-parameterType": "InputParameter",
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"x-valueType": [
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"http://identifiers.org/hgnc.symbol",
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"http://identifiers.org/refseq",
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"http://identifiers.org/unigene",
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"http://identifiers.org/uniprot",
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"http://identifiers.org/pdb' x-defaultValue: CDK2 x-exampleValue: CDK2 operationId: queryGene responses: responses: "
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]
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}
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],
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"operationId": "add operation id here",
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"responses": {
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"200": {
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"description": "Successful response.",
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"content": {
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"application/json": {
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"x-responseProfile": "http://www.w3.org/ns/anno.jsonld",
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"x-responseValueType": [
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{
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"path": "a.id",
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"valueType": "http://example.org/a.id"
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},
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{
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"path": "a.b.c.id",
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"valueType": "http://example.org/c.id"
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}
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]
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}
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}
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}
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}
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}
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},
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"/gene/{geneid}": {
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"get": {
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"tags": [
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"gene"
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],
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"parameters": [
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{
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"name": "geneid",
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"in": "path",
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"description": "Entrez or Ensembl gene id, e.g., 1017, ENSG00000170248. A retired Entrez Gene id works too if it is replaced by a new one, e.g., 245794",
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"required": true,
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"x-parameterType": "InputParameter",
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"x-valueType": [
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"http://identifiers.org/ncbigene",
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"http://identifiers.org/ensembl"
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],
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"x-defaultValue": "add default",
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"x-exampleValue": "1017"
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}
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],
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"operationId": "getAnnotation",
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"summary": "add summary",
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"responses": {
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"200": {
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"description": "Successful response",
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"content": {
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"application/json": {
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"x-responseSchema": {
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"properties": {
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"reporter": {
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"properties": {
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"HTA-2_0": {
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"type": "string"
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},
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"HG-U133_Plus_2": {
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"items": {
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"type": "string"
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},
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"type": "array"
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},
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"HuEx-1_0": {
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"type": "integer"
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},
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"HuGene-1_1": {
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"type": "integer"
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},
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"HuGene-2_1": {
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"type": "integer"
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},
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"HG-U95Av2": {
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"items": {
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"type": "string"
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},
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"type": "array"
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}
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},
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"type": "object"
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}
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}
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},
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"x-responseValueType": [
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{
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"path": "ec",
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"valueType": "http://identifiers.org/ec-code/"
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},
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{
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"path": "ensembl.gene",
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"valueType": "http://identifiers.org/ensembl/"
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},
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{
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"path": "ensembl.translation.protein",
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"valueType": "http://identifiers.org/ensembl/"
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},
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{
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"path": "ensembl.translation.rna",
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"valueType": "http://identifiers.org/ensembl/"
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},
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{
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"path": "entrezgene",
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"valueType": "http://identifiers.org/ncbigene/"
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},
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{
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"path": "generif.pubmed",
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"valueType": "http://identifiers.org/pubmed/"
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}
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]
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}
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}
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}
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}
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}
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}
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}
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}

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