diff --git a/.github/workflows/docker-build-push-ghcr.yml b/.github/workflows/docker-build-push-ghcr.yml index 43a2486..4e6b02c 100644 --- a/.github/workflows/docker-build-push-ghcr.yml +++ b/.github/workflows/docker-build-push-ghcr.yml @@ -7,7 +7,8 @@ name: Docker-ghcr on: push: - branches: [ "dev", "staging", "main", local-dev ] + branches: [ "dev", "staging", "main", local-stg ] + # Publish semver tags as releases. tags: [ 'v*.*.*' ] diff --git a/public/docs/bioactivity.json b/public/docs/bioactivity.json index 8c5b635..4fc8110 100644 --- a/public/docs/bioactivity.json +++ b/public/docs/bioactivity.json @@ -7,8 +7,8 @@ }, "servers": [ { - "url": "https://ctx-api-dev.ccte.epa.gov", - "description": "Development Environment" + "url": "https://ctx-api-stg.ccte.epa.gov", + "description": "Staging Environment" } ], "tags": [ diff --git a/public/docs/bioactivity.yaml b/public/docs/bioactivity.yaml index f85a683..2cea930 100644 --- a/public/docs/bioactivity.yaml +++ b/public/docs/bioactivity.yaml @@ -1,25 +1,394 @@ -openapi: 3.0.1 +--- +openapi: 3.1.0 info: title: Computational Toxicology and Exposure Data APIs - Bioactivity - description: >- - The Bioactivity APIs are part of a set of public computational toxicology - and exposure APIs and provide bioactivity data through a set of API - endpoints. + description: The Bioactivity APIs are part of a set of public computational toxicology + and exposure APIs and provide bioactivity data through a set of API endpoints. version: 1.0.0 servers: - - url: https://api-ccte-stg.epa.gov + - url: https://ctx-api-stg.ccte.epa.gov description: Production Environment tags: + - name: Assay Search Resource + description: API endpoints for searching assays (starts-with, exact, contains. - name: Bioactivity Assay Resource description: API endpoints for collecting Assay annotations. + - name: Analytical QC Resource + description: API endpoints for Analytical QC data. - name: Bioactivity Data Resource description: API endpoints for collecting bioactivity data. + - name: Bioactivity AOP Data Resource + description: API endpoints for collecting bioactivity AOP data. paths: - /bioactivity/data/summary/search/by-aeid/{aeid}: + "/bioactivity/data/search/by-spid/": + post: + tags: + - Bioactivity Data Resource + summary: Find bioactivity data by batch of spids + description: return bioactivity data for requested spids. + operationId: batchSearchDataBySpid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["EPAPLT0232A03","TP0000311A04"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" + security: + - api_key: [] + "/bioactivity/data/search/by-m4id/": + post: + tags: + - Bioactivity Data Resource + summary: Find bioactivity data by batch of m4ids + description: return bioactivity data for requested m4ids. + operationId: batchSearchDataByM4id + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["1135145","394876"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" + security: + - api_key: [] + "/bioactivity/data/search/by-dtxsid/": + post: + tags: + - Bioactivity Data Resource + summary: Find bioactivity data by batch of dtxsids + description: return bioactivity data for requested dtxsids. + operationId: batchSearchDataByDtxsid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID9026974","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" + security: + - api_key: [] + "/bioactivity/data/search/by-aeid/": + post: + tags: + - Bioactivity Data Resource + summary: Find bioactivity data by batch of aeids + description: return bioactivity data for requested aeids. + operationId: batchSearchDataByAeid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["3032","755"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" + security: + - api_key: [] + "/bioactivity/data/aed/search/by-dtxsid": + post: + tags: + - Bioactivity Data Resource + - bioactivity + - data + summary: Batch fetch AED data by DTXSIDs + description: Returns AED bioactivity data for a list of DTXSIDs + operationId: getAedDataForBatchDtxsids + requestBody: + description: List of DTXSIDs + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + "$ref": "#/components/schemas/AedData" + security: + - api_key: [] + "/bioactivity/assay/search/by-aeid/": + post: + tags: + - Bioactivity Assay Resource + summary: Find assay annotations by batch of aeids + description: return assay annotations for requested aeids. + operationId: batchSearchAssayByAeid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["111","3032"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/AssayAll" + security: + - api_key: [] + "/bioactivity/search/start-with/{value}": + get: + tags: + - Assay Search Resource + summary: Search by starting value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: assayStartWith + parameters: + - name: value + in: path + description: Starting characters for search value + required: true + schema: + type: string + examples: + Search Value: + description: Search Value + value: ATG_S + - name: top + in: query + required: false + schema: + type: integer + format: int32 + default: 500 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SearchAssay" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/bioactivity/search/equal/{value}": + get: + tags: + - Assay Search Resource + summary: Search by exact value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: assayEqual + parameters: + - name: value + in: path + description: Exact match of search value + required: true + schema: + type: string + examples: + Search Value: + description: Search Value + value: ATG_STAT3_CIS + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SearchAssay" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/bioactivity/search/contain/{value}": + get: + tags: + - Assay Search Resource + summary: Search by substring value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: assayContain + parameters: + - name: value + in: path + description: Substring of search word + required: true + schema: + type: string + examples: + Search Value: + description: Search Value + value: AT3_CIS + Synonym: + description: Synonym + value: razine + - name: top + in: query + required: false + schema: + type: integer + format: int32 + default: 0 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SearchAssay" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/bioactivity/data/summary/search/by-tissue/": + get: + tags: + - Bioactivity Data Resource + - bioactivity + - data + summary: Get summary by dtxsid + description: Return summary data for given dtxsid + operationId: summaryByDtxsidAndTissue + parameters: + - name: dtxsid + in: query + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7024241 + - name: tissue + in: query + description: Tissue of origin + required: true + schema: + type: string + example: liver + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SummaryByTissue" + security: + - api_key: [] + "/bioactivity/data/summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - Bioactivity Data Resource + - bioactivity + - data + summary: Get summary by dtxsid + description: Return summary data for given dtxsid + operationId: summaryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID9026974 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalAgg" + security: + - api_key: [] + "/bioactivity/data/summary/search/by-aeid/{aeid}": get: tags: - Bioactivity Data Resource + - bioactivity + - data summary: Get summary by aeid + description: Return summary data for given aeid operationId: summaryByAeid parameters: - name: aeid @@ -29,21 +398,26 @@ paths: schema: type: integer format: int32 - example: 1386 + example: 3032 responses: '200': description: OK content: - application/hal+json: + application/json: schema: - $ref: '#/components/schemas/AssayListCount' + type: string + oneOf: + - "$ref": "#/components/schemas/AssayListCount" security: - api_key: [] - /bioactivity/data/search/by-spid/{spid}: + "/bioactivity/data/search/by-spid/{spid}": get: tags: - Bioactivity Data Resource + - bioactivity + - data summary: Get data by spid + description: Return data for given spid operationId: dataBySpid parameters: - name: spid @@ -52,23 +426,26 @@ paths: required: true schema: type: string - example: spid + example: EPAPLT0232A03 responses: '200': description: OK content: - application/hal+json: + application/json: schema: type: array items: - type: object + "$ref": "#/components/schemas/BioactivityDataAll" security: - api_key: [] - /bioactivity/data/search/by-m4id/{m4id}: + "/bioactivity/data/search/by-m4id/{m4id}": get: tags: - Bioactivity Data Resource + - bioactivity + - data summary: Get data by m4id + description: Return single data row for given m4id operationId: dataByM4Id parameters: - name: m4id @@ -78,21 +455,26 @@ paths: schema: type: integer format: int32 - example: 392006 + example: 1135145 responses: '200': description: OK content: - application/hal+json: + application/json: schema: - $ref: '#/components/schemas/BioactivityDataBase' + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" security: - api_key: [] - /bioactivity/data/search/by-dtxsid/{dtxsid}: + "/bioactivity/data/search/by-dtxsid/{dtxsid}": get: tags: - Bioactivity Data Resource - summary: Get data by dtxsid + - bioactivity + - data + summary: Get data by dtxsid with or without projection + description: Return data for given DTXSID operationId: dataByDtxsid parameters: - name: dtxsid @@ -101,23 +483,35 @@ paths: required: true schema: type: string - example: DTXSID0021125 + example: DTXSID7020182 + - name: projection + in: query + description: 'Specifies if projection is used. Option: toxcast-summary-plot. + If omitted, the default BioactivityDataAll data is returned.' + required: false + schema: + type: string responses: '200': description: OK content: - application/hal+json: + application/json: schema: type: array items: - type: object + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityDataAll" security: - api_key: [] - /bioactivity/data/search/by-aeid/{aeid}: + "/bioactivity/data/search/by-aeid/{aeid}": get: tags: - Bioactivity Data Resource + - bioactivity + - data summary: Get data by aeid + description: Return data for given aeid operationId: dataByAeid parameters: - name: aeid @@ -127,23 +521,109 @@ paths: schema: type: integer format: int32 - example: 1386 + example: 3032 responses: '200': description: OK content: - application/hal+json: + application/json: schema: type: array items: - type: object + "$ref": "#/components/schemas/BioactivityDataAll" + security: + - api_key: [] + "/bioactivity/data/aed/search/by-dtxsid/{dtxsid}": + get: + tags: + - Bioactivity Data Resource + - bioactivity + - data + summary: Get AED data by dtxsid + description: Returns AED data for given DTXSID + operationId: getAedDataByDtxsid + parameters: + - name: dtxsid + in: path + required: true + schema: + type: string + example: DTXSID5021209 + responses: + '200': + description: OK + content: + application/json: + schema: + "$ref": "#/components/schemas/AedData" + security: + - api_key: [] + "/bioactivity/assay/single-conc/search/by-aeid/{aeid}": + get: + tags: + - Bioactivity Assay Resource + summary: Get single conc data by aeid + operationId: singleConcDataByAeid + parameters: + - name: aeid + in: path + description: Numeric assay endpoint identifier + required: true + schema: + type: integer + format: int32 + example: 3032 + - name: projection + in: query + required: false + schema: + type: string + default: single-conc + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CcdSingleConcData" + security: + - api_key: [] + "/bioactivity/assay/search/by-gene/{geneSymbol}": + get: + tags: + - Bioactivity Assay Resource + summary: Get assay endpoints list + operationId: assayEndpointsListByGene + parameters: + - name: geneSymbol + in: path + description: Gene Symbol + required: true + schema: + type: string + example: TUBA1A + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/AssayEndpointsList" security: - api_key: [] - /bioactivity/assay/search/by-aeid/{aeid}: + "/bioactivity/assay/search/by-aeid/{aeid}": get: tags: - Bioactivity Assay Resource - summary: Get annotation by aeid + summary: Get assay data by aeid with projections + description: 'Fetches assay data based on the specified projection. Available + projections: ccd-assay-annotation, ccd-assay-gene, ccd-assay-citations, ccd-assay-tcpl, + ccd-assay-reagents, assay-all. If no projection is specified, the default + full assay data will be returned.' operationId: assayByAeid parameters: - name: aeid @@ -153,57 +633,1409 @@ paths: schema: type: integer format: int32 - example: 1386 + example: 3032 + - name: projection + in: query + description: 'Specifies which projection to use. Options: ccd-assay-annotation, + ccd-assay-gene, ccd-assay-citations, ccd-assay-tcpl, ccd-assay-reagents, + assay-all. If omitted, the full assay data is returned.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/AssayAnnotation" + - "$ref": "#/components/schemas/CcDAssayAnnotation" + - "$ref": "#/components/schemas/CcdAssayGene" + - "$ref": "#/components/schemas/CcdAssayCitation" + - "$ref": "#/components/schemas/CcdTcplData" + - "$ref": "#/components/schemas/CcdReagents" + '400': + description: Invalid projection type + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + '404': + description: No data found for the given aeid + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/bioactivity/assay/count": + get: + tags: + - Bioactivity Assay Resource + summary: Get count of all available assays + operationId: assayCount + responses: + '200': + description: OK + content: + application/json: + schema: + type: integer + format: int64 + security: + - api_key: [] + "/bioactivity/assay/chemicals/search/by-aeid/{aeid}": + get: + tags: + - Bioactivity Assay Resource + summary: Get list of DTXSIDs by aeid + operationId: chemicalsByAeid + parameters: + - name: aeid + in: path + description: Numeric assay endpoint identifier + required: true + schema: + type: integer + format: int32 + example: 3032 responses: '200': description: OK content: - application/hal+json: + application/json: schema: - $ref: '#/components/schemas/AssayBase' + type: string + oneOf: + - "$ref": "#/components/schemas/BioactivityAgg" security: - api_key: [] - /bioactivity/assay/: + "/bioactivity/assay/": get: tags: - Bioactivity Assay Resource summary: Get all assays operationId: allAssays + parameters: + - name: projection + in: query + required: false + schema: + type: string + default: assay-all + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/AssayAnnotation" + security: + - api_key: [] + "/bioactivity/aop/search/by-toxcast-aeid/{toxcastAeid}": + get: + tags: + - Bioactivity AOP Data Resource + - aop + - bioactivity + summary: Get aop data by toxcast aeid + description: Return aop data for given toxcast aeid + operationId: dataByToxcastAeid + parameters: + - name: toxcastAeid + in: path + description: Toxcast Aeid + required: true + schema: + type: integer + format: int32 + example: 63 responses: '200': description: OK content: - application/hal+json: + application/json: schema: type: array items: - type: object + "$ref": "#/components/schemas/AOP" security: - api_key: [] -components: - schemas: - AssayListCount: - type: object - properties: + "/bioactivity/aop/search/by-event-number/{eventNumber}": + get: + tags: + - Bioactivity AOP Data Resource + - aop + - bioactivity + summary: Get aop data by event number + description: Return aop data for given event number + operationId: dataByEventNumber + parameters: + - name: eventNumber + in: path + description: Event Number + required: true + schema: + type: integer + format: int32 + example: 18 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + "$ref": "#/components/schemas/AOP" + security: + - api_key: [] + "/bioactivity/aop/search/by-entrez-gene-id/{entrezGeneId}": + get: + tags: + - Bioactivity AOP Data Resource + - aop + - bioactivity + summary: Get aop data by entrez gene id + description: Return aop data for given entrez gene id + operationId: dataByEntrezGeneId + parameters: + - name: entrezGeneId + in: path + description: Entrez Gene Id + required: true + schema: + type: integer + format: int32 + example: 196 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + "$ref": "#/components/schemas/AOP" + security: + - api_key: [] + "/bioactivity/analyticalqc/search/by-dtxsid/{dtxsid}": + get: + tags: + - Analytical QC Resource + summary: Get analytical QC data by DTXSID + operationId: findByDsstoxSubstanceId + parameters: + - name: dtxsid + in: path + required: true + schema: + type: string + responses: + '200': + description: Successful retrieval + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/AnalyticalQC" + '404': + description: Data not found + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" +components: + schemas: + BioactivityDataAll: + type: object + properties: aeid: + type: integer + format: int64 + maxMedConc: + type: number + format: double + nmedGtblPos: type: integer format: int32 + nmedGtblNeg: + type: integer + format: int32 + modelType: + type: integer + format: int32 + stkcUnit: + type: string + testedConcUnit: + type: string + mc3Param: + "$ref": "#/components/schemas/Mc3Param" + mc4Param: + type: object + additionalProperties: + type: number + mc6Param: + "$ref": "#/components/schemas/Mc6Param" + maxMeanConc: + type: number + format: double + mc5Param: + type: object + additionalProperties: + type: number + chnm: + type: string + spid: + type: string + dtxsid: + type: string + casn: + type: string + bmad: + type: number + format: double + respMin: + type: number + format: double + respMax: + type: number + format: double + m4id: + type: integer + format: int64 + chid: + type: integer + format: int32 + actp: + type: number + format: double + nrep: + type: number + format: double + stkc: + type: number + format: double + chidRep: + type: integer + format: int32 + maxMed: + type: number + format: double + hitc: + type: number + format: double + m5id: + type: integer + format: int64 + modl: + type: string + maxMean: + type: number + format: double + concMax: + type: number + format: double + fitc: + type: integer + format: int32 + coff: + type: number + format: double + concMin: + type: number + format: double + nconc: + type: integer + format: int32 + npts: + type: integer + format: int32 + Mc3Param: + type: object + properties: + conc: + type: array + items: + type: number + resp: + type: array + items: + type: number + Mc6Param: + type: object + properties: + flag: + type: array + items: + type: string + mc6MthdId: + type: array + items: + type: integer + format: int32 + AedData: + type: object + properties: + dtxsid: + type: string + preferredName: + type: string + aeid: + type: integer + format: int32 + aenm: + type: string + aedVal: + type: array + items: + type: number + format: double + aedType: + type: array + items: + type: string + httkModel: + type: array + items: + type: string + aedValUnit: + type: array + items: + type: string + httkVersion: + type: array + items: + type: string + potencyValType: + type: array + items: + type: string + invitrodbVersion: + type: array + items: + type: string + interindividualVarPerc: + type: array + items: + type: number + format: double + AssayAll: + type: object + properties: + dilutionSolventPercentMax: + type: number + format: double + assayComponentTargetDesc: + type: string + technologicalTargetTypeSub: + type: string + detectionTechnologyTypeSub: + type: string + assayName: + type: string + assayList: + type: array + items: + "$ref": "#/components/schemas/AssayList" + aeid: + type: integer + format: int64 + assayComponentName: + type: string + assayComponentEndpointName: + type: string + assayComponentEndpointDesc: + type: string + intendedTargetTypeSub: + type: string + intendedTargetFamilySub: + type: string + detectionTechnologyType: + type: string + detectionTechnology: + type: string + assayFormatTypeSub: + type: string + assayFunctionType: + type: string + intendedTargetType: + type: string + normalizedDataType: + type: string + parameterReadoutType: + type: string + biologicalProcessTarget: + type: string + technologicalTargetType: + type: string + keyPositiveControl: + type: string + contentReadoutType: + type: string + assayDesignTypeSub: + type: string + cellViabilityAssay: + type: integer + format: int32 + cellFreeComponentSource: + type: string + intendedTargetFamily: + type: string + keyAssayReagentType: + type: string + assaySourceLongName: + type: string + assayComponentDesc: + type: string + organism: + type: string + burstAssay: + type: integer + format: int32 + cellShortName: + type: string + assayFootprint: + type: string + dilutionSolvent: + type: string + assayDesignType: + type: string + keyAssayReagent: + type: string + citations: + type: array + items: + "$ref": "#/components/schemas/Citation" + timepointHr: + type: number + format: double + assayFormatType: + type: string + organismId: + type: integer + format: int32 + assayDesc: + type: string + cellFormat: + type: string + assaySourceName: + type: string + assaySourceDesc: + type: string + signalDirection: + type: string + cellGrowthMode: + type: string + asid: + type: integer + format: int32 + gene: + type: array + items: + "$ref": "#/components/schemas/Gene" + aid: + type: integer + format: int32 + tissue: + type: string + acid: + type: integer + format: int32 + AssayList: + type: object + properties: + name: + type: string + description: + type: string + Citation: + type: object + properties: + doi: + type: string + url: + type: string + pmid: + type: integer + format: int32 + title: + type: string + author: + type: string + citation: + type: string + otherId: + type: string + citationId: + type: integer + format: int32 + otherSource: + type: string + Gene: + type: object + properties: + geneId: + type: integer + format: int32 + geneName: + type: string + description: + type: string + geneSymbol: + type: string + organismId: + type: integer + format: int32 + trackStatus: + type: string + entrezGeneId: + type: integer + format: int32 + officialSymbol: + type: string + officialFullName: + type: string + uniprotAccessionNumber: + type: string + SearchAssay: + type: object + properties: + id: + type: integer + format: int32 + searchName: + type: string + maxLength: 50 + minLength: 0 + searchValue: + type: string + maxLength: 200 + minLength: 0 + searchValueDesc: + type: string + modifiedValue: + type: string + required: + - id + ProblemDetail: + type: object + properties: + type: + type: string + format: uri + title: + type: string + status: + type: integer + format: int32 + detail: + type: string + instance: + type: string + format: uri + properties: + type: object + additionalProperties: {} + SummaryByTissue: + type: object + properties: + intendedTargetFamily: + type: string + maxMedConc: + type: number + format: float + dtxsid: + type: string + tissue: + type: string + continuousHitCall: + type: number + format: float + cutOff: + type: number + format: float + ac50: + type: number + format: float + logAC50: + type: number + format: float + hitCall: + type: string + acc: + type: number + format: float + chemicalName: + type: string + ChemicalAgg: + type: object + properties: + dtxsid: + type: string + maxLength: 255 + minLength: 0 + activeMc: + type: integer + format: int32 + totalMc: + type: integer + format: int32 + activeSc: + type: integer + format: int32 + totalSc: + type: integer + format: int32 + cytotoxMedianRaw: + type: number + format: float + cytotoxMad: + type: number + format: float + globalMad: + type: number + format: float + cytotoxMedianLog: + type: number + format: float + cytotoxMedianUm: + type: number + format: float + cytotoxLowerUm: + type: number + format: float + cytotoxLowerLog: + type: number + format: float + ntested: + type: number + format: float + nhit: + type: number + format: float + AssayListCount: + type: object + description: US EPA's Toxicity Forecaster (ToxCast) program makes invitro medium- + and high-throughput screening assay data publicly available for prioritization + and hazard characterization.The summary endpoint returns the number of active + hits and total multi- and single-concentration chemicals tested for specific + ‘aeids’. For multi-concentration data, a continuous hit call value greater + than or equal to 0.9 is considered active, whereas values less than 0.9 are + considered inactive. For single concentration data, the hit call value is + binary where 1 is active and 0 is inactive. Multiple samples of the same chemical + may be tested for a given assay endpoint, and all samples per endpoint are + reflected in these counts. + properties: + aeid: + type: integer + format: int32 + description: Assay component endpoint ID activeMc: type: integer format: int64 + description: Number of active representative samples tested at multiple + concentrations per endpoint (aeid) totalMc: type: integer format: int64 + description: Total count of samples tested at multiple concentrations per + endpoint (aeid) activeSc: type: integer format: int64 + description: Number of active representative samples tested at single concentration + per endpoint (aeid) totalSc: type: integer format: int64 - BioactivityDataBase: + description: Total count of samples tested at single concentration per endpoint + (aeid) + CcdSingleConcData: type: object - AssayBase: + properties: + preferredName: + type: string + aeid: + type: integer + format: int32 + dtxsid: + type: string + casn: + type: string + bmad: + type: number + format: double + hitc: + type: number + format: double + s2id: + type: integer + format: int64 + coff: + type: number + format: double + maxMedVal: + type: number + format: double + endpointName: + type: string + AssayEndpointsList: + type: object + properties: + geneSymbol: + type: string + assayComponentEndpointName: + type: string + assayComponentEndpointDesc: + type: string + multiConcActives: + type: string + getsingleConcActive: + type: string + AssayAnnotation: + type: object + description: 'US EPA''s Toxicity Forecaster (ToxCast) program makes invitro + medium- and high-throughput screening assay data publicly available for prioritization + and hazard characterization. Given ToxCast includes a heterogeneous set of + assays across a diverse biological space, annotations in the database help + flexibly aggregate and differentiate processed data. The definition of an + “assay” is, in ToxCast, broken into 4 assay elements: assay source: the vendor/origination + of the data, assay: the procedure to generate the component data, assay component: + the raw data readout(s), assay component endpoint: the normalized component + data. The assay element annotations are often short in a standardized format + or use a controlled term list. Assay” resource endpoints provide assay metadata + for specific or all invitrodb ‘aeids’ (assay endpoint ids). These include + annotations from invitrodb’s assay, assay_component, assay_component_endpoint, + assay_list, assay_source, and gene tables, all returned in a by-aeid format. + Regular ToxCast/invitrodb users may find it easier to use the tcpl R package, + which has integrated to make API data retrievable in a familiar format. See + the tcpl vignette regarding data retrieval via API for more information.' + properties: + aeid: + type: integer + format: int64 + description: Assay component endpoint ID + assayComponentEndpointName: + type: string + description: Assay component endpoint name (abbreviated 'aenm' within the + package) + maxLength: 255 + minLength: 0 + assayComponentEndpointDesc: + type: string + description: Assay component endpoint description + assayFunctionType: + type: string + description: Description of targeted mechanism and the purpose of the analyzed + readout in relation to others from the same assay + maxLength: 255 + minLength: 0 + normalizedDataType: + type: string + description: Normalization approach for which the data is displayed + maxLength: 255 + minLength: 0 + burstAssay: + type: integer + format: int32 + description: Indicator if endpoint is included in the burst distribution + (1) or not (0); Burst phenomenon can describe confounding activity, such + as cytotoxicity due to non-specific activation of many targets at certain + concentrations + keyPositiveControl: + type: string + description: Tested chemical sample expected to produce activity; Used to + assess assay validity + maxLength: 255 + minLength: 0 + signalDirection: + type: string + description: Directionality of raw data signals from assay (gain or loss); + Defines analysis direction + maxLength: 255 + minLength: 0 + intendedTargetType: + type: string + description: General group of intended targets measured + maxLength: 255 + minLength: 0 + intendedTargetTypeSub: + type: string + description: Specific subgroup of intended targets measured + maxLength: 255 + minLength: 0 + intendedTargetFamily: + type: string + description: Family of intended target measured; Populated on ToxCast chemical + activity plot within CompTox dashboard + maxLength: 255 + minLength: 0 + intendedTargetFamilySub: + type: string + description: Specific subfamily of intended target measured + maxLength: 255 + minLength: 0 + cellViabilityAssay: + type: integer + format: int32 + description: Indicator of the impact of cytotoxicity in confounding (1) + or no cytotoxic impact (0) + acid: + type: integer + format: int32 + description: Assay component ID + assayComponentName: + type: string + description: Assay component name (abbreviated 'acnm' within the package) + maxLength: 255 + minLength: 0 + assayComponentDesc: + type: string + description: Assay component description + assayComponentTargetDesc: + type: string + description: Assay component target description. Generally includes information + about mechanism of action with assay target, how disruption is detected, + or significance of target disruption. + parameterReadoutType: + type: string + description: Description of parameters measured + maxLength: 255 + minLength: 0 + assayDesignType: + type: string + description: General description of the biological or physical process is + translated into a detectable signal by assay mechanism + maxLength: 255 + minLength: 0 + assayDesignTypeSub: + type: string + description: Specific description of method through which a biological or + physical process is translated into a detectable signal measured + maxLength: 255 + minLength: 0 + biologicalProcessTarget: + type: string + description: General biological process being chemically disrupted + maxLength: 255 + minLength: 0 + detectionTechnologyType: + type: string + description: General description of assay platform or detection signals + measured + maxLength: 255 + minLength: 0 + detectionTechnologyTypeSub: + type: string + description: Description of signals measured in assay platform + maxLength: 255 + minLength: 0 + detectionTechnology: + type: string + description: Specific description of assay platform used + maxLength: 255 + minLength: 0 + keyAssayReagentType: + type: string + description: Type of critical reactant being measured + maxLength: 255 + minLength: 0 + keyAssayReagent: + type: string + description: Critical reactant measured + maxLength: 255 + minLength: 0 + technologicalTargetType: + type: string + description: General description of technological target measured in assay + platform + maxLength: 255 + minLength: 0 + technologicalTargetTypeSub: + type: string + description: Specific description of technological target measured in assay + platform + maxLength: 255 + minLength: 0 + aid: + type: integer + format: int32 + description: Assay ID + assayName: + type: string + description: Assay name (abbreviated 'anm' within the package) + maxLength: 255 + minLength: 0 + assayDesc: + type: string + description: Assay description + timepointHr: + type: number + format: double + description: Treatment duration in hours + organismId: + type: integer + format: int32 + description: NCBI taxonomic identifier, available here https://www.ncbi.nlm.nih.gov/taxonomy + organism: + type: string + description: Organism of origin + maxLength: 255 + minLength: 0 + ncbiTaxonId: + type: integer + format: int32 + taxonName: + type: string + maxLength: 255 + minLength: 0 + commonName: + type: string + maxLength: 255 + minLength: 0 + lineage: + type: string + maxLength: 255 + minLength: 0 + tissue: + type: string + description: Tissue of origin + maxLength: 255 + minLength: 0 + cellFormat: + type: string + description: Description of cell format + maxLength: 255 + minLength: 0 + cellFreeComponentSource: + type: string + description: Description of source for targeted cell-free components + maxLength: 255 + minLength: 0 + cellShortName: + type: string + description: Abbreviation of cell line + maxLength: 255 + minLength: 0 + cellGrowthMode: + type: string + description: Cell growth modality + maxLength: 255 + minLength: 0 + assayFootprint: + type: string + description: Microtiter plate size + maxLength: 255 + minLength: 0 + assayFormatType: + type: string + description: General description of assay format + maxLength: 255 + minLength: 0 + assayFormatTypeSub: + type: string + description: Specific description of assay format + maxLength: 255 + minLength: 0 + contentReadoutType: + type: string + description: Description of well characteristics being measured + maxLength: 255 + minLength: 0 + dilutionSolvent: + type: string + description: Solvent used in sample dilution + maxLength: 255 + minLength: 0 + dilutionSolventPercentMax: + type: number + format: double + description: Maximum percent of dilution solvent used, from 0 to 1. + asid: + type: integer + format: int32 + description: Assay source ID + assaySourceName: + type: string + description: Assay source name (typically an abbreviation of the assay_source_long_name, + abbreviated 'asnm' within the package) + maxLength: 255 + minLength: 0 + assaySourceLongName: + type: string + description: Full assay source name + maxLength: 255 + minLength: 0 + assaySourceDesc: + type: string + description: Assay source description + maxLength: 255 + minLength: 0 + gene: + type: array + description: JSON object containing gene mappings + items: + "$ref": "#/components/schemas/Gene" + assayList: + type: array + description: JSON object containing curated groupings of endpoints anchored + by use in CCTE publications and/or projects + items: + "$ref": "#/components/schemas/AssayList" + citations: + type: array + description: JSON object containing references to assay-specific publications + describing assay design or results + items: + "$ref": "#/components/schemas/Citation" + mc2Methods: + type: array + description: JSON object containing Level 2 Multi-concentration (MC2) + items: + "$ref": "#/components/schemas/Mc2Method" + mc3Methods: + type: array + description: JSON object containing Level 3 Multi-concentration (MC3) normalized + concentration-response data + items: + "$ref": "#/components/schemas/Mc3Method" + mc4Methods: + type: array + description: JSON object containing Level 4 Multi-concentration (MC4) All + Models Fitting Parameters + items: + "$ref": "#/components/schemas/Mc4Method" + mc5Methods: + type: array + description: JSON object containing Level 5 Multi-concentration (MC5) Winning + Model Fitting Parameters + items: + "$ref": "#/components/schemas/Mc5Method" + mc6Methods: + type: array + description: JSON object containing Level 6 Multi-concentration (MC6) Flags + items: + "$ref": "#/components/schemas/Mc6Method" + sc1Methods: + type: array + items: + "$ref": "#/components/schemas/Sc1Method" + sc2Methods: + type: array + items: + "$ref": "#/components/schemas/Sc2Method" + Mc2Method: + type: object + properties: + desc: + type: string + mc2_mthd: + type: string + exec_ordr: + type: integer + format: int32 + mc2_mthd_id: + type: integer + format: int32 + Mc3Method: + type: object + properties: + desc: + type: string + mc3_mthd: + type: string + mc3_mthd_id: + type: integer + format: int32 + Mc4Method: + type: object + properties: + desc: + type: string + mc4_mthd: + type: string + mc4_mthd_id: + type: integer + format: int32 + Mc5Method: + type: object + properties: + desc: + type: string + mc5_mthd: + type: string + mc5_mthd_id: + type: integer + format: int32 + Mc6Method: + type: object + properties: + desc: + type: string + mc6_mthd: + type: string + mc6_mthd_id: + type: integer + format: int32 + Sc1Method: + type: object + properties: + desc: + type: string + sc1_mthd: + type: string + sc1_mthd_id: + type: integer + format: int32 + Sc2Method: + type: object + properties: + desc: + type: string + sc2_mthd: + type: string + sc2_mthd_id: + type: integer + format: int32 + CcDAssayAnnotation: + type: object + properties: + dilutionSolventPercentMax: + type: number + format: double + assayComponentTargetDesc: + type: string + technologicalTargetTypeSub: + type: string + detectionTechnologyTypeSub: + type: string + assayName: + type: string + aeid: + type: integer + format: int64 + assayComponentName: + type: string + assayComponentEndpointName: + type: string + assayComponentEndpointDesc: + type: string + intendedTargetTypeSub: + type: string + intendedTargetFamilySub: + type: string + detectionTechnologyType: + type: string + detectionTechnology: + type: string + assayFormatTypeSub: + type: string + assayFunctionType: + type: string + intendedTargetType: + type: string + normalizedDataType: + type: string + parameterReadoutType: + type: string + biologicalProcessTarget: + type: string + technologicalTargetType: + type: string + keyPositiveControl: + type: string + contentReadoutType: + type: string + assayDesignTypeSub: + type: string + cellFreeComponentSource: + type: string + intendedTargetFamily: + type: string + keyAssayReagentType: + type: string + assaySourceLongName: + type: string + assayComponentDesc: + type: string + organism: + type: string + burstAssay: + type: integer + format: int32 + cellShortName: + type: string + assayFootprint: + type: string + dilutionSolvent: + type: string + assayDesignType: + type: string + keyAssayReagent: + type: string + timepointHr: + type: number + format: double + assayFormatType: + type: string + assayDesc: + type: string + cellFormat: + type: string + assaySourceName: + type: string + assaySourceDesc: + type: string + signalDirection: + type: string + cellGrowthMode: + type: string + tissue: + type: string + toxCastAssayDescription: + type: string + CcdAssayGene: + type: object + properties: + entrezGeneId: + type: integer + format: int32 + geneSymbol: + type: string + geneName: + type: string + CcdAssayCitation: + type: object + properties: + url: + type: string + title: + type: string + aeid: + type: integer + format: int64 + assayComponentEndpointName: + type: string + author: + type: string + otherId: + type: string + doi: + type: string + pmid: + type: string + citation: + type: string + otherSource: + type: string + CcdTcplData: + type: object + properties: + methodName: + type: string + orderId: + type: integer + format: int32 + assayRunType: + type: string + levelApplied: + type: integer + format: int32 + description: + type: string + CcdReagents: + type: object + properties: + orderId: + type: integer + format: int32 + cultureOrAssay: + type: string + reagentType: + type: string + reagentValue: + type: string + BioactivityAgg: + type: object + properties: + aeid: + type: integer + format: int32 + description: Assay component endpoint ID + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id, also + known as DTXSID + maxLength: 255 + minLength: 0 + AOP: type: object + properties: + toxcastAeid: + type: integer + format: int32 + entrezGeneId: + type: integer + format: int32 + eventNumber: + type: integer + format: int32 + eventLink: + type: string + aopNumber: + type: integer + format: int32 + aopLink: + type: string + AnalyticalQC: + type: object + properties: + analyticalQcId: + type: integer + format: int64 + dtxsid: + type: string + chnm: + type: string + spid: + type: string + qcLevel: + type: string + t0: + type: string + t4: + type: string + call: + type: string + annotation: + type: string + flags: + type: string + averageMass: + type: string + log10VaporPressureOperaPred: + type: string + logkowOctanolWaterOperaPred: + type: string + exportDate: + type: string + format: date + dataVersion: + type: string + porCaution: + type: string Link: type: object properties: @@ -226,12 +2058,11 @@ components: Links: type: object additionalProperties: - $ref: '#/components/schemas/Link' + "$ref": "#/components/schemas/Link" securitySchemes: api_key: type: apiKey - description: >- - Each API call should have api_key, Contact author for getting the new - api_key. + description: 'Each API call should have api_key, Contact author for getting + the new api_key. ' name: x-api-key in: header diff --git a/public/docs/chemical.json b/public/docs/chemical.json index 56effe5..5e5b8f4 100644 --- a/public/docs/chemical.json +++ b/public/docs/chemical.json @@ -7,7 +7,7 @@ }, "servers": [ { - "url": "https://ctx-api-dev.ccte.epa.gov", + "url": "https://ctx-api-stg.ccte.epa.gov", "description": "Staging Environment" } ], @@ -39,62 +39,9 @@ { "name": "Lit Search Data Resource", "description": "Collection of endpoints containing extra chemical data pertaining to literature and patents." - }, - { - "name": "PubChem to GHS Classification Resource", - "description": "Collection of endpoints to check if GHS classification safety data in available in PubChem." - }, - { - "name": "Wikipedia to GHS Classification Resource", - "description": "Collection of endpoints to check if GHS classification safety data is available on Wikipedia." } ], "paths": { - "/chemical/wikipedia/by-dtxsid/": { - "post": { - "tags": [ - "Wikipedia to GHS Classification Resource" - ], - "summary": "Check for link for a batch of DTXSIDs", - "description": "This endpoint will return Y if Wikipedia has GHS Safety data, otherwise N.", - "operationId": "byBatchDtxsid", - "requestBody": { - "description": "JSON array of DSSTox Substance Identifiers", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - }, - "example": "[\"DTXSID7020182\",\"DTXSID9020112\"]" - } - }, - "required": true - }, - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/WikipediaLinkResponse" - } - } - } - } - } - }, - "security": [ - { - "api_key": [] - } - ] - } - }, "/chemical/synonym/search/by-dtxsid/": { "post": { "tags": [ @@ -441,51 +388,6 @@ ] } }, - "/chemical/ghslink/to-dtxsid/": { - "post": { - "tags": [ - "PubChem to GHS Classification Resource" - ], - "summary": "Check for link for a batch of DTXSIDs", - "description": "This endpoint will return Y if Pubchem has GHS Safety data, otherwise N.", - "operationId": "byBatchDtxsid_1", - "requestBody": { - "description": "JSON array of DSSTox Substance Identifiers", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "type": "string" - } - }, - "example": "[\"DTXSID7020182\",\"DTXSID9020112\"]" - } - }, - "required": true - }, - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "array", - "items": { - "$ref": "#/components/schemas/GhsLinkResponse" - } - } - } - } - } - }, - "security": [ - { - "api_key": [] - } - ] - } - }, "/chemical/fate/search/by-dtxsid/": { "post": { "tags": [ @@ -768,45 +670,6 @@ ] } }, - "/chemical/wikipedia/by-dtxsid/{dtxsid}": { - "get": { - "tags": [ - "Wikipedia to GHS Classification Resource" - ], - "summary": "Check for link by DTXSID", - "description": "This endpoint will return Y if Wikipedia has GHS Safety data, otherwise N.", - "operationId": "byDtxsid", - "parameters": [ - { - "name": "dtxsid", - "in": "path", - "description": "DSSTox Substance Identifier", - "required": true, - "schema": { - "type": "string" - }, - "example": "DTXSID7020182" - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/WikipediaLinkResponse" - } - } - } - } - }, - "security": [ - { - "api_key": [] - } - ] - } - }, "/chemical/synonym/search/by-dtxsid/{dtxsid}": { "get": { "tags": [ @@ -2218,45 +2081,6 @@ ] } }, - "/chemical/ghslink/to-dtxsid/{dtxsid}": { - "get": { - "tags": [ - "PubChem to GHS Classification Resource" - ], - "summary": "Check for link by DTXSID", - "description": "This endpoint will return Y if Pubchem has GHS Safety data, otherwise N.", - "operationId": "byDtxsid_1", - "parameters": [ - { - "name": "dtxsid", - "in": "path", - "description": "DSSTox Substance Identifier", - "required": true, - "schema": { - "type": "string" - }, - "example": "DTXSID7020182" - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "$ref": "#/components/schemas/GhsLinkResponse" - } - } - } - } - }, - "security": [ - { - "api_key": [] - } - ] - } - }, "/chemical/file/mol/search/by-dtxsid/{dtxsid}": { "get": { "tags": [ @@ -3000,77 +2824,10 @@ } ] } - }, - "/chemical/all": { - "get": { - "tags": [ - "Chemical Details Resource" - ], - "summary": "Get all data", - "description": "return all chemical details. The next parameter allows pagination for retrieval, but retrieval is limited to batches of 1000 per request. Please consider downloading the DSSTOX database instead accessing this information via API.", - "operationId": "getAllChemicalDetails", - "parameters": [ - { - "name": "next", - "in": "query", - "required": false, - "schema": { - "type": "integer", - "format": "int64", - "default": 1 - } - }, - { - "name": "projection", - "in": "query", - "description": "Specifies if projection is used. Option: all-ids. If omitted, the default ChemicalDetailStandard2 data is returned.", - "required": false, - "schema": { - "type": "string" - } - } - ], - "responses": { - "200": { - "description": "OK", - "content": { - "application/json": { - "schema": { - "type": "string", - "oneOf": [ - { - "$ref": "#/components/schemas/ChemicalDetailStandard2" - }, - { - "$ref": "#/components/schemas/ChemicalDetailAllIds" - } - ] - } - } - } - } - }, - "security": [ - { - "api_key": [] - } - ] - } } }, "components": { "schemas": { - "WikipediaLinkResponse": { - "type": "object", - "properties": { - "dtxsid": { - "type": "string" - }, - "safetyUrl": { - "type": "string" - } - } - }, "ChemicalSynonymAll": { "type": "object", "description": "Different types of synonyms for request dtxsid", @@ -3525,20 +3282,6 @@ "masses" ] }, - "GhsLinkResponse": { - "type": "object", - "properties": { - "dtxsid": { - "type": "string" - }, - "isSafetyData": { - "type": "boolean" - }, - "safetyUrl": { - "type": "string" - } - } - }, "ChemicalFateBatchDto": { "type": "object", "properties": { @@ -4506,21 +4249,6 @@ } } }, - "ChemicalDetailAllIds": { - "type": "object", - "properties": { - "id": { - "type": "integer", - "format": "int64" - }, - "dtxcid": { - "type": "string" - }, - "dtxsid": { - "type": "string" - } - } - }, "Link": { "type": "object", "properties": { diff --git a/public/docs/chemical.yaml b/public/docs/chemical.yaml new file mode 100644 index 0000000..6435ae3 --- /dev/null +++ b/public/docs/chemical.yaml @@ -0,0 +1,2914 @@ +--- +openapi: 3.1.0 +info: + title: Computational Toxicology and Exposure Data APIs - Chemical + description: 'The Chemical APIs are part of a set of public computational toxicology + and exposure APIs and provide a variety of chemical information through a set + of API endpoints. These APIs allow users to easily access and utilize a wide range + of chemical information, including the ability to: search for chemicals, retrieve + chemical structure files in various formats, access both experimental and predictive + chemical properties, obtain fate data, and access other chemical-related data.' + version: 1.0.0 +servers: + - url: https://ctx-api-stg.ccte.epa.gov + description: Production Environment +tags: + - name: Chemical Details Resource + description: API endpoints for collecting data for given chemical(s). + - name: Extra Data Resource + description: API endpoints for returning extra data relating to chemical(s) identified + by DTXSID(s) + - name: 'Wikipedia link to GHS Classification ' + description: 'API endpoints for checking if chemical has GHS classification safety + data in Wikipedia. ' + - name: Chemical Property Resource + description: API endpoints for getting chemical properties (experimental and/or + predictive) for a given DTXSID (Chemical Identifier). + - name: Pubchem link to GHS Classification + description: API endpoints for checking if chemical has GHS classification safety + data in Pubchem. + - name: Chemical Search Resource + description: API endpoints for searching chemicals using different identifiers or + characteristics. + - name: Chemical List Resource + description: API endpoints for getting chemical lists and chemicals in those lists. + - name: OPSIN Resource + description: 'API endpoints for getting chemical structure data through Systematic + IUPAC name using OPSIN. ' + - name: Chemical File Resource + description: API endpoints for getting chemical structure data in mol, mrv and image + (png or svg format) for given Chemical Identifier (DTXSID or DTXCID). + - name: Chemical Synonym Resource + description: API endpoints for getting chemical synonym for given DTXSID (Chemical + Identifier). + - name: Indigo Service + description: API endpoints for getting chemical info from Indigo Toolkit. +paths: + "/chemical/wikipedia/by-dtxsid/": + post: + tags: + - 'Wikipedia link to GHS Classification ' + summary: Check existence for batch of dtxsid + description: This endpoint will return Y if Wikipedia has GHS Safety data otherwise + it will return N. + operationId: byBatchDtxsid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + "$ref": "#/components/schemas/WikipediaLinkResponse" + security: + - api_key: [] + "/chemical/synonym/search/by-dtxsid/": + post: + tags: + - Chemical Synonym Resource + summary: Get synonyms by the batch of dtxsids + operationId: synoymsByBatchDtxsid + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalSynonymAll" + security: + - api_key: [] + "/chemical/search/equal/": + post: + tags: + - Chemical Search Resource + summary: Search by exact batch of values + description: 'NOTE: Search batch of values (values are separated by EOL character + and maximum 200 values are allowed).' + operationId: chemicalBatchEqual + requestBody: + content: + application/json: + schema: + type: string + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalBatchSearchResult" + security: + - api_key: [] + "/chemical/property/predicted/search/by-dtxsid/": + post: + tags: + - Chemical Property Resource + summary: Get predicted properties by the batch of dtxsid(s) + description: 'Note: Maximum 1000 DTXSIDs per request' + operationId: predictedBatchSearch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: Successfull + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyPredicted" + '400': + description: When user has submitted more then allowed number (1000) of + DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/chemical/property/experimental/search/by-dtxsid/": + post: + tags: + - Chemical Property Resource + summary: Get experimental properties by the batch of dtxsid(s) + description: 'Note: Maximum 1000 DTXSIDs per request' + operationId: experimentalBatchSearch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: Successfull + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyAll" + '400': + description: When user has submitted more then allowed number (1000) of + DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/chemical/msready/search/by-mass/": + post: + tags: + - Chemical Search Resource + summary: Search ms ready chemicals using bacth of mass ranges + operationId: msReadyByBatchMass + requestBody: + content: + application/json: + schema: + "$ref": "#/components/schemas/BatchMsReadyMassForm" + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: object + additionalProperties: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/msready/search/by-dtxcid/": + post: + tags: + - Chemical Search Resource + summary: Search ms ready chemicals by bacth of DTXCIDs + operationId: msReadyByBatchDtxcid + requestBody: + content: + application/json: + schema: + type: array + items: + type: string + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: {} + security: + - api_key: [] + "/chemical/indigo/to-smiles": + post: + tags: + - Indigo Service + summary: Get Smiles from mol + description: return Smiles for given mol file. + operationId: toSmiles + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + Smiles: + description: Smiles + value: C(C)(C)(C1C=CC(O)=CC=1)C1C=CC(O)=CC=1 + security: + - api_key: [] + "/chemical/indigo/to-molweight": + post: + tags: + - Indigo Service + summary: Get molecular weight from mol + description: return molecular weight for given mol file. + operationId: toMolecularWeight + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/indigo/to-mol3000": + post: + tags: + - Indigo Service + summary: Get mol file v3000 from mol + description: return mol file v3000 for given mol file. + operationId: toMol3000 + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + mol file v3000: + description: mol file v3000 + security: + - api_key: [] + "/chemical/indigo/to-mol2000": + post: + tags: + - Indigo Service + summary: Get mol file v2000 from mol + description: return mol file v2000 for given mol file. + operationId: toMol2000 + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + mol file v2000: + description: mol file v2000 + security: + - api_key: [] + "/chemical/indigo/to-inchikey": + post: + tags: + - Indigo Service + summary: Get InChIKey from mol + description: return InChIKey for given mol file. + operationId: toInChIkey + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + InChIKey: + description: InChIKey + value: DLFVBJFMPXGRIB-UHFFFAOYSA-N + security: + - api_key: [] + "/chemical/indigo/to-inchi": + post: + tags: + - Indigo Service + summary: Get InChI from mol + description: return InChI for given mol file. + operationId: toInChI + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + InChI: + description: InChI + value: InChI=1/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)/f/h3H2 + security: + - api_key: [] + "/chemical/indigo/to-canonicalsmiles": + post: + tags: + - Indigo Service + summary: Get Canonical Smiles from mol + description: return Canonical Smiles for given mol file. + operationId: toCanonicalSmiles + requestBody: + content: + application/json: + schema: + type: string + description: mol file + required: true + responses: + '200': + description: OK + content: + application/json: + examples: + Canonical Smiles: + description: Canonical Smiles + security: + - api_key: [] + "/chemical/ghslink/to-dtxsid/": + post: + tags: + - Pubchem link to GHS Classification + summary: Check existence for batch of dtxsid + description: This endpoint will return Y if Pubchem has GHS Safety data otherwise + it will return N. + operationId: byBatchDtxsid_1 + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + "$ref": "#/components/schemas/GhsLinkResponse" + security: + - api_key: [] + "/chemical/fate/search/by-dtxsid/": + post: + tags: + - Chemical Property Resource + summary: Get fate by the batch of dtxsid(s) (Env. Fate/transport) + description: 'Note: Maximum 1000 DTXSIDs per request' + operationId: fateBatchSearch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: Successfull + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyAll" + '400': + description: When user has submitted more then allowed number (1000) of + DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/chemical/extra-data/search/by-dtxsid/": + post: + tags: + - Extra Data Resource + summary: Get data by dtxsid + description: Specify the dtxsid as part of the path. + operationId: batchSearchExtraData + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID101296374","DTXSID10612113","DTXSID20635878"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ExtraData" + security: + - api_key: [] + "/chemical/detail/search/by-dtxsid/": + post: + tags: + - Chemical Details Resource + summary: Get data by the batch of dtxsids + description: 'Besides batch of the values, the user can also define projection + (set of attributes to return). Note: Maximum 1000 DTXSIDs per request' + operationId: batchDtxsidSearch + parameters: + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalDetailProjection" + default: chemicaldetailall + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalDetailStandard" + - "$ref": "#/components/schemas/ChemicalIdentifier" + - "$ref": "#/components/schemas/ChemicalStructure" + '400': + description: When user has submitted more then allowed number (1000) of + DTXSID(s). + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/chemical/detail/search/by-dtxcid/": + post: + tags: + - Chemical Details Resource + summary: Get data by the batch of dtxcids + description: 'Besides batch of the values, the user can also define projection + (set of attributes to return). Note: Maximum 1000 DTXCIDs per request' + operationId: batchDtxcidSearch + parameters: + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalDetailProjection" + default: chemicaldetailall + requestBody: + description: JSON array of DSSTox Compound Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXCID505","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalDetailStandard" + - "$ref": "#/components/schemas/ChemicalIdentifier" + - "$ref": "#/components/schemas/ChemicalStructure" + '400': + description: When user has submitted more then allowed number (1000) of + DTXCID(s). + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '${application.batch-size}' dtxsid at + one time, '${application.batch-size+1}' are submitted. + security: + - api_key: [] + "/chemical/wikipedia/by-dtxsid/{dtxsid}": + get: + tags: + - 'Wikipedia link to GHS Classification ' + summary: Check existence by dtxsid + description: This endpoint will return Y if Wikipedia has GHS Safety data otherwise + it will return N. + operationId: byDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + "$ref": "#/components/schemas/WikipediaLinkResponse" + security: + - api_key: [] + "/chemical/synonym/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Synonym Resource + summary: Get synonym by dtxsid + operationId: synoymsByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalSynonymAll" + security: + - api_key: [] + "/chemical/search/start-with/{word}": + get: + tags: + - Chemical Search Resource + summary: Search by starting value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: chemicalStartWith + parameters: + - name: word + in: path + description: Starting characters for search word + required: true + schema: + type: string + examples: + DSSTox Substance Identifier: + description: DSSTox Substance Identifier + value: DTXSID7020182 + CASRN: + description: CASRN + value: 1912-24 + - name: top + in: query + required: false + schema: + type: integer + format: int32 + default: 500 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalSearchAll" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/chemical/search/equal/{word}": + get: + tags: + - Chemical Search Resource + summary: Search by exact value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: chemicalEqual + parameters: + - name: word + in: path + description: Exact match of search word + required: true + schema: + type: string + examples: + DSSTox Substance Identifier: + description: DSSTox Substance Identifier + value: DTXSID7020182 + CASRN: + description: CASRN + value: 1912-24-9 + - name: projection + in: query + required: false + schema: + type: string + default: chemicalsearchall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalSearchAll" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/chemical/search/contain/{word}": + get: + tags: + - Chemical Search Resource + summary: Search by substring value + description: 'NOTE: Search value needs to be URL encoded for synonyms' + operationId: chemicalContain + parameters: + - name: word + in: path + description: Substring of search word + required: true + schema: + type: string + examples: + DSSTox Compound Identifier: + description: DSSTox Compound Identifier + value: DTXCID505 + Synonym: + description: Synonym + value: razine + - name: top + in: query + required: false + schema: + type: integer + format: int32 + default: 0 + - name: projection + in: query + required: false + schema: + type: string + default: chemicalsearchall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalSearchAll" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + security: + - api_key: [] + "/chemical/search/by-msready-formula/{formula}": + get: + tags: + - Chemical Search Resource + summary: Search chemicals by ms ready formula + operationId: getChemicalsForMsreadyFormula + parameters: + - name: formula + in: path + description: Chemical formula + required: true + schema: + type: string + example: C15H16O2 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/search/by-exact-formula/{formula}": + get: + tags: + - Chemical Search Resource + summary: Search chemicals by exact formula + operationId: getChemicalsForExactFormula + parameters: + - name: formula + in: path + description: Chemical formula + required: true + schema: + type: string + example: C15H16O2 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/property/summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Property Resource + summary: Get property summary by dtxsid (Physchem) + description: Specify the dtxsid as part of the path. + operationId: propertySummaryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertySummary" + security: + - api_key: [] + "/chemical/property/summary/search/": + get: + tags: + - Chemical Property Resource + summary: Get summary by dtxsid and property name (Physchem) + description: Specify the dtxsid and propertyName as parameters. + operationId: propertySummaryByDtxsidAndName + parameters: + - name: dtxsid + in: query + required: true + schema: + type: string + - name: propName + in: query + required: true + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertySummary" + security: + - api_key: [] + "/chemical/property/predicted/search/by-range/{propertyId}/{start}/{end}": + get: + tags: + - Chemical Property Resource + summary: Get predicted properties by propertyName and range(start,end) + description: Specify the propertyName, start, and end as part of the path. + operationId: predictedPropertyByRange + parameters: + - name: propertyId + in: path + required: true + schema: + type: string + - name: start + in: path + required: true + schema: + type: number + format: double + - name: end + in: path + required: true + schema: + type: number + format: double + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyPredicted" + security: + - api_key: [] + "/chemical/property/predicted/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Property Resource + summary: Get predicted properties by dtxsid + description: Specify the dtxsid as part of the path. + operationId: predictedPropertyByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyPredicted" + security: + - api_key: [] + "/chemical/property/predicted/name": + get: + tags: + - Chemical Property Resource + summary: Get all predicted property names + operationId: predictedPropertyNames + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyName" + security: + - api_key: [] + "/chemical/property/experimental/search/by-range/{propertyName}/{start}/{end}": + get: + tags: + - Chemical Property Resource + summary: Get experimental properties by propertyName and range(start,end) (Physchem) + description: Specify the propertyName, start, and end as part of the path. + operationId: experimentalPropertyByRange + parameters: + - name: propertyName + in: path + required: true + schema: + type: string + - name: start + in: path + required: true + schema: + type: number + format: double + - name: end + in: path + required: true + schema: + type: number + format: double + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyAll" + security: + - api_key: [] + "/chemical/property/experimental/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Property Resource + summary: Get experimental properties by dtxsid (Physchem) + description: Specify the dtxsid as part of the path. + operationId: experimentalPropertyByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyAll" + security: + - api_key: [] + "/chemical/property/experimental/name": + get: + tags: + - Chemical Property Resource + summary: Get all experimental property names (Physchem) + operationId: experimentalPropertyNames + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyName" + security: + - api_key: [] + "/chemical/opsin/to-smiles/{name}": + get: + tags: + - OPSIN Resource + summary: Get Smiles + description: return Smiles for given Systematic IUPAC Name. + operationId: toSmiles_1 + parameters: + - name: name + in: path + description: Systematic IUPAC Name + required: true + schema: + type: string + example: acetamide + responses: + '200': + description: OK + content: + application/json: + examples: + Smiles: + description: Smiles + value: C(C)(=O)N + security: + - api_key: [] + "/chemical/opsin/to-inchikey/{name}": + get: + tags: + - OPSIN Resource + summary: Get InChIKey + description: return InChIKey for given Systematic IUPAC Name. + operationId: toInChIKey + parameters: + - name: name + in: path + description: Systematic IUPAC Name + required: true + schema: + type: string + example: acetamide + responses: + '200': + description: OK + content: + application/json: + examples: + InChIKey: + description: InChIKey + value: DLFVBJFMPXGRIB-UHFFFAOYSA-N + security: + - api_key: [] + "/chemical/opsin/to-inchi/{name}": + get: + tags: + - OPSIN Resource + summary: Get InChI + description: return InChI for given Systematic IUPAC Name. + operationId: toInChI_1 + parameters: + - name: name + in: path + description: Systematic IUPAC Name + required: true + schema: + type: string + example: acetamide + responses: + '200': + description: OK + content: + application/json: + examples: + InChI: + description: InChI + value: InChI=1/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)/f/h3H2 + security: + - api_key: [] + "/chemical/msready/search/by-mass/{start}/{end}": + get: + tags: + - Chemical Search Resource + summary: Search ms ready chemicals using mass range + operationId: msReadyByMass + parameters: + - name: start + in: path + description: Starting mass value + required: true + schema: + type: number + format: double + example: 200.9 + - name: end + in: path + description: Ending mass value + required: true + schema: + type: number + format: double + example: 200.95 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/msready/search/by-formula/{formula}": + get: + tags: + - Chemical Search Resource + summary: Search ms ready chemicals by formula + operationId: msReadyByFormula + parameters: + - name: formula + in: path + description: Chemical formula + required: true + schema: + type: string + example: C16H24N2O5S + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/msready/search/by-dtxcid/{dtxcid}": + get: + tags: + - Chemical Search Resource + summary: Search ms ready chemicals by DTXCID + operationId: msReadyByDtxcid + parameters: + - name: dtxcid + in: path + description: DSSTox Compound Identifier + required: true + schema: + type: string + example: DTXCID30182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/type": + get: + tags: + - Chemical List Resource + summary: Get all list types + operationId: getAllType + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/search/by-type/{type}": + get: + tags: + - Chemical List Resource + summary: Get public lists by type + operationId: listByType + parameters: + - name: type + in: path + description: Chemical List Type + required: true + schema: + type: string + example: other + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalListProjection" + default: chemicallistall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalListAll" + - "$ref": "#/components/schemas/ChemicalListName" + security: + - api_key: [] + "/chemical/list/search/by-name/{listName}": + get: + tags: + - Chemical List Resource + summary: Get public lists by name + operationId: listByName + parameters: + - name: listName + in: path + description: Chemical List Name + required: true + schema: + type: string + example: 40CFR1164 + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalListProjection" + default: chemicallistall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalListAll" + - "$ref": "#/components/schemas/ChemicalListName" + security: + - api_key: [] + "/chemical/list/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical List Resource + summary: Get public lists by dtxsid + operationId: listByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID1020560 + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalListProjection" + default: chemicallistall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalListAll" + - "$ref": "#/components/schemas/ChemicalListName" + security: + - api_key: [] + "/chemical/list/chemicals/search/start-with/{list}/{word}": + get: + tags: + - Chemical List Resource + summary: Get DTXSIDs for a list name and starting value of chemical name + operationId: startWith + parameters: + - name: list + in: path + description: List Name + required: true + schema: + type: string + example: 40CFR1164 + - name: word + in: path + description: Chemical Name + required: true + schema: + type: string + example: ammo + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/chemicals/search/equal/{list}/{word}": + get: + tags: + - Chemical List Resource + summary: Get DTXSIDs for a list name and exact match of chemical name + operationId: exact + parameters: + - name: list + in: path + description: List Name + required: true + schema: + type: string + example: ANTMIC + - name: word + in: path + description: Chemical Name + required: true + schema: + type: string + example: PHOSPHORIC ACID + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/chemicals/search/contain/{list}/{word}": + get: + tags: + - Chemical List Resource + summary: Get DTXSIDs for a list name and substring match of chemical name + operationId: contain + parameters: + - name: list + in: path + description: List Name + required: true + schema: + type: string + example: ANTMIC + - name: word + in: path + description: Chemical Name + required: true + schema: + type: string + example: PHOSPHORIC ACID + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/chemicals/search/by-listname/{list}": + get: + tags: + - Chemical List Resource + summary: Get DTXSIDs for a specific list name + operationId: listDtxsids + parameters: + - name: list + in: path + required: true + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: array + items: + type: string + security: + - api_key: [] + "/chemical/list/": + get: + tags: + - Chemical List Resource + summary: Get all public lists + operationId: listAll + parameters: + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalListProjection" + default: chemicallistall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalListAll" + - "$ref": "#/components/schemas/ChemicalListName" + security: + - api_key: [] + "/chemical/ghslink/to-dtxsid/{dtxsid}": + get: + tags: + - Pubchem link to GHS Classification + summary: Check existence by dtxsid + description: This endpoint will return Y if Pubchem has GHS Safety data otherwise + it will return N. + operationId: byDtxsid_1 + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + "$ref": "#/components/schemas/GhsLinkResponse" + security: + - api_key: [] + "/chemical/file/mrv/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical File Resource + summary: Get mrv file by dtxsid + description: Specify the dtxsid as part of the path. + operationId: mrvByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/mrv/search/by-dtxcid/{dtxcid}": + get: + tags: + - Chemical File Resource + summary: Get mrv file by dtxcid + description: Specify the dtxcid as part of the path. + operationId: mrvByDtxcid + parameters: + - name: dtxcid + in: path + description: DSSTox Compound Identifier + required: true + schema: + type: string + example: DTXCID505 + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/mol/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical File Resource + summary: Get mol file by dtxsid + description: Specify the dtxsid as part of the path. + operationId: molByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/mol/search/by-dtxcid/{dtxcid}": + get: + tags: + - Chemical File Resource + summary: Get mol file by dtxcid + description: Specify the dtxcid as part of the path. + operationId: molByDtxcid + parameters: + - name: dtxcid + in: path + description: DSSTox Compound Identifier + required: true + schema: + type: string + example: DTXCID505 + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/image/search/by-gsid/{gsid}": + get: + tags: + - Chemical File Resource + summary: Get structure image by gsid + description: Specify the gsid as part of the path. + operationId: imageByGsid + parameters: + - name: gsid + in: path + description: Generic Substance Id + required: true + schema: + type: string + example: 20182 + - name: Image Format + in: query + description: In case of absence, it will return png image + required: false + schema: + "$ref": "#/components/schemas/ImageFormat" + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/image/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical File Resource + summary: Get structure image by dtxsid + description: Specify the dtxsid as part of the path. + operationId: imageByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + - name: Image Format + in: query + description: In case of absence, it will return png image + required: false + schema: + "$ref": "#/components/schemas/ImageFormat" + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/image/search/by-dtxcid/{dtxcid}": + get: + tags: + - Chemical File Resource + summary: Get structure image by dtxcid + description: Specify the dtxcid as part of the path. + operationId: imageByDtxcid + parameters: + - name: dtxcid + in: path + description: DSSTox Compound Identifier + required: true + schema: + type: string + example: DTXCID505 + - name: Image Format + in: query + description: In case of absence, it will return png image + required: false + schema: + "$ref": "#/components/schemas/ImageFormat" + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/file/image/generate": + get: + tags: + - Chemical File Resource + summary: Get generated structure image for smiles + description: User can use generate structure image by providing smiles string. + operationId: generateImageBySmiles + parameters: + - name: smiles + in: query + description: SMILES String + required: true + schema: + type: string + example: CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1 + - name: Image Format + in: query + description: In case of absence, it will return png image + required: false + schema: + "$ref": "#/components/schemas/ImageFormat" + default: PNG + responses: + '200': + description: OK + content: + application/json: {} + security: + - api_key: [] + "/chemical/fate/summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Property Resource + summary: Get fate summary by dtxsid (Env. Fate/transport) + description: Specify the dtxsid as part of the path. + operationId: fateSummaryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertySummary" + security: + - api_key: [] + "/chemical/fate/summary/search/": + get: + tags: + - Chemical Property Resource + summary: Get fate summary by dtxsid and property name (Env. Fate/transport) + description: Specify the dtxsid and propertyName as parameters. + operationId: fateSummaryByDtxsidAndName + parameters: + - name: dtxsid + in: query + required: true + schema: + type: string + - name: propName + in: query + required: true + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertySummary" + security: + - api_key: [] + "/chemical/fate/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Property Resource + summary: Get chemical fate by dtxsid (Env. Fate/transport) + description: Specify the dtxsid as part of the path. + operationId: fateByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalPropertyAll" + security: + - api_key: [] + "/chemical/extra-data/search/by-dtxsid/{dtxsid}": + get: + tags: + - Extra Data Resource + summary: Get data by dtxsid + description: Specify the dtxsid as part of the path. + operationId: extraDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID101296374 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ExtraData" + '400': + description: Data not found. + content: + application/problem+json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ExtraData" + example: + title: Bad Request + status: 400 + detail: dtxsid with value (${application.dtxsid}) not found. + instance: + - "/chemical/extra-data/search/by-dtxsid/($application.dtxsid})" + security: + - api_key: [] + "/chemical/detail/search/by-dtxsid/{dtxsid}": + get: + tags: + - Chemical Details Resource + summary: Get data by dtxsid + description: Specify the dtxsid as part of the path, and optionally user can + also define projection (set of attributes to return). + operationId: detailByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalDetailProjection" + default: chemicaldetailall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalDetailStandard" + - "$ref": "#/components/schemas/ChemicalIdentifier" + - "$ref": "#/components/schemas/ChemicalStructure" + security: + - api_key: [] + "/chemical/detail/search/by-dtxcid/{dtxcid}": + get: + tags: + - Chemical Details Resource + summary: Get data by dtxcid + description: Specify the dtxcid as part of the path, and optionally user can + also define projection (set of attributes to return). + operationId: detailsByDtxcid + parameters: + - name: dtxcid + in: path + description: DSSTox Compound Identifier + required: true + schema: + type: string + example: DTXCID505 + - name: projection + in: query + required: false + schema: + "$ref": "#/components/schemas/ChemicalDetailProjection" + default: chemicaldetailall + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalDetailStandard" + - "$ref": "#/components/schemas/ChemicalIdentifier" + - "$ref": "#/components/schemas/ChemicalStructure" + - "$ref": "#/components/schemas/chemicaldetailall" + - "$ref": "#/components/schemas/NtaToolkit" + security: + - api_key: [] + "/chemical/count/by-msready-formula/{formula}": + get: + tags: + - Chemical Search Resource + summary: Search chemicals Count by ms ready formula + operationId: getChemicalsCountForMsreadyFormula + parameters: + - name: formula + in: path + description: Chemical formula + required: true + schema: + type: string + example: C15H16O2 + - name: projection + in: query + required: false + schema: + type: string + default: count + responses: + '200': + description: OK + content: + application/hal+json: + schema: + type: integer + format: int64 + security: + - api_key: [] + "/chemical/count/by-exact-formula/{formula}": + get: + tags: + - Chemical Search Resource + summary: Search chemicals Count by exact formula + operationId: getChemicalsCountForExactFormula + parameters: + - name: formula + in: path + description: Chemical formula + required: true + schema: + type: string + example: C15H16O2 + - name: projection + in: query + required: false + schema: + type: string + default: count + responses: + '200': + description: OK + content: + application/hal+json: + schema: + type: integer + format: int64 + security: + - api_key: [] + "/chemical/all": + get: + tags: + - Chemical Details Resource + summary: Find all chemical details + description: return all chemical details. + operationId: getAllChemicalDetails + parameters: + - name: next + in: query + required: false + schema: + type: integer + format: int64 + default: 1 + - name: projection + in: query + description: 'Specifies if projection is used. Option: all-ids. If omitted, + the default ChemicalDetailStandard2 data is returned.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ChemicalDetailStandard2" + - "$ref": "#/components/schemas/ChemicalDetailAllIds" + security: + - api_key: [] +components: + schemas: + WikipediaLinkResponse: + type: object + properties: + dtxsid: + type: string + safetyUrl: + type: string + ChemicalSynonymAll: + type: object + description: Different types of synonyms for request dtxsid + properties: + dtxsid: + type: string + pcCode: + type: string + other: + type: array + items: + type: string + valid: + type: array + items: + type: string + good: + type: array + items: + type: string + deletedCasrn: + type: array + items: + type: string + beilstein: + type: array + items: + type: string + alternateCasrn: + type: array + items: + type: string + ChemicalBatchSearchResult: + type: object + properties: + dtxsid: + type: string + maxLength: 20 + minLength: 0 + dtxcid: + type: string + maxLength: 20 + minLength: 0 + casrn: + type: string + maxLength: 255 + minLength: 0 + smiles: + type: string + preferredName: + type: string + maxLength: 255 + minLength: 0 + searchName: + type: string + maxLength: 50 + minLength: 0 + searchValue: + type: string + rank: + type: integer + format: int32 + hasStructureImage: + type: integer + format: int32 + isMarkush: + type: boolean + searchMsgs: + type: array + description: Message about the search + items: + type: string + suggestions: + type: array + description: List of suggestions in case there is no match found + items: + type: string + isDuplicate: + type: boolean + ChemicalPropertyPredicted: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 255 + minLength: 0 + dtxcid: + type: string + maxLength: 255 + minLength: 0 + smiles: + type: string + maxLength: 2000 + minLength: 0 + canonQsarSmiles: + type: string + maxLength: 1000 + minLength: 0 + genericSubstanceUpdatedAt: + type: string + format: date-time + propName: + type: string + maxLength: 255 + minLength: 0 + propCategory: + type: string + maxLength: 255 + minLength: 0 + propDescription: + type: string + maxLength: 255 + minLength: 0 + modelName: + type: string + maxLength: 255 + minLength: 0 + modelId: + type: integer + format: int64 + sourceName: + type: string + maxLength: 255 + minLength: 0 + sourceDescription: + type: string + maxLength: 1000 + minLength: 0 + propValueExperimental: + type: number + format: double + propValueExperimentalString: + type: string + maxLength: 255 + minLength: 0 + propValue: + type: number + format: double + propUnit: + type: string + propValueString: + type: string + maxLength: 255 + minLength: 0 + propValueError: + type: string + maxLength: 255 + minLength: 0 + adMethod: + type: string + maxLength: 255 + minLength: 0 + adValue: + type: number + format: double + adConclusion: + type: string + maxLength: 255 + minLength: 0 + adReasoning: + type: string + maxLength: 255 + minLength: 0 + adMethodGlobal: + type: string + adValueGlobal: + type: number + format: double + adConclusionGlobal: + type: string + maxLength: 255 + minLength: 0 + adReasoningGlobal: + type: string + maxLength: 255 + minLength: 0 + hasQmrf: + type: boolean + qmrfUrl: + type: string + required: + - id + ProblemDetail: + type: object + properties: + type: + type: string + format: uri + title: + type: string + status: + type: integer + format: int32 + detail: + type: string + instance: + type: string + format: uri + properties: + type: object + additionalProperties: {} + ChemicalPropertyAll: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + dtxcid: + type: string + smiles: + type: string + expDetailsSpeciesSupercategory: + type: string + publicSourceOriginalDescription: + type: string + publicSourceOriginalName: + type: string + propName: + type: string + propValue: + type: number + format: double + propValueId: + type: integer + format: int64 + propValueText: + type: string + publicSourceUrl: + type: string + lsCitation: + type: string + directUrl: + type: string + propUnit: + type: string + briefCitation: + type: string + sourceName: + type: string + expDetailsPh: + type: integer + format: int64 + dataset: + type: string + lsName: + type: string + lsDoi: + type: string + expDetailsResponseSite: + type: string + propValueOriginal: + type: string + expDetailsPressureMmhg: + type: integer + format: int64 + publicSourceDescription: + type: string + expDetailsSpeciesLatin: + type: string + publicSourceOriginalUrl: + type: string + expDetailsSpeciesCommon: + type: string + sourceDescription: + type: string + expDetailsTemperatureC: + type: integer + format: int64 + publicSourceName: + type: string + BatchMsReadyMassForm: + type: object + properties: + masses: + type: array + items: + type: number + format: double + minItems: 1 + error: + type: integer + format: int32 + required: + - error + - masses + GhsLinkResponse: + type: object + properties: + dtxsid: + type: string + isSafetyData: + type: boolean + safetyUrl: + type: string + ExtraData: + type: object + properties: + dtxsid: + type: string + maxLength: 45 + minLength: 0 + dtxcid: + type: integer + format: int32 + maximum: 45 + minimum: 0 + refs: + type: integer + format: int32 + maximum: 255 + minimum: 0 + googlePatent: + type: integer + format: int32 + literature: + type: integer + format: int32 + pubmed: + type: integer + format: int32 + ChemicalDetailProjection: + type: string + description: 'Projection options for chemical details APIs ' + enum: + - chemicaldetailstandard + - chemicalidentifier + - chemicalstructure + - ntatoolkit + - ccdchemicaldetails + - chemicaldetailall + - compact + ChemicalDetailStandard: + type: object + description: Standard attributes available for chemical details APIs + properties: + id: + type: string + compoundId: + type: integer + format: int32 + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + dtxcid: + type: string + qcLevel: + type: integer + format: int32 + relatedStructureCount: + type: integer + format: int64 + hasStructureImage: + type: integer + format: int32 + relatedSubstanceCount: + type: integer + format: int64 + wikipediaArticle: + type: string + descriptorStringTsv: + type: string + monoisotopicMass: + type: number + format: double + genericSubstanceId: + type: integer + format: int32 + cpdataCount: + type: integer + format: int64 + isMarkush: + type: boolean + iupacName: + type: string + toxcastSelect: + type: string + qsarReadySmiles: + type: string + inchikey: + type: string + activeAssays: + type: integer + format: int32 + molFormula: + type: string + pubmedCount: + type: number + format: double + qcLevelDesc: + type: string + sourcesCount: + type: integer + format: int64 + pubchemCount: + type: integer + format: int32 + totalAssays: + type: integer + format: int32 + pubchemCid: + type: integer + format: int32 + percentAssays: + type: number + format: double + inchiString: + type: string + irisLink: + type: string + pprtvLink: + type: string + multicomponent: + type: integer + format: int32 + msReadySmiles: + type: string + isotope: + type: integer + format: int32 + smiles: + type: string + qcNotes: + type: string + ChemicalIdentifier: + type: object + description: Attributes related to chemical identification for chemical details + APIs + properties: + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + dtxcid: + type: string + iupacName: + type: string + inchikey: + type: string + ChemicalStructure: + type: object + description: Attributes related to chemical structure for chemical details APIs + properties: + id: + type: string + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + dtxcid: + type: string + hasStructureImage: + type: integer + format: int32 + qsarReadySmiles: + type: string + inchikey: + type: string + inchiString: + type: string + msReadySmiles: + type: string + smiles: + type: string + ChemicalSearchAll: + type: object + properties: + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + dtxcid: + type: string + hasStructureImage: + type: integer + format: int32 + isMarkush: + type: boolean + searchName: + type: string + searchValue: + type: string + smiles: + type: string + rank: + type: integer + format: int32 + ChemicalPropertySummary: + type: object + properties: + propName: + type: string + experimentalRange: + type: string + experimentalAverage: + type: string + experimentalMedian: + type: number + format: float + predictedAverage: + type: string + unit: + type: string + predictedRange: + type: string + predictedMedian: + type: number + format: float + ChemicalPropertyName: + type: object + description: Attributes for chemical property names for chemical property APIs + properties: + propertyName: + type: string + ChemicalListProjection: + type: string + description: 'Projection options for chemical List APIs ' + enum: + - chemicallistall + - chemicallistwithdtxsids + - chemicallistname + - ccdchemicaldetaillists + ChemicalListAll: + type: object + properties: + label: + type: string + id: + type: integer + format: int32 + type: + type: string + shortDescription: + type: string + longDescription: + type: string + visibility: + type: string + listName: + type: string + createdAt: + type: string + format: date-time + chemicalCount: + type: integer + format: int64 + updatedAt: + type: string + format: date-time + ChemicalListName: + type: object + properties: + listName: + type: string + ImageFormat: + type: string + enum: + - PNG + - SVG + chemicaldetailall: + type: object + description: All attributes available for chemical details APIs + properties: + id: + type: string + thermalConductivity: + type: number + format: double + compoundId: + type: integer + format: int32 + preferredName: + type: string + dtxsid: + type: string + stereo: + type: string + casrn: + type: string + dtxcid: + type: string + qcLevel: + type: integer + format: int32 + relatedStructureCount: + type: integer + format: int64 + hasStructureImage: + type: integer + format: int32 + relatedSubstanceCount: + type: integer + format: int64 + wikipediaArticle: + type: string + descriptorStringTsv: + type: string + monoisotopicMass: + type: number + format: double + genericSubstanceId: + type: integer + format: int32 + cpdataCount: + type: integer + format: int64 + isMarkush: + type: boolean + iupacName: + type: string + toxcastSelect: + type: string + qsarReadySmiles: + type: string + inchikey: + type: string + activeAssays: + type: integer + format: int32 + molFormula: + type: string + pubmedCount: + type: number + format: double + qcLevelDesc: + type: string + sourcesCount: + type: integer + format: int64 + pubchemCount: + type: integer + format: int32 + totalAssays: + type: integer + format: int32 + pubchemCid: + type: integer + format: int32 + averageMass: + type: number + format: double + percentAssays: + type: number + format: double + inchiString: + type: string + irisLink: + type: string + pprtvLink: + type: string + multicomponent: + type: integer + format: int32 + msReadySmiles: + type: string + isotope: + type: integer + format: int32 + smiles: + type: string + qcNotes: + type: string + viscosityCpCpTestPred: + type: number + format: double + waterSolubilityOpera: + type: number + format: double + biodegradationHalfLifeDays: + type: number + format: double + octanolAirPartitionCoeff: + type: number + format: double + bioconcentrationFactorTestPred: + type: number + format: double + amesMutagenicityTestPred: + type: number + format: double + vaporPressureMmhgOperaPred: + type: number + format: double + boilingPointDegcOperaPred: + type: number + format: double + bioconcentrationFactorOperaPred: + type: number + format: double + meltingPointDegcOperaPred: + type: number + format: double + vaporPressureMmhgTestPred: + type: number + format: double + boilingPointDegcTestPred: + type: number + format: double + meltingPointDegcTestPred: + type: number + format: double + soilAdsorptionCoefficient: + type: number + format: double + atmosphericHydroxylationRate: + type: number + format: double + toxvalData: + type: string + surfaceTension: + type: number + format: double + oralRatLd50Mol: + type: number + format: double + hrDiphniaLc50: + type: number + format: double + henrysLawAtm: + type: number + format: double + devtoxTestPred: + type: number + format: double + pkaaOperaPred: + type: number + format: double + pkabOperaPred: + type: number + format: double + hrFatheadMinnow: + type: number + format: double + expocatMedianPrediction: + type: string + waterSolubilityTest: + type: number + format: double + expocat: + type: string + nhanes: + type: string + density: + type: number + format: double + flashPointDegcTestPred: + type: number + format: double + octanolWaterPartition: + type: number + format: double + tetrahymenaPyriformis: + type: number + format: double + operaKmDaysOperaPred: + type: number + format: double + NtaToolkit: + type: object + description: All attributes use for NTA Informatics Toolkit. + properties: + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + dtxcid: + type: string + monoisotopicMass: + type: number + format: double + cpdataCount: + type: integer + format: int64 + inchikey: + type: string + activeAssays: + type: integer + format: int32 + molFormula: + type: string + sourcesCount: + type: integer + format: int64 + totalAssays: + type: integer + format: int32 + percentAssays: + type: number + format: double + msReadySmiles: + type: string + smiles: + type: string + expocatMedianPrediction: + type: string + expocat: + type: string + nhanes: + type: string + ChemicalDetailStandard2: + type: object + properties: + id: + type: integer + format: int64 + preferredName: + type: string + dtxsid: + type: string + casrn: + type: string + qcLevel: + type: integer + format: int32 + monoisotopicMass: + type: number + format: double + iupacName: + type: string + inchikey: + type: string + molFormula: + type: string + qcLevelDesc: + type: string + averageMass: + type: number + format: double + inchiString: + type: string + smiles: + type: string + ChemicalDetailAllIds: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + dtxcid: + type: string + Link: + type: object + properties: + href: + type: string + hreflang: + type: string + title: + type: string + type: + type: string + deprecation: + type: string + profile: + type: string + name: + type: string + templated: + type: boolean + Links: + type: object + additionalProperties: + "$ref": "#/components/schemas/Link" + securitySchemes: + api_key: + type: apiKey + description: 'Each API call should have api_key, Contact author for getting + the new api_key. ' + name: x-api-key + in: header diff --git a/public/docs/exposure.json b/public/docs/exposure.json index cca01b6..3ecb360 100644 --- a/public/docs/exposure.json +++ b/public/docs/exposure.json @@ -7,8 +7,8 @@ }, "servers": [ { - "url": "https://ctx-api-dev.ccte.epa.gov", - "description": "Development Environment" + "url": "https://ctx-api-stg.ccte.epa.gov", + "description": "Staging Environment" } ], "tags": [ diff --git a/public/docs/exposure.yaml b/public/docs/exposure.yaml new file mode 100644 index 0000000..a50cfe5 --- /dev/null +++ b/public/docs/exposure.yaml @@ -0,0 +1,1681 @@ +--- +openapi: 3.1.0 +info: + title: Computational Toxicology and Exposure Data APIs - Exposure + description: The Exposure APIs are part of a set of public computational toxicology + and exposure APIs and provide exposure data through a set of API endpoints. + version: 1.0.0 +servers: + - url: https://ctx-api-stg.ccte.epa.gov + description: Production Environment +tags: + - name: CCD Data Resource + description: API endpoints for CompTox Chemicals Dashboard exposure tabs. + - name: MMDB Resource + description: API endpoints for collecting data for MMDB database. + - name: Functional Use Resource + description: API endpoints for functional use in exposure data. + - name: Product Data Resource + description: API endpoints for product data in exposure data. + - name: Httk Data Resource + description: API endpoints for httk data in exposure data. + - name: List Presence Resource + description: API endpoints for list presence in exposure data. + - name: General Exposure Prediction Resource + description: API endpoints for general prediction in exposure data. + - name: Demographic Exposure Prediction Resource + description: API endpoints for demographic prediction in exposure data. +paths: + "/exposure/seem/general/search/by-dtxsid/": + post: + tags: + - General Exposure Prediction Resource + summary: Find general exposure prediction SEEMs data by batch of dtxsids + description: return general prediction SEEMs data for requested dtxsids + operationId: batchSearchGenExpoPrediction + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID00195485","DTXSID00195400"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenExpoPrediction" + security: + - api_key: [] + "/exposure/seem/demographic/search/by-dtxsid/": + post: + tags: + - Demographic Exposure Prediction Resource + summary: Find demographic prediction SEEMs data by batch of dtxsids + description: return demographic prediction SEEMs data for requested dtxsids + operationId: batchSearchDemoExpoPrediction + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID00195506","DTXSID0027301"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/DemoExpoPrediction" + security: + - api_key: [] + "/exposure/product-data/search/by-dtxsid/": + post: + tags: + - Product Data Resource + summary: Find product data by batch dtxsids + description: return product data for requested dtxsids + operationId: batchSearchProductData + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProductData" + security: + - api_key: [] + "/exposure/list-presence/search/by-dtxsid/": + post: + tags: + - List Presence Resource + summary: Find list presence data by batch of dtxsids + description: return list presence data for requested dtxsids + operationId: batchSearchListPresence + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ListPresence" + security: + - api_key: [] + "/exposure/httk/search/by-dtxsid/": + post: + tags: + - Httk Data Resource + summary: Find httk data by batch of dtxsids + description: return httk data for requested dtxsids + operationId: batchSearchHttk + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID0027301","DTXSID0027272"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/HttkData" + security: + - api_key: [] + "/exposure/functional-use/search/by-dtxsid/": + post: + tags: + - Functional Use Resource + summary: Find functional-use data by batch of dtxsids + description: return functional-use data for requested dtxsids. + operationId: batchSearchFunctionalUse + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/FunctionalUseAll" + security: + - api_key: [] + "/exposure/seem/general/search/by-dtxsid/{dtxsid}": + get: + tags: + - General Exposure Prediction Resource + summary: Find general prediction SEEMs data by dtxsid + description: return demographic prediction SEEMs data for requested dtxsid + operationId: getGenExpoPredictionByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + - name: projection + in: query + description: 'Specifies whether to use projection. Optional: ccd-general.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenExpoPrediction" + security: + - api_key: [] + "/exposure/seem/demographic/search/by-dtxsid/{dtxsid}": + get: + tags: + - Demographic Exposure Prediction Resource + summary: Find demographic prediction SEEMs data by dtxsid + description: return demographic prediction SEEMs data for requested dtxsid + operationId: getDemoExpoPredictionByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + - name: projection + in: query + description: 'Specifies whether to use projection. Optional: ccd-demographic.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/DemoExpoPrediction" + security: + - api_key: [] + "/exposure/product-data/search/by-dtxsid/{dtxsid}": + get: + tags: + - Product Data Resource + summary: Find product data by dtxsid + description: return product data for requested dtxsid + operationId: getProductDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProductData" + security: + - api_key: [] + "/exposure/product-data/puc": + get: + tags: + - Product Data Resource + summary: List all puc product data + description: return all puc product data. + operationId: getProductDataPuc + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/Puc" + security: + - api_key: [] + "/exposure/mmdb/single-sample/by-medium": + get: + tags: + - MMDB Resource + summary: Get harmonized single-sample records by medium + description: Specify the medium as part of the path. + operationId: getHarmonizedSingleSampleDataByMedium + parameters: + - name: medium + in: query + description: harmonized medium + required: true + schema: + type: string + example: surface water + - name: pageNumber + in: query + required: false + schema: + type: integer + format: int32 + default: 1 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/MMDBSingleSample" + security: + - api_key: [] + "/exposure/mmdb/single-sample/by-dtxsid/{dtxsid}": + get: + tags: + - MMDB Resource + summary: Get harmonized single-sample records by dtxsid + description: Specify the dtxsid as part of the path. + operationId: getHarmonizedSingleSampleDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/MMDBSingleSample" + security: + - api_key: [] + "/exposure/mmdb/mediums": + get: + tags: + - MMDB Resource + summary: Get all searchable harmonized medium categories and their corresponding + definitions + operationId: getAllHarmonizedMedia + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/MMDBMediaDescSummary" + security: + - api_key: [] + "/exposure/mmdb/aggregate/by-medium": + get: + tags: + - MMDB Resource + summary: Get harmonized aggregate records by medium + description: Specify the medium as part of the path. + operationId: getHarmonizedAggregateDataByMedium + parameters: + - name: medium + in: query + description: harmonized medium + required: true + schema: + type: string + example: surface water + - name: pageNumber + in: query + required: false + schema: + type: integer + format: int32 + default: 1 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/MMDBAggregate" + security: + - api_key: [] + "/exposure/mmdb/aggregate/by-dtxsid/{dtxsid}": + get: + tags: + - MMDB Resource + summary: Get harmonized aggregate records by dtxsid + description: Specify the dtxsid as part of the path. + operationId: getHarmonizedAggregateDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/MMDBAggregate" + security: + - api_key: [] + "/exposure/list-presence/tags": + get: + tags: + - List Presence Resource + summary: Produce list presence tags + description: return list presence tags + operationId: getListPresenceTags + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ListPresenceTag" + security: + - api_key: [] + "/exposure/list-presence/search/by-dtxsid/{dtxsid}": + get: + tags: + - List Presence Resource + summary: Find list presence data by dtxsid + description: return list presence data for requested dtxsid + operationId: getListPresenceByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ListPresence" + security: + - api_key: [] + "/exposure/httk/search/by-dtxsid/{dtxsid}": + get: + tags: + - Httk Data Resource + summary: Find httk data by dtxsid + description: return httk data for requested dtxsid + operationId: getHttkDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/HttkData" + security: + - api_key: [] + "/exposure/functional-use/search/by-dtxsid/{dtxsid}": + get: + tags: + - Functional Use Resource + summary: Find functional-use data by dtxsid + description: return functional-use data for requested dtxsid + operationId: getFunctionalUseByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/FunctionalUseAll" + security: + - api_key: [] + "/exposure/functional-use/probability/search/by-dtxsid/{dtxsid}": + get: + tags: + - Functional Use Resource + summary: Find functional-use probability by dtxsid + description: return functional-use probability for requested dtxsid + operationId: getFunctionalUseProbabilityByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/QsurDataAll" + security: + - api_key: [] + "/exposure/functional-use/category": + get: + tags: + - Functional Use Resource + summary: Find functional-use categories + description: return all functional-use categories + operationId: getFunctionalUseCategory + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/FunctionalUseCategoryAll" + security: + - api_key: [] + "/exposure/ccd/puc/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find Product Use Category data by dtxsid + description: return Product Use Category data for requested dtxsid + operationId: getProductUseCategoryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDProductUseCategory" + security: + - api_key: [] + "/exposure/ccd/production-volume/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find Production Volume data by dtxsid + description: return Production Volume data for requested dtxsid + operationId: getProductionVolumeDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDProductionVolume" + security: + - api_key: [] + "/exposure/ccd/monitoring-data/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find Biomonitoring data by dtxsid with ccd projection + description: return NHANES Inferences for requested dtxsidthere is an available + projection for ccd exposure biomonitoring page:ccd-biomonitoringIf no projection + is specified, the default CCDBiomonitoring data will be returned + operationId: getBiomonitoringDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + - name: projection + in: query + description: 'Specifies if projection is used. Option: ccd-biomonitoring, + If omitted, the default CCDBiomonitoring data is returned.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDBiomonitoring" + - "$ref": "#/components/schemas/CCDBiomonitoringAll" + security: + - api_key: [] + "/exposure/ccd/keywords/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find General Use Keywords data by dtxsid + description: return General Use Keywords data for requested dtxsid + operationId: getGeneralUseKeywordsByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDGeneralUseKeywords" + security: + - api_key: [] + "/exposure/ccd/functional-use/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find Reported Functional Use data by dtxsid + description: return Reported Functional Use data for requested dtxsid + operationId: getReportedFunctionalUseByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDReportedFunctionalUse" + security: + - api_key: [] + "/exposure/ccd/chem-weight-fractions/search/by-dtxsid/{dtxsid}": + get: + tags: + - CCD Data Resource + summary: Find Chemical Weight Fractions data by dtxsid + description: return Chemical Weight Fractions data for requested dtxsid + operationId: getChemicalWeightFractionsByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0020232 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CCDChemicalWeightFractions" + security: + - api_key: [] +components: + schemas: + GenExpoPrediction: + type: object + description: These are estimates of the average (geometric mean) exposure rate + (mg/kg bodyweight/day) for the U.S. population. We are 50% confident that + the exposure for the chemical is below the median estimate, and we are 95% + confident that the average exposure rate is below the upper 95th percent estimate. + Total population predictions are based upon consensus exposure model predictions + and the similarity of the compound to those chemicals monitored by NHANES. + The method for the total U.S. population was described in a 2018 publication, + "Consensus Modeling of Median Chemical Intake for the U.S. Population Based + on Predictions of Exposure Pathways". + properties: + dtxsid: + type: string + description: Chemical identifier + maxLength: 20 + minLength: 0 + productionVolume: + type: number + description: How much chemical is produced or imported in the United States + units: + type: string + description: Units on production volume + maxLength: 7 + minLength: 0 + stockholmConvention: + type: integer + format: int32 + description: Whether (1) or not (0) the chemical is banned by the Stockholm + Convention on persistent organic pollutants + probabilityDietary: + type: number + description: QSPR-predicted probability that the chemical has human exposure + via a dietary pathway + probabilityResidential: + type: number + description: QSPR-predicted probability that the chemical has human exposure + via a consumer use pathway + probabilityPesticde: + type: number + description: QSPR-predicted probability that the chemical has human exposure + via a far-field pesticide pathway + probabilityIndustrial: + type: number + description: QSPR-predicted probability that the chemical has human exposure + via a far-field industrial pathway + DemoExpoPrediction: + type: object + description: These are estimates of the average (geometric mean) exposure rate + (mg/kg bodyweight/day) for the U.S. population. We are 50% confident that + the exposure for the chemical is below the median estimate, and we are 95% + confident that the average exposure rate is below the upper 95th percent estimate. + Total population predictions are based upon consensus exposure model predictions + and the similarity of the compound to those chemicals monitored by NHANES. + The method for the demographic-specific predictions are based upon a simpler, + heuristic model described in the 2014 publication "High Throughput Heuristics + for Prioritizing Human Exposure to Environmental Chemicals". + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Chemical identifier + maxLength: 20 + minLength: 0 + demographic: + type: string + description: Which portion of the U.S. population these values refer to + maxLength: 25 + minLength: 0 + predictor: + type: string + description: The model/approach used to make a prediction + maxLength: 25 + minLength: 0 + median: + type: number + format: double + description: The median predicted value + medianText: + type: string + maxLength: 25 + minLength: 0 + l95: + type: number + format: double + description: The lower 95th percentile confidence value (uncertainty) for + the prediction + l95Text: + type: string + maxLength: 25 + minLength: 0 + u95: + type: number + format: double + description: The upper 95th percentile confidence value (uncertainty) for + the prediction + u95Text: + type: string + maxLength: 25 + minLength: 0 + units: + type: string + description: The units of the prediction + maxLength: 20 + minLength: 0 + ad: + type: integer + format: int32 + description: Whether (1) or not (0) the chemical is within the applicability + domain of the predictor + reference: + type: string + description: The peer reviewed journal article explaining how the prediction + was made + maxLength: 20 + minLength: 0 + ProductData: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + docid: + type: integer + format: int32 + doctitle: + type: string + maxLength: 500 + minLength: 0 + docdate: + type: string + maxLength: 25 + minLength: 0 + productname: + type: string + maxLength: 255 + minLength: 0 + gencat: + type: string + maxLength: 50 + minLength: 0 + prodfam: + type: string + maxLength: 50 + minLength: 0 + prodtype: + type: string + maxLength: 100 + minLength: 0 + classificationmethod: + type: string + maxLength: 100 + minLength: 0 + rawmincomp: + type: string + maxLength: 100 + minLength: 0 + rawmaxcomp: + type: string + maxLength: 100 + minLength: 0 + rawcentralcomp: + type: string + maxLength: 100 + minLength: 0 + unittype: + type: string + maxLength: 50 + minLength: 0 + lowerweightfraction: + type: number + upperweightfraction: + type: number + centralweightfraction: + type: number + weightfractiontype: + type: string + maxLength: 50 + minLength: 0 + component: + type: string + maxLength: 200 + minLength: 0 + ListPresence: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + docid: + type: integer + format: int32 + doctitle: + type: string + maxLength: 500 + minLength: 0 + docsubtitle: + type: string + maxLength: 250 + minLength: 0 + docdate: + type: string + maxLength: 25 + minLength: 0 + organization: + type: string + maxLength: 255 + minLength: 0 + reportedfunction: + type: string + maxLength: 255 + minLength: 0 + functioncategory: + type: string + maxLength: 100 + minLength: 0 + component: + type: string + maxLength: 200 + minLength: 0 + keywordset: + type: string + HttkData: + type: object + description: 'The information here describes toxicokinetics in humans. Values + are 1) measured either in vitro or in vivo, 2) predicted from chemical properties + using in silico tools, or 3) computed with mathematical models simulating + toxicokinetics. Note: intrinsic hepatic clearance and fraction unbound in + plasma values can have measured values listed, but these may be assumed from + measured data using a surrogate species. The Data Source Species column identifies + the measured data species source. We use these assumed measured values in + calculations to estimate other outcomes, such as volume of distribution, PK + half life, and steady-state plasma concentration. The in vitro measured values + reflect the value curated for the open source R package “httk”. The computed + values are generated with httk using the reported in vitro values. "https://CRAN.R-project.org/package=httk". + The in vivo measured values are estimated from toxicokinetic concentration + vs. time contained in the CvTdb (https://doi.org/10.1038/s41597-020-0455-1). + In vivo estimates are calculated using R package “invivoPKfit” (https://github.com/USEPA/CompTox-ExpoCast-invivoPKfit)' + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Chemical identifier + maxLength: 20 + minLength: 0 + parameter: + type: string + description: The toxicokinetic parameter. Clint = Intrinsic hepatic clearance + rate, Fup = fraction unbound in plasma, Vd = effective volume of distribution, + Days.Css = number of days to reach steady-state from constant exposure, + Css = plasma concentration after reaching steady-state, TK.Half.Life = + number of hours for half of chemical in body to be eliminated + maxLength: 15 + minLength: 0 + measuredText: + type: string + maxLength: 15 + minLength: 0 + measured: + type: number + description: Experimentally measured value for the parameter + predictedText: + type: string + maxLength: 15 + minLength: 0 + predicted: + type: number + description: The predicted value for the parameter + units: + type: string + description: Units on the predicted parameter + maxLength: 30 + minLength: 0 + model: + type: string + description: The toxicokinetic model used to predict the parameter + maxLength: 15 + minLength: 0 + reference: + type: string + description: Peer reviewed journal article(s) from which measured or predicted + value was derived + maxLength: 150 + minLength: 0 + percentile: + type: string + description: For humans, what fraction of the population have a lower value + given the same dose. Not relevant to animal species + maxLength: 5 + minLength: 0 + species: + type: string + maxLength: 10 + minLength: 0 + dataSourceSpecies: + type: string + maxLength: 10 + minLength: 0 + FunctionalUseAll: + type: object + properties: + id: + type: integer + format: int64 + reportedfunction: + type: string + functioncategory: + type: string + doctitle: + type: string + datatype: + type: string + dtxsid: + type: string + docdate: + type: string + docid: + type: integer + format: int32 + Puc: + type: object + properties: + id: + type: integer + format: int64 + kindName: + type: string + maxLength: 50 + minLength: 0 + genCat: + type: string + maxLength: 50 + minLength: 0 + prodfam: + type: string + maxLength: 50 + minLength: 0 + prodtype: + type: string + maxLength: 100 + minLength: 0 + definition: + type: string + MMDBSingleSample: + type: object + description: The information here describes harmonized single-sample records + associated with studies that report sample-level results in MMDB with their + associated source and metadata information. + properties: + id: + type: integer + format: int64 + description: Unique database ID for this individual table record + fullSourceName: + type: string + description: Full name of the data source + maxLength: 120 + minLength: 0 + chemicalName: + type: string + description: Any reported chemical name reported in the raw data + maxLength: 200 + minLength: 0 + dtxsid: + type: string + description: DSSTox chemical structure ID + maxLength: 20 + minLength: 0 + preferredName: + type: string + description: Preferred chemical name for this DTXSID + maxLength: 300 + minLength: 0 + casrn: + type: string + description: CASRN associated with this DTXSID + maxLength: 20 + minLength: 0 + result: + type: string + description: Any reported concentration or sample result included in the + raw data (any format) + maxLength: 100 + minLength: 0 + units: + type: string + description: Any reported units included in the raw data (any format) + maxLength: 100 + minLength: 0 + cleanedUnits: + type: string + description: Units from the raw data formatted for consistency + lod: + type: string + description: Limit of detection associated witht he study, if available + maxLength: 45 + minLength: 0 + loq: + type: string + description: Limit of quantification associated witht he study, if available + maxLength: 45 + minLength: 0 + detectionFlag: + type: string + description: Flag indicating if raw data indicated a measurement below limit + of detection + maxLength: 100 + minLength: 0 + resultFlag: + type: string + description: Any reported flags associated with the reported concentrationresult + in the raw data + maxLength: 500 + minLength: 0 + detected: + type: integer + format: int32 + description: Single variable indicating whether observation is associated + with detection of the chemical (1:yes; 2:no; NA:could not be determined + conclusively) + detectedConflict: + type: integer + format: int32 + description: A quality flag to note if fields used to determine if a chemical + was detected were in conflict, resulting in less certain detected field + designation (1:the detected field for a chemical sample is less certain; + 0:no conflict) + notesDetects: + type: string + description: Description of detected status + species: + type: string + description: Any species name (biota) reported in the raw data + maxLength: 200 + minLength: 0 + media: + type: string + description: Any media name reported in the raw data + maxLength: 120 + minLength: 0 + harmonizedMedium: + type: string + description: Harmonized medium associated with the reported_media + maxLength: 200 + minLength: 0 + method: + type: string + description: Any reported analytical method information included in the + raw data (any format) + maxLength: 1000 + minLength: 0 + collectionActivityId: + type: string + description: Any reported collection activity ID reported in the raw data + maxLength: 100 + minLength: 0 + sampleId: + type: string + description: Any reported sample ID reported in the raw data + maxLength: 100 + minLength: 0 + mmdbSampleId: + type: string + description: Standardized sample ID issued for unique combinations of sample + and source for single-sample data + dates: + type: string + description: Any reported date of sample collection in the raw data (any + format) + maxLength: 45 + minLength: 0 + year: + type: string + description: Year of sample collection + maxLength: 4 + minLength: 0 + month: + type: string + description: Month of sample collection (any format) + maxLength: 4 + minLength: 0 + time: + type: string + description: Time of sample collection (any format) + location: + type: string + description: Any specific location reported in the raw data that does not + fit other location variables (any format) + maxLength: 250 + minLength: 0 + stateOrProvince: + type: string + description: U.S. state or international province where sample was collected + county: + type: string + description: U.S. county where sample was collected + maxLength: 60 + minLength: 0 + country: + type: string + description: Country where sample was collected + maxLength: 100 + minLength: 0 + qualityFlag: + type: string + description: Flag indicating if raw data included any quality flags for + the record + maxLength: 100 + minLength: 0 + link: + type: string + description: Any web link to location of the record in the original data + source + maxLength: 500 + minLength: 0 + reference: + type: string + description: Any literature reference included in the raw data (any format) + maxLength: 300 + minLength: 0 + version: + type: string + description: Release version of the data + exportDate: + type: string + format: date + description: Date this data was inserted into a materialized view + casnumber: + type: string + MMDBMediaDescSummary: + type: object + properties: + harmonizedMedium: + type: string + harmonizedMediumDesc: + type: string + MMDBAggregate: + type: object + description: The information here describes records associated with reported + statistics from aggregate studies in MMDB with their associated source and + metadata information. + properties: + id: + type: integer + format: int64 + description: Unique database ID for this individual table record + fullSourceName: + type: string + description: Full name of the data source + maxLength: 120 + minLength: 0 + chemicalName: + type: string + description: Any reported chemical name reported in the raw data + maxLength: 200 + minLength: 0 + dtxsid: + type: string + description: DSSTox chemical structure ID + maxLength: 20 + minLength: 0 + preferredName: + type: string + description: Preferred chemical name for this DTXSID + maxLength: 300 + minLength: 0 + casrn: + type: string + description: CASRN associated with this DTXSID + maxLength: 20 + minLength: 0 + result: + type: string + description: Reported value (any format) for reported_statistic + units: + type: string + description: Any reported units included in the raw data (any format) + maxLength: 100 + minLength: 0 + cleanedUnits: + type: string + description: Units from the raw data formatted for consistency + statistic: + type: string + description: Name of the reported statistic in the raw data + maxLength: 100 + minLength: 0 + sampleSize: + type: string + description: Reported sample size + lod: + type: string + description: Limit of detection associated witht he study, if available + loq: + type: string + description: Limit of quantification associated witht he study, if available + numDetects: + type: string + description: Reported number of detections + numNonDetects: + type: string + description: Any reported number of nondetects in the raw data + rateDetects: + type: string + description: Reported rate of detection (percent or fraction) included in + the raw data (any format) + detected: + type: integer + format: int32 + description: Single variable indicating whether observation is associated + with detection of the chemical (1:yes; 2:no; NA:could not be determined + conclusively) + detectedConflict: + type: integer + format: int32 + description: A quality flag to note if fields used to determine if a chemical + was detected were in conflict, resulting in less certain detected field + designation (1:the detected field for a chemical sample is less certain; + 0:no conflict) + notesDetects: + type: string + description: Description of detected status + species: + type: string + description: Any species name (biota) reported in the raw data + maxLength: 200 + minLength: 0 + media: + type: string + description: Any media name reported in the raw data + maxLength: 120 + minLength: 0 + harmonizedMedium: + type: string + description: Harmonized medium associated with the reported_media + maxLength: 200 + minLength: 0 + population: + type: string + description: Any reported description of the population studied + maxLength: 500 + minLength: 0 + subPopulation: + type: string + description: Any reported subpopulation of human subjects included in the + raw data (any format) + collectionActivityId: + type: string + description: Any reported collection activity ID reported in the raw data + maxLength: 100 + minLength: 0 + dates: + type: string + description: Any reported date information for sample collection in the + raw data (any format) + years: + type: string + description: Inclusive year range of sample collection in the raw data (any + format) + location: + type: string + description: Any specific location reported in the raw data that does not + fit other location variables (any format) + maxLength: 500 + minLength: 0 + stateOrProvince: + type: string + description: U.S. state or international province where sample was collected + county: + type: string + description: U.S. county where sample was collected + maxLength: 60 + minLength: 0 + country: + type: string + description: Country where sample was collected + qualityFlag: + type: string + description: Flag indicating if raw data included any quality flags for + the record + maxLength: 200 + minLength: 0 + link: + type: string + description: Any web link to location of the record in the original data + source + maxLength: 500 + minLength: 0 + reference: + type: string + description: Any literature reference included in the raw data (any format) + maxLength: 300 + minLength: 0 + version: + type: string + description: Release version of the data + exportDate: + type: string + format: date + description: Date this data was inserted into a materialized view + casnumber: + type: string + ListPresenceTag: + type: object + properties: + id: + type: integer + format: int64 + tagName: + type: string + maxLength: 100 + minLength: 0 + tagDefinition: + type: string + maxLength: 750 + minLength: 0 + tagKind: + type: string + maxLength: 50 + minLength: 0 + QsurDataAll: + type: object + properties: + harmonizedFunctionalUse: + type: string + dtxsid: + type: string + probability: + type: number + FunctionalUseCategoryAll: + type: object + properties: + id: + type: integer + format: int64 + definition: + type: string + category: + type: string + CCDProductUseCategory: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + displayPuc: + type: string + maxLength: 202 + minLength: 0 + pucKind: + type: string + maxLength: 50 + minLength: 0 + prodCount: + type: integer + format: int64 + genCat: + type: string + maxLength: 50 + minLength: 0 + prodfam: + type: string + maxLength: 50 + minLength: 0 + prodtype: + type: string + maxLength: 100 + minLength: 0 + definition: + type: string + CCDProductionVolume: + type: object + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + name: + type: string + amount: + type: string + CCDBiomonitoring: + type: object + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + demographic: + type: string + median: + type: number + upperBound: + type: number + lowerBound: + type: number + nhanesCohort: + type: string + CCDBiomonitoringAll: + type: object + properties: + label: + type: string + median: + type: number + dtxsid: + type: string + hoverMsg: + type: string + upper95th: + type: number + lower95th: + type: number + CCDGeneralUseKeywords: + type: object + properties: + id: + type: integer + format: int64 + keywordset: + type: string + sourceCount: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + CCDReportedFunctionalUse: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + category: + type: string + maxLength: 100 + minLength: 0 + definition: + type: string + maxLength: 255 + minLength: 0 + CCDChemicalWeightFractions: + type: object + properties: + id: + type: integer + format: int64 + dtxsid: + type: string + maxLength: 50 + minLength: 0 + prodName: + type: string + maxLength: 255 + minLength: 0 + displayPuc: + type: string + maxLength: 202 + minLength: 0 + pucKind: + type: string + maxLength: 50 + minLength: 0 + lowerweightfraction: + type: number + upperweightfraction: + type: number + weightfractiontype: + type: string + maxLength: 50 + minLength: 0 + gencat: + type: string + maxLength: 50 + minLength: 0 + prodfam: + type: string + maxLength: 50 + minLength: 0 + prod_type: + type: string + maxLength: 100 + minLength: 0 + pucDefinition: + type: string + sourceName: + type: string + maxLength: 50 + minLength: 0 + sourceDescription: + type: string + sourceUrl: + type: string + maxLength: 150 + minLength: 0 + sourceDownloadDate: + type: string + format: date-time + productCount: + type: integer + format: int64 + securitySchemes: + api_key: + type: apiKey + description: 'Each API call should have api_key, Contact author for getting + the new api_key. ' + name: x-api-key + in: header diff --git a/public/docs/hazard.json b/public/docs/hazard.json index 123e46d..64ba61e 100644 --- a/public/docs/hazard.json +++ b/public/docs/hazard.json @@ -7,8 +7,8 @@ }, "servers": [ { - "url": "https://ctx-api-dev.ccte.epa.gov", - "description": "Development Environment" + "url": "https://ctx-api-stg.ccte.epa.gov", + "description": "Staging Environment" } ], "tags": [ diff --git a/public/docs/hazard.yaml b/public/docs/hazard.yaml new file mode 100644 index 0000000..8c0f722 --- /dev/null +++ b/public/docs/hazard.yaml @@ -0,0 +1,3155 @@ +--- +openapi: 3.1.0 +info: + title: Computational Toxicology and Exposure Data APIs - Hazard + description: The Hazard APIs are part of a set of public computational toxicology + and exposure APIs and provide hazard data through a set of API endpoints. Users + have the option to get all the data or only data related to human health or related + to ecotoxicology. + version: 1.0.0 +servers: + - url: https://ctx-api-stg.ccte.epa.gov + description: Production Environment +tags: + - name: PPRTV Resource + description: API endpoints for collecting pprtv chemical data for specified chemical + identifier (DTXSID). + - name: ToxValDb Cancer Summary Resource + description: API endpoints for collecting cancer summary data. + - name: ToxRefDb Effects Resource + description: API endpoints for collecting ToxRefDB effects data. + - name: ToxValDb Skin Eye Resource + description: API endpoints for collecting skin eye data. + - name: ToxValDb Resource + description: API endpoints for collecting ToxValDb data for specified chemical identifier + (DTXSID). + - name: HAWC Resource + description: API endpoints for collecting CCD - EPA HAWC link mapper for specified + chemical identifier (DTXSID). + - name: ToxRefDB Summary Resource + description: API endpoints for collecting ToxRefDB summary data. + - name: ToxRefDB Batch Resource + description: API endpoints for collecting ToxRef data by batch of dtxsids. + - name: IRIS Resource + description: API endpoints for collecting IRIS data for specified chemical identifier + (DTXSID). + - name: ToxValDb Genetox Resource + description: API endpoints for collecting Genetox data. + - name: ToxRefDB Data Resource + description: API endpoints for collecting ToxRefDB data. + - name: ADME - IVIVE Resource + description: API endpoints for collecting adme - ivive data for specified chemical + identifier (DTXSID). + - name: ToxRefDB Observation Resource + description: API endpoints for collecting ToxRefDB observation data. +paths: + "/hazard/toxval/search/by-dtxsid/": + post: + tags: + - ToxValDb Resource + summary: Get all data by batch of dtxsid(s). + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: hazardBatch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxValDb" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/toxref/search/by-dtxsid/": + post: + tags: + - ToxRefDB Batch Resource + summary: Get data by batch of dtxsid(s) + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: toxRefBatch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID5034307","DTXSID2040363"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefBatch" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/skin-eye/search/by-dtxsid/": + post: + tags: + - ToxValDb Skin Eye Resource + summary: Get data by batch of dtxsid(s) + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: skinEyedBatch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SkinEye" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/genetox/summary/search/by-dtxsid/": + post: + tags: + - ToxValDb Genetox Resource + summary: Get summary data by batch of dtxsid(s). + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: batchSearchSummary + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenetoxSummary" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/genetox/details/search/by-dtxsid/": + post: + tags: + - ToxValDb Genetox Resource + summary: Get detail data by batch of dtxsid(s) + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: batchSearch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenetoxDetail" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/cancer-summary/search/by-dtxsid/": + post: + tags: + - ToxValDb Cancer Summary Resource + summary: Get data by batch of dtxsid(s) + description: 'Note: Maximum 200 DTXSIDs per request' + operationId: cancerSummaryBatch + requestBody: + description: JSON array of DSSTox Substance Identifier + content: + application/json: + schema: + type: array + items: + type: string + example: '["DTXSID7020182","DTXSID9020112"]' + required: true + responses: + '200': + description: Successfull + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CancerSummary" + '400': + description: When user has submitted more then allowed number (200) of DTXSID(s). + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ProblemDetail" + example: + title: Validation Error + status: 400 + detail: System supports only '200' dtxsid at one time, '202' are submitted. + security: + - api_key: [] + "/hazard/toxval/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxValDb Resource + summary: Get all data by dtxsid + operationId: hazardByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0021125 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxValDb" + security: + - api_key: [] + "/hazard/toxref/summary/search/by-study-type/{studyType}": + get: + tags: + - ToxRefDB Summary Resource + summary: Get data by study type + operationId: toxRefSummaryByStudyType + parameters: + - name: studyType + in: path + description: Study Type + required: true + schema: + type: string + example: DEV + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefSummary" + security: + - api_key: [] + "/hazard/toxref/summary/search/by-study-id/{studyId}": + get: + tags: + - ToxRefDB Summary Resource + summary: Get data by study id + operationId: toxRefSummaryByStudyId + parameters: + - name: studyId + in: path + description: Study ID + required: true + schema: + type: integer + format: int32 + example: 63 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefSummary" + security: + - api_key: [] + "/hazard/toxref/summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxRefDB Summary Resource + summary: Get data by dtxsid + operationId: toxRefSummaryByDtxsid + parameters: + - name: dtxsid + in: path + description: dtxsid + required: true + schema: + type: string + example: DTXSID1037806 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefSummary" + security: + - api_key: [] + "/hazard/toxref/observations/search/by-study-type/{studyType}": + get: + tags: + - ToxRefDB Observation Resource + summary: Get observations by study type + operationId: toxRefObsByStudyType + parameters: + - name: studyType + in: path + description: Study Type + required: true + schema: + type: string + example: DEV + - name: pageNumber + in: query + required: false + schema: + type: integer + format: int32 + default: 1 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefObs" + security: + - api_key: [] + "/hazard/toxref/observations/search/by-study-id/{studyId}": + get: + tags: + - ToxRefDB Observation Resource + summary: Get observations by study id + operationId: toxRefObsByStudyId + parameters: + - name: studyId + in: path + description: Study ID + required: true + schema: + type: integer + format: int32 + example: 63 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefObs" + security: + - api_key: [] + "/hazard/toxref/observations/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxRefDB Observation Resource + summary: Get observations by dtxsid + operationId: toxRefObsByDtxsid + parameters: + - name: dtxsid + in: path + description: dtxsid + required: true + schema: + type: string + example: DTXSID1037806 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefObs" + security: + - api_key: [] + "/hazard/toxref/effects/search/by-study-type/{studyType}": + get: + tags: + - ToxRefDb Effects Resource + summary: Get data by study type + operationId: toxRefEffectsByStudyType + parameters: + - name: studyType + in: path + description: Study Type + required: true + schema: + type: string + example: DEV + - name: pageNumber + in: query + required: false + schema: + type: integer + format: int32 + default: 1 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefEffects" + security: + - api_key: [] + "/hazard/toxref/effects/search/by-study-id/{studyId}": + get: + tags: + - ToxRefDb Effects Resource + summary: Get data by study id + operationId: toxRefEffectsByStudyId + parameters: + - name: studyId + in: path + description: Study ID + required: true + schema: + type: integer + format: int32 + example: 63 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefEffects" + security: + - api_key: [] + "/hazard/toxref/effects/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxRefDb Effects Resource + summary: Get data by dtxsid + operationId: toxRefEffectsByDtxsid + parameters: + - name: dtxsid + in: path + description: dtxsid + required: true + schema: + type: string + example: DTXSID1037806 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefEffects" + security: + - api_key: [] + "/hazard/toxref/data/search/by-study-type/{studyType}": + get: + tags: + - ToxRefDB Data Resource + summary: Get data by study type + operationId: toxRefDataByStudyType + parameters: + - name: studyType + in: path + description: Study Type + required: true + schema: + type: string + example: DEV + - name: pageNumber + in: query + required: false + schema: + type: integer + format: int32 + default: 1 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefData" + security: + - api_key: [] + "/hazard/toxref/data/search/by-study-id/{studyId}": + get: + tags: + - ToxRefDB Data Resource + summary: Get data by study id + operationId: toxRefDataByStudyId + parameters: + - name: studyId + in: path + description: Study ID + required: true + schema: + type: integer + format: int32 + example: 63 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefData" + security: + - api_key: [] + "/hazard/toxref/data/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxRefDB Data Resource + summary: Get data by dtxsid + operationId: toxRefDataByDtxsid + parameters: + - name: dtxsid + in: path + description: dtxsid + required: true + schema: + type: string + example: DTXSID1037806 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/ToxRefData" + security: + - api_key: [] + "/hazard/skin-eye/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxValDb Skin Eye Resource + summary: Get data by dtxsid + operationId: skinEyedByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0021125 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/SkinEye" + security: + - api_key: [] + "/hazard/pprtv/search/by-dtxsid/{dtxsid}": + get: + tags: + - PPRTV Resource + summary: Get all pprtv chemical data by dtxsid + operationId: pprtvChemicalsByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/Pprtv" + security: + - api_key: [] + "/hazard/iris/search/by-dtxsid/{dtxsid}": + get: + tags: + - IRIS Resource + summary: Get all iris data by dtxsid + operationId: irisDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/Iris" + security: + - api_key: [] + "/hazard/hawc/search/by-dtxsid/{dtxsid}": + get: + tags: + - HAWC Resource + summary: Get CCD - EPA HAWC link mapper by dtxsid + operationId: hawcDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/Hawc" + security: + - api_key: [] + "/hazard/genetox/summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxValDb Genetox Resource + summary: Get summary data by dtxsid + operationId: genetoxSummaryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0021125 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenetoxSummary" + security: + - api_key: [] + "/hazard/genetox/details/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxValDb Genetox Resource + summary: Get detail data by dtxsid with ccd projection + description: return genetox details for requested dtxsidthere is an available + projection for ccd Genetoxicity Details page:ccd-genetox-detailsIf no projection + is specified, the default GenetoxDetails data will be returned + operationId: getGenetoxDetailsByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + - name: projection + in: query + description: 'Specifies if projection is used. Option: ccd-genetox-details, + If omitted, the default GenetoxDetail data is returned.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/GenetoxDetail" + - "$ref": "#/components/schemas/CcdGenetoxDetail" + security: + - api_key: [] + "/hazard/cancer-summary/search/by-dtxsid/{dtxsid}": + get: + tags: + - ToxValDb Cancer Summary Resource + summary: Get data by dtxsid + operationId: cancerSummaryByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID0021125 + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/CancerSummary" + security: + - api_key: [] + "/hazard/adme-ivive/search/by-dtxsid/{dtxsid}": + get: + tags: + - ADME - IVIVE Resource + summary: Get all adme - ivive data by dtxsid with ccd projection + description: return adme - ivive data for requested dtxsidthere is an available + projection for ccd ADME - IVIVE page:ccd-adme-dataIf no projection is specified, + the default ADME data will be returned + operationId: admeDataByDtxsid + parameters: + - name: dtxsid + in: path + description: DSSTox Substance Identifier + required: true + schema: + type: string + example: DTXSID7020182 + - name: projection + in: query + description: 'Specifies if projection is used. Option: ccd-adme-data, If omitted, + the default ADME-IVIVE data is returned.' + required: false + schema: + type: string + responses: + '200': + description: OK + content: + application/json: + schema: + type: string + oneOf: + - "$ref": "#/components/schemas/Adme" + - "$ref": "#/components/schemas/CcdADME" + security: + - api_key: [] +components: + schemas: + ToxValDb: + type: object + description: The Toxicity Values Database (ToxValDB) is a compilation of toxicity + information from world-wide sites, databases, and sources, which can save + the user time by providing information in one location. The data are largely + limited to summary values from individual studies or chemical-level assessments, + and is focused on quantitative values such as LOAELs, NOAELs, BMDs, LD50s + and RfDs. The user must apply judgment in use of the information and should + consult the original scientific paper or data source, if possible, to ensure + an understanding of the context of the data. The ToxValDB SQL download is + available at https://www.epa.gov/comptox-tools/downloadable-computational-toxicology-data#AT + . + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + maxLength: 45 + minLength: 0 + casrn: + type: string + name: + type: string + source: + type: string + description: Originator of source data + maxLength: 255 + minLength: 0 + subsource: + type: string + description: Additional source reference + maxLength: 255 + minLength: 0 + toxvalType: + type: string + description: 'Categorization of records based on POD or effect level. Categories + include: Point of Departure (The quantitative result of an in vivo repeat + dose study, such as a LOAEL, NOAEL or BMDL), Lethality Effect Level (The + quantitative result of an in vivo acute study, such as a LD50 or LC50), + Toxicity Value (A risk assessment summary value for a chemical, such as + an RFD or cancer slope factor), Screening Level (An environmentally safe + concentration, primarily EPA Regional Screening levels), Exposure Limit + (Exposure levels of concern in air, water, or other media), Effect Time + (A time when an effect is seen for a fixed concentration. These values + all come from the ECOTOX Knowledgebase), Effect Level (A value similar + to a Point of Departure, but not linked to a critical effect), Effect + Dose (Similar to a Lethality Effect Level but for non-lethal ecotoxicology + endpoints in acute studies), Inhibition Concentration (Similar to a Lethality + Effect Level but for non-lethal ecotoxicology endpoints, focused on inhibition + of growth), Other (Other uncharacterized classes of records)' + maxLength: 255 + minLength: 0 + toxvalTypeDefinition: + type: string + toxvalSubtype: + type: string + description: Effect subtype or value subtype + maxLength: 255 + minLength: 0 + toxvalTypeSuperCategory: + type: string + maxLength: 255 + minLength: 0 + qualifier: + type: string + description: Operators (<, <=, >, >=, =) to contextualize level of certainty + in estimates + maxLength: 255 + minLength: 0 + toxvalNumeric: + type: number + format: double + description: Concentration of a test chemical, typically reported in ppm + within the exposure matrix (e.g., feed or water), or the an adjusted amount + of the chemical administered in mg/kg of body weight/day (mg/kg/day) + toxvalUnits: + type: string + description: Unit associated with the concentration or adjusted dose of + a chemical + maxLength: 255 + minLength: 0 + riskAssessmentClass: + type: string + description: Designation of cancer or non-cancer for toxicity values or + media associated with exposure guideline values + maxLength: 255 + minLength: 0 + humanEco: + type: string + maxLength: 255 + minLength: 0 + studyType: + type: string + description: Classification to describe toxicity testing that was conducted + maxLength: 255 + minLength: 0 + studyDurationClass: + type: string + description: 'Categorical description of exposure duration ' + maxLength: 255 + minLength: 0 + studyDurationValue: + type: number + format: double + description: Amount of time a group is dosed. This varies within studies + depending on the dose period of a particular treatment group + studyDurationUnits: + type: string + description: Unit of time associated with the dose duration. Typically in + days or months + maxLength: 255 + minLength: 0 + speciesCommon: + type: string + description: Species of the animal test subject used in a study + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform + maxLength: 255 + minLength: 0 + latinName: + type: string + maxLength: 255 + minLength: 0 + speciesSupercategory: + type: string + description: Categorization of effect or value type into one of five categories, + including dose response summary value, mortality response summary value, + toxicity value, media exposure guidelines, or acute exposure guidelines + maxLength: 255 + minLength: 0 + sex: + type: string + description: Gender of a test animal. The gender of fetal groups is denoted + as MF for both males and females + maxLength: 255 + minLength: 0 + generation: + type: string + description: Generation a test animal belongs to + maxLength: 255 + minLength: 0 + lifestage: + type: string + description: Stage of life that a measurement was taken + maxLength: 255 + minLength: 0 + exposureRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other + maxLength: 255 + minLength: 0 + exposureMethod: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical + maxLength: 255 + minLength: 0 + exposureForm: + type: string + description: The vehicle used in administration of the chemical + maxLength: 255 + minLength: 0 + media: + type: string + maxLength: 255 + minLength: 0 + toxicologicalEffect: + type: string + description: 'Treatment-associated effect ' + experimentalRecord: + type: string + studyGroup: + type: string + maxLength: 255 + minLength: 0 + longRef: + type: string + doi: + type: string + title: + type: string + author: + type: string + maxLength: 255 + minLength: 0 + year: + type: string + maxLength: 255 + minLength: 0 + guideline: + type: string + maxLength: 255 + minLength: 0 + quality: + type: string + maxLength: 255 + minLength: 0 + qcCategory: + type: string + sourceHash: + type: string + maxLength: 45 + minLength: 0 + externalSourceId: + type: string + externalSourceIdDesc: + type: string + sourceUrl: + type: string + description: URL for source data + maxLength: 255 + minLength: 0 + subsourceUrl: + type: string + description: Additional URL reference for source data + maxLength: 255 + minLength: 0 + storedSourceRecord: + type: string + maxLength: 255 + minLength: 0 + toxvalTypeOriginal: + type: string + description: 'Categorization of records based on POD or effect level. Categories + include: Point of Departure (The quantitative result of an in vivo repeat + dose study, such as a LOAEL, NOAEL or BMDL), Lethality Effect Level (The + quantitative result of an in vivo acute study, such as a LD50 or LC50), + Toxicity Value (A risk assessment summary value for a chemical, such as + an RFD or cancer slope factor), Screening Level (An environmentally safe + concentration, primarily EPA Regional Screening levels), Exposure Limit + (Exposure levels of concern in air, water, or other media), Effect Time + (A time when an effect is seen for a fixed concentration. These values + all come from the ECOTOX Knowledgebase), Effect Level (A value similar + to a Point of Departure, but not linked to a critical effect), Effect + Dose (Similar to a Lethality Effect Level but for non-lethal ecotoxicology + endpoints in acute studies), Inhibition Concentration (Similar to a Lethality + Effect Level but for non-lethal ecotoxicology endpoints, focused on inhibition + of growth), Other (Other uncharacterized classes of records) (original)' + maxLength: 255 + minLength: 0 + toxvalSubtypeOriginal: + type: string + description: Effect subtype or value subtype (original) + maxLength: 255 + minLength: 0 + toxvalNumericOriginal: + type: number + format: double + description: Concentration of a test chemical, typically reported in ppm + within the exposure matrix (e.g., feed or water), or the an adjusted amount + of the chemical administered in mg/kg of body weight/day (mg/kg/day) (original) + maximum: 255 + minimum: 0 + toxvalUnitsOriginal: + type: string + description: Unit associated with the concentration or adjusted dose of + a chemical (original) + maxLength: 255 + minLength: 0 + studyTypeOriginal: + type: string + description: Classification to describe toxicity testing that was conducted + (original) + maxLength: 255 + minLength: 0 + studyDurationClassOriginal: + type: string + description: Categorical description of exposure duration (original) + maxLength: 255 + minLength: 0 + studyDurationValueOriginal: + type: string + description: Amount of time a group is dosed. This varies within studies + depending on the dose period of a particular treatment group (original) + maxLength: 255 + minLength: 0 + studyDurationUnitsOriginal: + type: string + description: Unit of time associated with the dose duration. Typically in + days or months (original) + maxLength: 255 + minLength: 0 + speciesOriginal: + type: string + description: Species of the animal test subject used in a study (original) + maxLength: 255 + minLength: 0 + strainOriginal: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform (original) + maxLength: 255 + minLength: 0 + sexOriginal: + type: string + description: Gender of a test animal. The gender of fetal groups is denoted + as MF for both males and females (original) + maxLength: 255 + minLength: 0 + generationOriginal: + type: string + description: Generation a test animal belongs to (original) + maxLength: 255 + minLength: 0 + lifestageOriginal: + type: string + description: Stage of life that a measurement was taken (original) + maxLength: 255 + minLength: 0 + exposureRouteOriginal: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other (original) + maxLength: 255 + minLength: 0 + exposureMethodOriginal: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical (original + maxLength: 255 + minLength: 0 + exposureFormOriginal: + type: string + description: The vehicle used in administration of the chemical (original) + maxLength: 255 + minLength: 0 + mediaOriginal: + type: string + maxLength: 255 + minLength: 0 + toxicologicalEffectOriginal: + type: string + description: Treatment-associated effect (original) + originalYear: + type: string + description: Year in which the study was reported as finished + maxLength: 255 + minLength: 0 + required: + - id + ProblemDetail: + type: object + properties: + type: + type: string + format: uri + title: + type: string + status: + type: integer + format: int32 + detail: + type: string + instance: + type: string + format: uri + properties: + type: object + additionalProperties: {} + ToxRefBatch: + type: object + description: Export of all extracted dose-treatment group-effect information + as well as doses not eliciting effects from ToxRefDB for the dtxsids listed + in the input. Data from ToxRefDB is also summarized in ToxValDB, including + inferred NEL and NOAEL effect levels based on the reported LEL and LOAEL, + respectively. + properties: + studyId: + type: integer + format: int32 + description: A unique numeric identifier for each study in the database. + dtxsid: + type: string + description: Unique identifier from DSSTox + maxLength: 45 + minLength: 0 + casrn: + type: string + description: Curated casrn from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + name: + type: string + description: Curated chemical name from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + studySource: + type: string + description: Organization that provided or authored the document for curation. + maxLength: 255 + minLength: 0 + studySourceId: + type: string + description: Unique document identifier provided by the study source. + maxLength: 255 + minLength: 0 + citation: + type: string + description: Citation in source document + maxLength: 1024 + minLength: 0 + studyYear: + type: string + studyType: + type: string + description: 'Classification to describe animal toxicity testing that was + conducted. Based on either dose period, subjects involved, or measured + effects of interest, study types include: ACU (acute): Dose period typically + a day or less. Excludes developmental and neurological studies.; SAC (subacute): + Dose period is typically 21-28 days. Excludes developmental and neurological + studies.; SUB (subchronic): Dose period is typically 13 weeks, but may + be as long as 6 months. Excludes developmental and neurological studies.; + CHR (chronic): Dose period is typically 12, 18, or 24 months (generally + any dosing lasting a year or longer). Excludes developmental and neurological + studies.; DEV (developmental): Gestational (in utero) dose period. Sacrificed + prior to delivery.; MGR (multigenerational reproductive): Dose period + begins in adolescent F0 males and females and continues until terminal + generation. At least some of the litters deliver their pups, some may + be sacrificed prior to delivery.; NEU (neurological): Study contains functional + observation battery or other battery of behavioral testing that occurs + during or after dosing. Pathology has specific interest in the brain (i.e. + regions, morphology, biochemistry, et cetera). excludes developmental + studies; DNT (developmental neurotoxicity): dose period occurs anytime + during development (i.e. in utero, lactational, adolescent [after weaning, + before adulthood]). Study contains functional observation battery or other + battery of behavioral testing that occurs during or after dosing, typically + during adulthood. Pathology has specific interest in the brain (i.e. regions, + morphology, biochemistry, etc.)' + maxLength: 255 + minLength: 0 + studyTypeGuideline: + type: string + description: Description that combines the study_type and guideline name + for a study. + maxLength: 255 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study. + maxLength: 255 + minLength: 0 + strainGroup: + type: string + description: 'Descriptive category for a group of test animals that is more + general than the strain. ' + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform. + maxLength: 255 + minLength: 0 + adminRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other. + maxLength: 255 + minLength: 0 + adminMethod: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical. + maxLength: 255 + minLength: 0 + doseDuration: + type: string + description: Amount of time a group is dosed. This varies within studies + depending on the dose period of a particular treatment group. + doseDurationUnit: + type: string + description: Unit of time associated with the dose duration. Typically in + days or months. + maxLength: 16 + minLength: 0 + doseStart: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance began. + doseStartUnit: + type: string + description: Unit of time associated with the start of the dose (dose_start). + maxLength: 255 + minLength: 0 + doseEnd: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance stopped. + doseEndUnit: + type: string + description: Unit of time associated with the end of the dose (dose_end). + maxLength: 255 + minLength: 0 + dosePeriod: + type: string + description: Period within a group's lifetime that the animals were dosed + and the sample for an endpoint's data was taken (when the animals were + sacrificed). + maxLength: 32 + minLength: 0 + doseLevel: + type: integer + format: int32 + description: 'Numeric rank indicating the level of dose administered to + test animals, with lower dose levels indicating lower concentrations of + a chemical (e.g., 0 = vehicle, 1 = lowest dose, etc.). The dose level + for some studies may be staggered since concentrations may vary by sex + (e.g, male treatment group: 0 = vehicle, 1 = lowest dose, 3 = second lowest + dose, etc.).' + conc: + type: string + description: Concentration of a test chemical, typically reported in ppm + within the exposure matrix (e.g., feed or water). + concUnit: + type: string + description: Unit associated with a concentration of a test chemical, typically + reported as ppm. + maxLength: 255 + minLength: 0 + vehicle: + type: string + description: The media used in administration of the chemical. + maxLength: 255 + minLength: 0 + doseComment: + type: string + description: NULL if no additional comment needed. Field can be used to + explain any differences in dosing over the dosing interval and/or clarifying + comments on how the dose was administered. + maxLength: 1024 + minLength: 0 + doseAdjusted: + type: string + description: The amount of the chemical administered in mg/kg of body weight/day + (mg/kg/day). This value is typically different between male and female + groups receiving the same dose concentration (conc) due to differences + in bodyweight. If dose_adjusted values were not provided in a study, then + they were calculated using species scaling factors (FAO/WHO, 2000). + doseAdjustedUnit: + type: string + description: Unit associated with the adjusted dose of a chemical, typically + reported in mg/kg/day. + maxLength: 32 + minLength: 0 + sex: + type: string + description: Gender of a test animal. The gender of fetal groups is denoted + as MF for both males and females. + maxLength: 8 + minLength: 0 + generation: + type: string + description: Generation a test animal belongs to. The F0 generation is the + first generation mating group for MGR studies and is the default for non-reproductive + studies (CHR, SUB, SAC). F1 is the second generation mating group, selected + from either F1a or F1b litters. F2 is the third generation mating group, + selected from either F2a or F2b litters. F1a and F1b are the first and + second litter groups produced by F0 matings, F2a and F2b are the first + and second litter groups produced by F1 matings, and F3a and F3b are the + first and second litter groups produced by F2 matings. The fetal generation + is the group produced by F0 matings in DEV studies, and are typically + removed from a female via cesarean section in DEV studies. + maxLength: 16 + minLength: 0 + lifeStage: + type: string + description: 'Stage of life that a measurement was taken. CHR, SUB, and + SAC studies typically only have adult for life_stage, whereas DEV and + MGR studies will always be characterized by multiple life stages. The + different life stages in the database include: fetal, juvenile, adult, + adult-pregnancy and pregnancy.' + maxLength: 32 + minLength: 0 + numAnimals: + type: string + description: Number of animals per treatment group + maxLength: 255 + minLength: 0 + tgComment: + type: string + description: 'NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group (e.g. animals dosed via capsule so concentration + not reported, added recovery groups, etc.). ' + maxLength: 1024 + minLength: 0 + endpointCategory: + type: string + description: 'The broadest descriptive term for an endpoint. Possible endpoint + categories include: systemic, developmental, reproductive, and cholinesterase.' + maxLength: 255 + minLength: 0 + endpointType: + type: string + description: The subcategory for endpoint_category, which is more descriptive + for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive + performance, etc.) + maxLength: 255 + minLength: 0 + endpointTarget: + type: string + description: More specific description than endpoint_type, often indicating + where or how the sample was collected to supply data for a particular + endpoint. Target may describe an organ, tissue, metabolite or protein + measured. + maxLength: 255 + minLength: 0 + effectDesc: + type: string + description: More specific description for an effect than endpoint_category, + usually detailing a specific condition associated with an endpoint_target + (e.g. dysplasia, atrophy, necrosis, etc.). + maxLength: 255 + minLength: 0 + effectDescFree: + type: string + description: Brief verbatim text from study file that was entered if the + effect description differed from predetermined endpoint terminology. + maxLength: 255 + minLength: 0 + cancerRelated: + type: boolean + description: Indicates if effect is considered cancer related (1) or not. + targetSite: + type: string + description: A more specific description than effect_target. Can describe + a specific tissue within an organ, type of cell, etc. + maxLength: 64 + minLength: 0 + direction: + type: integer + format: int32 + description: Description of the net change across all doses that indicates + whether the numerical data increased, decreased, or stayed the same. Also + can be used to describe effects that did not have numerical data, but + were still described in the study source. + effectComment: + type: string + description: NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group-effect (e.g. units not reported, effect only reported + for certain treatment groups, etc.). + maxLength: 1024 + minLength: 0 + treatmentRelated: + type: string + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D indicates there was a statistically significant difference + from the control group for the effect; “FALSEâ€\x9D indicates there + was no difference from control group. The highest dose level at which + no significant observable adverse effects were observed corresponds to + the no effect level (NEL). The lowest effect level (LEL) can be inferred + by treatment related effects." + criticalEffect: + type: boolean + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D corresponds to a toxic or adverse effect denoted in the + study summary or via expert judgement using a weight-of-evidence approach. + “FALSEâ€\x9D indicates that although an effect is produced at this level, + it is not considered adverse, nor immediate precursors to specific adverse + effects. If there are several critical effects, the no observed adverse + effect level (NOAEL) is determined from the highest dose level without + critical effects. The lowest dose level at which the critical effect was + observed in a study is the lowest observed adverse effect level (LOAEL.)" + sampleSize: + type: string + description: Number of animals used for an examination for a particular + effect. + maxLength: 8 + minLength: 0 + effectVal: + type: string + description: Numeric value of a measured effect, can be continuous or dichotomous + (incidence) data. + effectValUnit: + type: string + description: Unit associated with the effect value. + maxLength: 128 + minLength: 0 + effectVar: + type: string + description: Measurement of the variance for a set of data associated with + a measured effect, generally reported as the standard deviation (SD) or + standard error (SE). + effectVarType: + type: string + description: 'Name of the variance metric used to determine the effect variance, + typically the standard deviation (SD) or standard error (SE). Other effect_var + types include: interquartile range, 95% confidence limit, and none.' + maxLength: 32 + minLength: 0 + time: + type: string + description: Numeric value associated with the duration of the exposure + at which a particular effect was measured or observed, typically reported + in hours, days, weeks, or months. + timeUnit: + type: string + description: " Unit associated with the duration of the exposure at which + a particular effect was measured or observed, typically reported in hours, + days, weeks, or months." + maxLength: 64 + minLength: 0 + noQuantDataReported: + type: boolean + description: Indicates if qualitative (1) or quantitative (0) effect data + was reported. + tbsKey: + type: integer + format: int64 + description: Date view of ToxRefDB data was created for API + SkinEye: + type: object + description: Skin and eye irritation tests are used to assess the safety of + products and chemicals that may come into contact with the skin or eyes. These + tests are important for labeling and registering chemicals and agrochemicals, + and for developing drugs. Types of skin and eye irritation tests include Draize + test, EpiOcular Eye Irritation Test (EIT), Red blood cells test, or Patch + test + properties: + id: + type: integer + format: int32 + authority: + type: string + maxLength: 45 + minLength: 0 + classification: + type: string + description: Classification into hazard categories based on the severity + of the skin or eye irritation + maxLength: 255 + minLength: 0 + dtxsid: + type: string + description: 'Distributed Structure-Searchable Toxicity (DSSTox) id ' + maxLength: 255 + minLength: 0 + endpoint: + type: string + description: Skin sensitization or eye irritation + maxLength: 255 + minLength: 0 + glp: + type: string + guideline: + type: string + description: Number associated with the particular guideline that a test + adheres to or most closely adheres to + recordUrl: + type: string + maxLength: 1024 + minLength: 0 + reliability: + type: string + description: Ranking of reliability of results + maxLength: 45 + minLength: 0 + resultText: + type: string + description: Annotation describing results + maxLength: 1024 + minLength: 0 + score: + type: string + description: Hazard scoring based on classification + maxLength: 45 + minLength: 0 + skinEyeHash: + type: string + maxLength: 255 + minLength: 0 + skinEyeId: + type: integer + format: int32 + skinEyeUuid: + type: string + maxLength: 255 + minLength: 0 + source: + type: string + description: Originator of source data + maxLength: 45 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform + maxLength: 255 + minLength: 0 + studyType: + type: string + description: Classification to describe testing that was conducted + maxLength: 255 + minLength: 0 + year: + type: integer + format: int32 + description: Year in which the study was reported as finished + required: + - id + GenetoxSummary: + type: object + description: 'Description: Genotoxicity testing, also known as short-term assays, + is used to evaluate the potential adverse effects of chemicals on human health. + These tests can help identify carcinogens, as about 80% of known human carcinogens + are genotoxic. The results of genotoxicity tests are important because of + the irreversible nature and severity of the health effects that may result + from genotoxic events. There are many different techniques that can be used + for genotoxicity testing, notably including Ames test (comparative genetic + analysis using multiple bacterial strains of Salmonella typhimurium), Comet + assay (measurement DNA strand breaks), micronucleus test (cytogenetic assay + that uses fluorescence in situ hybridization and chromosome painting) and + chromosomal aberration test (cytogenetic assay that examines in vivo tissues + to reflect how chemicals are absorbed, excreted, distributed, and metabolized). + This endpoint provides summary-level genotoxicity data associated to a chemical.' + properties: + id: + type: integer + format: int32 + ames: + type: string + description: Average result in AMES test + maxLength: 255 + minLength: 0 + clowderDocId: + type: string + maxLength: 65 + minLength: 0 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + maxLength: 255 + minLength: 0 + genetoxCall: + type: string + maxLength: 255 + minLength: 0 + genetoxSummaryId: + type: integer + format: int32 + micronucleus: + type: string + description: Average result in Micronucleus test + maxLength: 255 + minLength: 0 + reportsNegative: + type: integer + format: int32 + description: Count of genetox records reporting negative results + reportsOther: + type: integer + format: int32 + description: Count of genetox records reporting ‘other’ in results + reportsPositive: + type: integer + format: int32 + description: Count of genetox records reporting positive results + required: + - id + GenetoxDetail: + type: object + description: 'Description: Genotoxicity testing, also known as short-term assays, + is used to evaluate the potential adverse effects of chemicals on human health. + These tests can help identify carcinogens, as about 80% of known human carcinogens + are genotoxic. The results of genotoxicity tests are important because of + the irreversible nature and severity of the health effects that may result + from genotoxic events. There are many different techniques that can be used + for genotoxicity testing, notably including Ames test (comparative genetic + analysis using multiple bacterial strains of Salmonella typhimurium), Comet + assay (measurement DNA strand breaks), micronucleus test (cytogenetic assay + that uses fluorescence in situ hybridization and chromosome painting) and + chromosomal aberration test (cytogenetic assay that examines in vivo tissues + to reflect how chemicals are absorbed, excreted, distributed, and metabolized). + This endpoint provides detailed genotoxicity data associated to a chemical.' + properties: + id: + type: integer + format: int32 + assayCategory: + type: string + description: 'Category of assay: in vitro or in vivo' + maxLength: 45 + minLength: 0 + assayCode: + type: string + maxLength: 45 + minLength: 0 + assayPotency: + type: integer + format: int32 + maximum: 45 + minimum: 0 + assayResult: + type: string + description: Result in assay (positive, negative, or other) + maxLength: 45 + minLength: 0 + assayType: + type: string + description: Type of genotoxicity assay + maxLength: 255 + minLength: 0 + assayTypeStandard: + type: string + maxLength: 255 + minLength: 0 + chemicalId: + type: string + maxLength: 255 + minLength: 0 + clowderDocId: + type: string + maxLength: 65 + minLength: 0 + comment: + type: string + cytotoxicity: + type: string + maxLength: 255 + minLength: 0 + dataQuality: + type: integer + format: int32 + maximum: 45 + minimum: 0 + documentNumber: + type: integer + format: int32 + maximum: 45 + minimum: 0 + documentSource: + type: string + maxLength: 45 + minLength: 0 + doseResponse: + type: string + maxLength: 45 + minLength: 0 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + maxLength: 255 + minLength: 0 + duration: + type: integer + format: int32 + maximum: 45 + minimum: 0 + genetoxCall: + type: string + maxLength: 255 + minLength: 0 + genetoxDetailsId: + type: integer + format: int32 + genetoxNote: + type: string + maxLength: 255 + minLength: 0 + genetoxResults: + type: string + maxLength: 255 + minLength: 0 + genetoxSummaryId: + type: integer + format: int32 + glp: + type: integer + format: int32 + guideline: + type: string + index: + type: string + metabolicActivation: + type: integer + format: int32 + description: Indicator if assay included metabolic activation + maximum: 45 + minimum: 0 + micronucleus: + type: string + panelReport: + type: string + maxLength: 255 + minLength: 0 + protocolEra: + type: string + maxLength: 45 + minLength: 0 + reference: + type: string + maxLength: 1024 + minLength: 0 + referenceUrl: + type: string + maxLength: 255 + minLength: 0 + reportsNeg: + type: string + reportsOther: + type: string + reportsPos: + type: string + sex: + type: string + maxLength: 45 + minLength: 0 + source: + type: string + description: Originator of source data + maxLength: 45 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study + maxLength: 45 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform + maxLength: 255 + minLength: 0 + title: + type: string + maxLength: 1024 + minLength: 0 + useme: + type: integer + format: int64 + description: Year in which the study was reported as finished + year: + type: integer + format: int32 + description: Year in which the study was reported as finished + required: + - id + CancerSummary: + type: object + description: A carcinogen is a substance that may cause cancer and pose a health + hazard. Carcinogens are subject to specific controls and regulations. National + and international health agencies evaluate new and existing chemicals to determine + if they are likely to be carcinogens through a process called cancer hazard + identification. This process combines human and animal data with supporting + evidence to characterize the weight-of-evidence (WOE) regarding the agent's + potential as a human carcinogen. The general categories recognized by the + guidelines are carcinogenic to humans, likely to be carcinogenic to humans, + and suggestive evidence of carcinogenic potential. This endpoint provides + summary-level cancer data associated to a chemical. + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + maxLength: 255 + minLength: 0 + source: + type: string + description: Originator of source data + maxLength: 255 + minLength: 0 + exposureRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other + maxLength: 255 + minLength: 0 + cancerCall: + type: string + description: Annotation indicating level of carcinogenicity + maxLength: 255 + minLength: 0 + url: + type: string + description: URL for source data + maxLength: 255 + minLength: 0 + required: + - id + ToxRefSummary: + type: object + properties: + id: + type: integer + format: int64 + studyId: + type: integer + format: int32 + description: A unique numeric identifier for each study in the database. + dtxsid: + type: string + description: Unique identifier from DSSTox + maxLength: 45 + minLength: 0 + casrn: + type: string + description: Curated casrn from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + name: + type: string + description: Curated chemical name from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + studySource: + type: string + description: Organization that provided or authored the document for curation. + maxLength: 255 + minLength: 0 + studySourceId: + type: string + description: Unique document identifier provided by the study source. + maxLength: 255 + minLength: 0 + citation: + type: string + description: Citation in source document + maxLength: 1024 + minLength: 0 + studyYear: + type: integer + format: int32 + studyType: + type: string + description: 'Classification to describe animal toxicity testing that was + conducted. Based on either dose period, subjects involved, or measured + effects of interest, study types include: ACU (acute): Dose period typically + a day or less. Excludes developmental and neurological studies.; SAC (subacute): + Dose period is typically 21-28 days. Excludes developmental and neurological + studies.; SUB (subchronic): Dose period is typically 13 weeks, but may + be as long as 6 months. Excludes developmental and neurological studies.; + CHR (chronic): Dose period is typically 12, 18, or 24 months (generally + any dosing lasting a year or longer). Excludes developmental and neurological + studies.; DEV (developmental): Gestational (in utero) dose period. Sacrificed + prior to delivery.; MGR (multigenerational reproductive): Dose period + begins in adolescent F0 males and females and continues until terminal + generation. At least some of the litters deliver their pups, some may + be sacrificed prior to delivery.; NEU (neurological): Study contains functional + observation battery or other battery of behavioral testing that occurs + during or after dosing. Pathology has specific interest in the brain (i.e. + regions, morphology, biochemistry, et cetera). excludes developmental + studies; DNT (developmental neurotoxicity): dose period occurs anytime + during development (i.e. in utero, lactational, adolescent [after weaning, + before adulthood]). Study contains functional observation battery or other + battery of behavioral testing that occurs during or after dosing, typically + during adulthood. Pathology has specific interest in the brain (i.e. regions, + morphology, biochemistry, etc.)' + maxLength: 255 + minLength: 0 + studyTypeGuideline: + type: string + description: Description that combines the study_type and guideline name + for a study. + maxLength: 255 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study. + maxLength: 255 + minLength: 0 + strainGroup: + type: string + description: 'Descriptive category for a group of test animals that is more + general than the strain. ' + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform. + maxLength: 255 + minLength: 0 + adminRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other. + maxLength: 255 + minLength: 0 + adminMethod: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical. + maxLength: 255 + minLength: 0 + doseStart: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance began. + doseStartUnit: + type: string + description: Unit of time associated with the start of the dose (dose_start). + maxLength: 255 + minLength: 0 + doseEnd: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance stopped. + doseEndUnit: + type: string + description: Unit of time associated with the end of the dose (dose_end). + maxLength: 255 + minLength: 0 + exportDate: + type: string + format: date + description: Date view of ToxRefDB data was created for API + version: + type: string + description: Version of ToxRefDB data + required: + - id + ToxRefObs: + type: object + description: Export of all observations and endpoint observation status according + to a relevant guideline profile for the chemicals, studies, or study types + listed in the input. Given ToxRefDB curations are guideline studies with specific + testing requirements, guideline profiles are used to populate a list of observations + that should be reported and tested within the study, i.e. endpoint observation + status. Endpoint Observation status enables automated distinction of true + negatives (i.e. tested with no effect observed) and better understanding of + false negative (i.e. missing) effects. + properties: + id: + type: integer + format: int32 + studyId: + type: integer + format: int32 + description: Autoincremented unique numeric identifier for each study in + ToxRefDB + dtxsid: + type: string + description: Identifier assigned through DSSTox chemical curation + maxLength: 45 + minLength: 0 + casrn: + type: string + description: Curated casrn from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + name: + type: string + description: Curated chemical name from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + studyType: + type: string + description: 'Classification to describe animal toxicity testing that was + conducted. Based on either dose period, subjects involved, or measured + effects of interest, study types include: ACU (acute): Dose period typically + a day or less. Excludes developmental and neurological studies.; SAC (subacute): + Dose period is typically 21-28 days. Excludes developmental and neurological + studies.; SUB (subchronic): Dose period is typically 13 weeks, but may + be as long as 6 months. Excludes developmental and neurological studies.; + CHR (chronic): Dose period is typically 12, 18, or 24 months (generally + any dosing lasting a year or longer). Excludes developmental and neurological + studies.; DEV (developmental): Gestational (in utero) dose period. Sacrificed + prior to delivery.; MGR (multigenerational reproductive): Dose period + begins in adolescent F0 males and females and continues until terminal + generation. At least some of the litters deliver their pups, some may + be sacrificed prior to delivery.; NEU (neurological): Study contains functional + observation battery or other battery of behavioral testing that occurs + during or after dosing. Pathology has specific interest in the brain (i.e. + regions, morphology, biochemistry, et cetera). excludes developmental + studies; DNT (developmental neurotoxicity): dose period occurs anytime + during development (i.e. in utero, lactational, adolescent [after weaning, + before adulthood]). Study contains functional observation battery or other + battery of behavioral testing that occurs during or after dosing, typically + during adulthood. Pathology has specific interest in the brain (i.e. regions, + morphology, biochemistry, etc.)' + maxLength: 255 + minLength: 0 + guidelineNumber: + type: string + description: Number associated with the guideline.OPP DERs follow the Series + 870 - Health Effects Test Guidelines. + maxLength: 64 + minLength: 0 + guidelineName: + type: string + description: Name of guideline, such as the particular Office of Chemical + Safety and Pollution Prevention (OCSPP) guideline or NTP specifications. + maxLength: 512 + minLength: 0 + endpointCategory: + type: string + description: 'The broadest descriptive term for an endpoint. Possible endpoint + categories include: systemic, developmental, reproductive, and cholinesterase.' + maxLength: 255 + minLength: 0 + endpointType: + type: string + description: The subcategory for endpoint_category, which is more descriptive + for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive + performance, etc.) + maxLength: 255 + minLength: 0 + endpointTarget: + type: string + description: More specific description than endpoint_type, often indicating + where or how the sample was collected to supply data for a particular + endpoint. Target may describe an organ, tissue, metabolite or protein + measured. + maxLength: 255 + minLength: 0 + status: + type: string + description: The status regarding whether or not an endpoint was required, + recommended, triggered, not required, or mentioned by the study's most + closely related guideline. Assumes that an endpoint was tested if the + guideline the study adheres to requires that endpoint to be tested. + maxLength: 64 + minLength: 0 + defaultStatus: + type: boolean + description: The status regarding whether or not an endpoint was tested + and reported in a study. Assumes that an endpoint was tested if the guideline + the study adheres to requires that endpoint to be tested. + testedStatus: + type: boolean + description: Indicates if an endpoint was tested (1) or not tested (0). + If an endpoint was tested, it was examined or measured in the study. + reportedStatus: + type: boolean + description: Indicates if an endpoint was reported (1) or not reported (0). + If an endpoint was reported, it appears somewhere in the text of the report. + exportDate: + type: string + format: date + description: Date view of ToxRefDB data was created for API + version: + type: string + description: Version of ToxRefDB data + required: + - id + ToxRefEffects: + type: object + description: Export of all extracted dose-treatment group-effect information + from ToxRefDB for the chemicals, studies, or study types listed in the input. + This view is available as an enhanced data sheet from batch search on the + CompTox Chemicals Dashboard. Data from ToxRefDB is also summarized in ToxValDB, + including inferred NEL and NOAEL effect levels based on the reported LEL and + LOAEL, respectively. + properties: + id: + type: integer + format: int32 + studyId: + type: integer + format: int32 + description: A unique numeric identifier for each study in the database. + dtxsid: + type: string + description: Unique identifier from DSSTox + maxLength: 45 + minLength: 0 + casrn: + type: string + description: Curated casrn from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + name: + type: string + description: Curated chemical name from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + studySource: + type: string + description: Organization that provided or authored the document for curation. + maxLength: 255 + minLength: 0 + studySourceId: + type: string + description: Unique document identifier provided by the study source. + maxLength: 255 + minLength: 0 + citation: + type: string + description: Citation in source document + maxLength: 1024 + minLength: 0 + studyYear: + type: integer + format: int32 + studyType: + type: string + description: 'Classification to describe animal toxicity testing that was + conducted. Based on either dose period, subjects involved, or measured + effects of interest, study types include: ACU (acute): Dose period typically + a day or less. Excludes developmental and neurological studies.; SAC (subacute): + Dose period is typically 21-28 days. Excludes developmental and neurological + studies.; SUB (subchronic): Dose period is typically 13 weeks, but may + be as long as 6 months. Excludes developmental and neurological studies.; + CHR (chronic): Dose period is typically 12, 18, or 24 months (generally + any dosing lasting a year or longer). Excludes developmental and neurological + studies.; DEV (developmental): Gestational (in utero) dose period. Sacrificed + prior to delivery.; MGR (multigenerational reproductive): Dose period + begins in adolescent F0 males and females and continues until terminal + generation. At least some of the litters deliver their pups, some may + be sacrificed prior to delivery.; NEU (neurological): Study contains functional + observation battery or other battery of behavioral testing that occurs + during or after dosing. Pathology has specific interest in the brain (i.e. + regions, morphology, biochemistry, et cetera). excludes developmental + studies; DNT (developmental neurotoxicity): dose period occurs anytime + during development (i.e. in utero, lactational, adolescent [after weaning, + before adulthood]). Study contains functional observation battery or other + battery of behavioral testing that occurs during or after dosing, typically + during adulthood. Pathology has specific interest in the brain (i.e. regions, + morphology, biochemistry, etc.)' + maxLength: 255 + minLength: 0 + studyTypeGuideline: + type: string + description: Description that combines the study_type and guideline name + for a study. + maxLength: 255 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study. + maxLength: 255 + minLength: 0 + strainGroup: + type: string + description: 'Descriptive category for a group of test animals that is more + general than the strain. ' + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform. + maxLength: 255 + minLength: 0 + adminRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other. + maxLength: 255 + minLength: 0 + adminMethod: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical. + maxLength: 255 + minLength: 0 + doseDuration: + type: integer + format: int32 + description: Amount of time a group is dosed. This varies within studies + depending on the dose period of a particular treatment group. + doseDurationUnit: + type: string + description: Unit of time associated with the dose duration. Typically in + days or months. + maxLength: 16 + minLength: 0 + doseStart: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance began. + doseStartUnit: + type: string + description: Unit of time associated with the start of the dose (dose_start). + maxLength: 255 + minLength: 0 + doseEnd: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance stopped. + doseEndUnit: + type: string + description: Unit of time associated with the end of the dose (dose_end). + maxLength: 255 + minLength: 0 + dosePeriod: + type: string + description: Period within a group's lifetime that the animals were dosed + and the sample for an endpoint's data was taken (when the animals were + sacrificed). + maxLength: 32 + minLength: 0 + doseLevel: + type: integer + format: int32 + description: 'Numeric rank indicating the level of dose administered to + test animals, with lower dose levels indicating lower concentrations of + a chemical (e.g., 0 = vehicle, 1 = lowest dose, etc.). The dose level + for some studies may be staggered since concentrations may vary by sex + (e.g, male treatment group: 0 = vehicle, 1 = lowest dose, 3 = second lowest + dose, etc.).' + conc: + type: number + format: double + description: Concentration of a test chemical, typically reported in ppm + within the exposure matrix (e.g., feed or water). + concUnit: + type: string + description: Unit associated with a concentration of a test chemical, typically + reported as ppm. + maxLength: 255 + minLength: 0 + vehicle: + type: string + description: The media used in administration of the chemical. + maxLength: 255 + minLength: 0 + doseComment: + type: string + description: NULL if no additional comment needed. Field can be used to + explain any differences in dosing over the dosing interval and/or clarifying + comments on how the dose was administered. + maxLength: 1024 + minLength: 0 + doseAdjusted: + type: number + description: The amount of the chemical administered in mg/kg of body weight/day + (mg/kg/day). This value is typically different between male and female + groups receiving the same dose concentration (conc) due to differences + in bodyweight. If dose_adjusted values were not provided in a study, then + they were calculated using species scaling factors (FAO/WHO, 2000). + doseAdjustedUnit: + type: string + description: Unit associated with the adjusted dose of a chemical, typically + reported in mg/kg/day. + maxLength: 32 + minLength: 0 + sex: + type: string + description: Gender of a test animal. The gender of fetal groups is denoted + as MF for both males and females. + maxLength: 8 + minLength: 0 + generation: + type: string + description: Generation a test animal belongs to. The F0 generation is the + first generation mating group for MGR studies and is the default for non-reproductive + studies (CHR, SUB, SAC). F1 is the second generation mating group, selected + from either F1a or F1b litters. F2 is the third generation mating group, + selected from either F2a or F2b litters. F1a and F1b are the first and + second litter groups produced by F0 matings, F2a and F2b are the first + and second litter groups produced by F1 matings, and F3a and F3b are the + first and second litter groups produced by F2 matings. The fetal generation + is the group produced by F0 matings in DEV studies, and are typically + removed from a female via cesarean section in DEV studies. + maxLength: 16 + minLength: 0 + lifeStage: + type: string + description: 'Stage of life that a measurement was taken. CHR, SUB, and + SAC studies typically only have adult for life_stage, whereas DEV and + MGR studies will always be characterized by multiple life stages. The + different life stages in the database include: fetal, juvenile, adult, + adult-pregnancy and pregnancy.' + maxLength: 32 + minLength: 0 + numAnimals: + type: number + description: Number of animals per treatment group + tgComment: + type: string + description: 'NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group (e.g. animals dosed via capsule so concentration + not reported, added recovery groups, etc.). ' + maxLength: 1024 + minLength: 0 + endpointCategory: + type: string + description: 'The broadest descriptive term for an endpoint. Possible endpoint + categories include: systemic, developmental, reproductive, and cholinesterase.' + maxLength: 255 + minLength: 0 + endpointType: + type: string + description: The subcategory for endpoint_category, which is more descriptive + for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive + performance, etc.) + maxLength: 255 + minLength: 0 + endpointTarget: + type: string + description: More specific description than endpoint_type, often indicating + where or how the sample was collected to supply data for a particular + endpoint. Target may describe an organ, tissue, metabolite or protein + measured. + maxLength: 255 + minLength: 0 + effectDesc: + type: string + description: More specific description for an effect than endpoint_category, + usually detailing a specific condition associated with an endpoint_target + (e.g. dysplasia, atrophy, necrosis, etc.). + maxLength: 255 + minLength: 0 + effectDescFree: + type: string + description: Brief verbatim text from study file that was entered if the + effect description differed from predetermined endpoint terminology. + maxLength: 255 + minLength: 0 + cancerRelated: + type: boolean + description: Indicates if effect is considered cancer related (1) or not. + targetSite: + type: string + description: A more specific description than effect_target. Can describe + a specific tissue within an organ, type of cell, etc. + maxLength: 64 + minLength: 0 + direction: + type: integer + format: int32 + description: Description of the net change across all doses that indicates + whether the numerical data increased, decreased, or stayed the same. Also + can be used to describe effects that did not have numerical data, but + were still described in the study source. + effectComment: + type: string + description: NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group-effect (e.g. units not reported, effect only reported + for certain treatment groups, etc.). + maxLength: 1024 + minLength: 0 + treatmentRelated: + type: boolean + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D indicates there was a statistically significant difference + from the control group for the effect; “FALSEâ€\x9D indicates there + was no difference from control group. The highest dose level at which + no significant observable adverse effects were observed corresponds to + the no effect level (NEL). The lowest effect level (LEL) can be inferred + by treatment related effects." + criticalEffect: + type: boolean + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D corresponds to a toxic or adverse effect denoted in the + study summary or via expert judgement using a weight-of-evidence approach. + “FALSEâ€\x9D indicates that although an effect is produced at this level, + it is not considered adverse, nor immediate precursors to specific adverse + effects. If there are several critical effects, the no observed adverse + effect level (NOAEL) is determined from the highest dose level without + critical effects. The lowest dose level at which the critical effect was + observed in a study is the lowest observed adverse effect level (LOAEL.)" + sampleSize: + type: string + description: Number of animals used for an examination for a particular + effect. + maxLength: 8 + minLength: 0 + effectVal: + type: number + format: double + description: Numeric value of a measured effect, can be continuous or dichotomous + (incidence) data. + effectValUnit: + type: string + description: Unit associated with the effect value. + maxLength: 128 + minLength: 0 + effectVar: + type: number + format: double + description: Measurement of the variance for a set of data associated with + a measured effect, generally reported as the standard deviation (SD) or + standard error (SE). + effectVarType: + type: string + description: 'Name of the variance metric used to determine the effect variance, + typically the standard deviation (SD) or standard error (SE). Other effect_var + types include: interquartile range, 95% confidence limit, and none.' + maxLength: 32 + minLength: 0 + time: + type: number + format: double + description: Numeric value associated with the duration of the exposure + at which a particular effect was measured or observed, typically reported + in hours, days, weeks, or months. + timeUnit: + type: string + description: " Unit associated with the duration of the exposure at which + a particular effect was measured or observed, typically reported in hours, + days, weeks, or months." + maxLength: 64 + minLength: 0 + noQuantDataReported: + type: boolean + description: Indicates if qualitative (1) or quantitative (0) effect data + was reported. + exportDate: + type: string + format: date + description: Date view of ToxRefDB data was created for API + version: + type: string + description: Version of ToxRefDB data + required: + - id + ToxRefData: + type: object + description: Export of all extracted dose-treatment group-effect information + as well as doses not eliciting effects from ToxRefDB for the chemicals, studies, + or study types listed in the input. Data from ToxRefDB is also summarized + in ToxValDB, including inferred NEL and NOAEL effect levels based on the reported + LEL and LOAEL, respectively. + properties: + id: + type: integer + format: int32 + studyId: + type: integer + format: int32 + description: A unique numeric identifier for each study in the database. + dtxsid: + type: string + description: Unique identifier from DSSTox + maxLength: 45 + minLength: 0 + casrn: + type: string + description: Curated casrn from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + name: + type: string + description: Curated chemical name from DSSTOX chemical curation + maxLength: 255 + minLength: 0 + studySource: + type: string + description: Organization that provided or authored the document for curation. + maxLength: 255 + minLength: 0 + studySourceId: + type: string + description: Unique document identifier provided by the study source. + maxLength: 255 + minLength: 0 + citation: + type: string + description: Citation in source document + maxLength: 1024 + minLength: 0 + studyYear: + type: integer + format: int32 + studyType: + type: string + description: 'Classification to describe animal toxicity testing that was + conducted. Based on either dose period, subjects involved, or measured + effects of interest, study types include: ACU (acute): Dose period typically + a day or less. Excludes developmental and neurological studies.; SAC (subacute): + Dose period is typically 21-28 days. Excludes developmental and neurological + studies.; SUB (subchronic): Dose period is typically 13 weeks, but may + be as long as 6 months. Excludes developmental and neurological studies.; + CHR (chronic): Dose period is typically 12, 18, or 24 months (generally + any dosing lasting a year or longer). Excludes developmental and neurological + studies.; DEV (developmental): Gestational (in utero) dose period. Sacrificed + prior to delivery.; MGR (multigenerational reproductive): Dose period + begins in adolescent F0 males and females and continues until terminal + generation. At least some of the litters deliver their pups, some may + be sacrificed prior to delivery.; NEU (neurological): Study contains functional + observation battery or other battery of behavioral testing that occurs + during or after dosing. Pathology has specific interest in the brain (i.e. + regions, morphology, biochemistry, et cetera). excludes developmental + studies; DNT (developmental neurotoxicity): dose period occurs anytime + during development (i.e. in utero, lactational, adolescent [after weaning, + before adulthood]). Study contains functional observation battery or other + battery of behavioral testing that occurs during or after dosing, typically + during adulthood. Pathology has specific interest in the brain (i.e. regions, + morphology, biochemistry, etc.)' + maxLength: 255 + minLength: 0 + studyTypeGuideline: + type: string + description: Description that combines the study_type and guideline name + for a study. + maxLength: 255 + minLength: 0 + species: + type: string + description: Species of the animal test subject used in a study. + maxLength: 255 + minLength: 0 + strainGroup: + type: string + description: 'Descriptive category for a group of test animals that is more + general than the strain. ' + maxLength: 255 + minLength: 0 + strain: + type: string + description: Intraspecific description of group of animals used in a study; + generally, a stock of animals that share a uniform morphological or physiological + character, or group that is genetically uniform. + maxLength: 255 + minLength: 0 + adminRoute: + type: string + description: Path by which test substance was administered to animal. Options + include oral, dermal, inhalation, injection, or other. + maxLength: 255 + minLength: 0 + adminMethod: + type: string + description: Specific path by which the test substance was administered + via the administration route. Examples include capsule, diet, gavage, + or topical. + maxLength: 255 + minLength: 0 + doseDuration: + type: integer + format: int32 + description: Amount of time a group is dosed. This varies within studies + depending on the dose period of a particular treatment group. + doseDurationUnit: + type: string + description: Unit of time associated with the dose duration. Typically in + days or months. + maxLength: 16 + minLength: 0 + doseStart: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance began. + doseStartUnit: + type: string + description: Unit of time associated with the start of the dose (dose_start). + maxLength: 255 + minLength: 0 + doseEnd: + type: integer + format: int32 + description: Time during an animal's life that the administration of a test + substance stopped. + doseEndUnit: + type: string + description: Unit of time associated with the end of the dose (dose_end). + maxLength: 255 + minLength: 0 + dosePeriod: + type: string + description: Period within a group's lifetime that the animals were dosed + and the sample for an endpoint's data was taken (when the animals were + sacrificed). + maxLength: 32 + minLength: 0 + doseLevel: + type: integer + format: int32 + description: 'Numeric rank indicating the level of dose administered to + test animals, with lower dose levels indicating lower concentrations of + a chemical (e.g., 0 = vehicle, 1 = lowest dose, etc.). The dose level + for some studies may be staggered since concentrations may vary by sex + (e.g, male treatment group: 0 = vehicle, 1 = lowest dose, 3 = second lowest + dose, etc.).' + conc: + type: number + format: double + description: Concentration of a test chemical, typically reported in ppm + within the exposure matrix (e.g., feed or water). + concUnit: + type: string + description: Unit associated with a concentration of a test chemical, typically + reported as ppm. + maxLength: 255 + minLength: 0 + vehicle: + type: string + description: The media used in administration of the chemical. + maxLength: 255 + minLength: 0 + doseComment: + type: string + description: NULL if no additional comment needed. Field can be used to + explain any differences in dosing over the dosing interval and/or clarifying + comments on how the dose was administered. + maxLength: 1024 + minLength: 0 + doseAdjusted: + type: number + description: The amount of the chemical administered in mg/kg of body weight/day + (mg/kg/day). This value is typically different between male and female + groups receiving the same dose concentration (conc) due to differences + in bodyweight. If dose_adjusted values were not provided in a study, then + they were calculated using species scaling factors (FAO/WHO, 2000). + doseAdjustedUnit: + type: string + description: Unit associated with the adjusted dose of a chemical, typically + reported in mg/kg/day. + maxLength: 32 + minLength: 0 + sex: + type: string + description: Gender of a test animal. The gender of fetal groups is denoted + as MF for both males and females. + maxLength: 8 + minLength: 0 + generation: + type: string + description: Generation a test animal belongs to. The F0 generation is the + first generation mating group for MGR studies and is the default for non-reproductive + studies (CHR, SUB, SAC). F1 is the second generation mating group, selected + from either F1a or F1b litters. F2 is the third generation mating group, + selected from either F2a or F2b litters. F1a and F1b are the first and + second litter groups produced by F0 matings, F2a and F2b are the first + and second litter groups produced by F1 matings, and F3a and F3b are the + first and second litter groups produced by F2 matings. The fetal generation + is the group produced by F0 matings in DEV studies, and are typically + removed from a female via cesarean section in DEV studies. + maxLength: 16 + minLength: 0 + lifeStage: + type: string + description: 'Stage of life that a measurement was taken. CHR, SUB, and + SAC studies typically only have adult for life_stage, whereas DEV and + MGR studies will always be characterized by multiple life stages. The + different life stages in the database include: fetal, juvenile, adult, + adult-pregnancy and pregnancy.' + maxLength: 32 + minLength: 0 + numAnimals: + type: number + description: Number of animals per treatment group + tgComment: + type: string + description: 'NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group (e.g. animals dosed via capsule so concentration + not reported, added recovery groups, etc.). ' + maxLength: 1024 + minLength: 0 + endpointCategory: + type: string + description: 'The broadest descriptive term for an endpoint. Possible endpoint + categories include: systemic, developmental, reproductive, and cholinesterase.' + maxLength: 255 + minLength: 0 + endpointType: + type: string + description: The subcategory for endpoint_category, which is more descriptive + for a particular endpoint (e.g. pathology gross, clinical chemistry, reproductive + performance, etc.) + maxLength: 255 + minLength: 0 + endpointTarget: + type: string + description: More specific description than endpoint_type, often indicating + where or how the sample was collected to supply data for a particular + endpoint. Target may describe an organ, tissue, metabolite or protein + measured. + maxLength: 255 + minLength: 0 + effectDesc: + type: string + description: More specific description for an effect than endpoint_category, + usually detailing a specific condition associated with an endpoint_target + (e.g. dysplasia, atrophy, necrosis, etc.). + maxLength: 255 + minLength: 0 + effectDescFree: + type: string + description: Brief verbatim text from study file that was entered if the + effect description differed from predetermined endpoint terminology. + maxLength: 255 + minLength: 0 + cancerRelated: + type: boolean + description: Indicates if effect is considered cancer related (1) or not. + targetSite: + type: string + description: A more specific description than effect_target. Can describe + a specific tissue within an organ, type of cell, etc. + maxLength: 64 + minLength: 0 + direction: + type: integer + format: int32 + description: Description of the net change across all doses that indicates + whether the numerical data increased, decreased, or stayed the same. Also + can be used to describe effects that did not have numerical data, but + were still described in the study source. + effectComment: + type: string + description: NULL if no additional comment needed; contains information + that the extractor/curator found helpful in describing issues related + to a treatment-group-effect (e.g. units not reported, effect only reported + for certain treatment groups, etc.). + maxLength: 1024 + minLength: 0 + treatmentRelated: + type: boolean + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D indicates there was a statistically significant difference + from the control group for the effect; “FALSEâ€\x9D indicates there + was no difference from control group. The highest dose level at which + no significant observable adverse effects were observed corresponds to + the no effect level (NEL). The lowest effect level (LEL) can be inferred + by treatment related effects." + criticalEffect: + type: boolean + description: "Boolean description for an effect by dose treatment group. + “TRUEâ€\x9D corresponds to a toxic or adverse effect denoted in the + study summary or via expert judgement using a weight-of-evidence approach. + “FALSEâ€\x9D indicates that although an effect is produced at this level, + it is not considered adverse, nor immediate precursors to specific adverse + effects. If there are several critical effects, the no observed adverse + effect level (NOAEL) is determined from the highest dose level without + critical effects. The lowest dose level at which the critical effect was + observed in a study is the lowest observed adverse effect level (LOAEL.)" + sampleSize: + type: string + description: Number of animals used for an examination for a particular + effect. + maxLength: 8 + minLength: 0 + effectVal: + type: number + format: double + description: Numeric value of a measured effect, can be continuous or dichotomous + (incidence) data. + effectValUnit: + type: string + description: Unit associated with the effect value. + maxLength: 128 + minLength: 0 + effectVar: + type: number + format: double + description: Measurement of the variance for a set of data associated with + a measured effect, generally reported as the standard deviation (SD) or + standard error (SE). + effectVarType: + type: string + description: 'Name of the variance metric used to determine the effect variance, + typically the standard deviation (SD) or standard error (SE). Other effect_var + types include: interquartile range, 95% confidence limit, and none.' + maxLength: 32 + minLength: 0 + time: + type: number + format: double + description: Numeric value associated with the duration of the exposure + at which a particular effect was measured or observed, typically reported + in hours, days, weeks, or months. + timeUnit: + type: string + description: " Unit associated with the duration of the exposure at which + a particular effect was measured or observed, typically reported in hours, + days, weeks, or months." + maxLength: 64 + minLength: 0 + noQuantDataReported: + type: boolean + description: Indicates if qualitative (1) or quantitative (0) effect data + was reported. + exportDate: + type: string + format: date + description: Date view of ToxRefDB data was created for API + version: + type: string + description: Version of ToxRefDB data + required: + - id + Pprtv: + type: object + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + maxLength: 45 + minLength: 0 + pprtvSubstanceId: + type: integer + format: int32 + name: + type: string + casrn: + type: string + lastReviosn: + type: integer + format: int32 + pprtvAssessment: + type: string + irisLink: + type: string + rfcValue: + type: string + rfdValue: + type: string + woe: + type: string + required: + - id + Iris: + type: object + description: 'Integrated Risk Information System (IRIS): EPA''s IRIS Program + identifies and characterizes the health hazards of chemicals found in the + environment. Each IRIS assessment can cover a chemical, a group of related + chemicals, or a complex mixture. IRIS assessments are an important source + of toxicity information used by EPA, state and local health agencies, other + federal agencies, and international health organizations.' + properties: + dtxsid: + type: string + chemicalName: + type: string + casrn: + type: string + lastSignificantRevision: + type: string + format: date-time + literatureScreeningReview: + type: string + criticalEffectsSystems: + type: string + rfdChronic: + type: string + rfdSubchronic: + type: string + rfcChronic: + type: string + rfcSubchronic: + type: string + tumorSite: + type: string + irisUrl: + type: string + required: + - dtxsid + Hawc: + type: object + description: EPA Health Assessment Workspace Collaborative (HAWC). EPA HAWC + is an interactive, expert-driven, content management system for EPA health + and environmental risk assessment programs that is intended to promote transparency, + data usability, and understanding of the data and decisions supporting health + and environmental assessments. Specifically, EPA HAWC is an application that + allows the data and decisions supporting an assessment to be evaluated and + managed in modules (e.g., study evaluation, summary study data) that can then + be publicly accessed online. + properties: + id: + type: integer + format: int32 + name: + type: string + year: + type: integer + format: int32 + dtxsid: + type: string + ccdUrl: + type: string + hawcUrl: + type: string + required: + - id + CcdGenetoxDetail: + type: object + properties: + year: + type: integer + format: int32 + source: + type: string + assayResult: + type: string + assayCategory: + type: string + assayType: + type: string + dtxsid: + type: string + species: + type: string + strain: + type: string + metabolicActivation: + type: string + Adme: + type: object + description: 'The information here describes toxicokinetics in humans. Values + are 1) measured either in vitro or in vivo, 2) predicted from chemical properties + using in silico tools, or 3) computed with mathematical models simulating + toxicokinetics. Note: intrinsic hepatic clearance and fraction unbound in + plasma values can have measured values listed, but these may be assumed from + measured data using a surrogate species. The Data Source Species column identifies + the measured data species source. We use these assumed measured values in + calculations to estimate other outcomes, such as volume of distribution, PK + half life, and steady-state plasma concentration. The in vitro measured values + reflect the value curated for the open source R package “httk”. The computed + values are generated with httk using the reported in vitro values. "https://CRAN.R-project.org/package=httk". + The in vivo measured values are estimated from toxicokinetic concentration + vs. time contained in the CvTdb (https://doi.org/10.1038/s41597-020-0455-1). + In vivo estimates are calculated using R package “invivoPKfit” (https://github.com/USEPA/CompTox-ExpoCast-invivoPKfit)' + properties: + id: + type: integer + format: int32 + dtxsid: + type: string + description: Distributed Structure-Searchable Toxicity (DSSTox) id + description: + type: string + measured: + type: string + predicted: + type: string + unit: + type: string + maxLength: 30 + minLength: 0 + model: + type: string + reference: + type: string + percentile: + type: string + species: + type: string + dataSourceSpecies: + type: string + required: + - id + CcdADME: + type: object + properties: + description: + type: string + label: + type: string + reference: + type: string + model: + type: string + percentile: + type: string + predicted: + type: string + measured: + type: string + dataSourceSpecies: + type: string + dtxsid: + type: string + unit: + type: string + species: + type: string + securitySchemes: + api_key: + type: apiKey + description: 'Each API call should have api_key, Contact author for getting + the new api_key. ' + name: x-api-key + in: header