ChEMBL PubChem Bioassay Sids API

openapi: 3.2.0
info:
  description: '# About CROssBAR & data

    **CROssBAR**: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations

    CROssBAR is a comprehensive system that integrates large-scale biomedical data from various resources e.g UniProt, ChEMBL, Drugbank, EFO, HPO, InterPro & PubChem and stores them in a new NoSQL database, enrich these data with deep learning based prediction of relations between numerous biomedical entities, rigorously analyse the enriched data to obtain biologically meaningful modules and display them to the user via easy to interpret, interactive and heterogeneous knowledge graphs.

    CROssBAR platform exposes a set of 12 endpoints to query data stored in the CROssBAR database. These endpoints help the user to find data of interest using different parameters provided by the API endpoint.

    For example,

    https://www.ebi.ac.uk/tools/crossbar/proteins?accession=A0A023GRW5 -> will provide protein information about accession ''A0A023GRW5'' including its interactions, functions, cross-references, variations and more.

    https://www.ebi.ac.uk/tools/crossbar/activities?moleculeChemblId=CHEMBL465983 -> will provide ChEMBL bio-interactions related information including targets and bio-activity measurements associated with molecule chembl id ''CHEMBL465983''


    **Knowledge graphs**

    Another use case of CROssBAR''s API endpoints is in building knowledge graphs. These endpoints can be *weaved* together (output from one API endpoint fed as input to another API endpoint) programmatically to link nodes like protein, disease, drugs etc. as nodes of the graph. The endpoints are designed to be independent from each other which allows users the flexibility to drive biological networks from any facet e.g drug-centric, disease-centric, gene-centric etc. Our service for knowledge graph construction is available at https://crossbar.kansil.org.

    An example for the part of the background queries on the CROssBAR API during the construction of a knowledge graph,

    (with the aim of keeping the example simple, we have only included the processes related to pathways, genes/proteins and drugs/compounds)

    In this example, we would like to find bio-active compounds (with a pChEMBL value threshold of at least 6.0) & drugs targeting all proteins belonging to "WNT ligand biogenesis and trafficking" pathway (based on Reactome pathway annotations).

    This can be achieved by using endpoints listed on this swagger documentation as illustrated in following steps-

    Find bio-active compounds (with a pChEMBL value threshold of at least 6.0) & drugs targeting all proteins belonging to "WNT ligand biogenesis and trafficking" pathway (based on Reactome annotations)

    This can be achieved by using endpoints listed on this swagger documentation as illustrated in following steps-

    1. Get all proteins from “/proteins” API endpoint which have a reactome pathway name equal to "WNT ligand biogenesis and trafficking".

    2. From the collection of uniprot protein accessions collected from step 1 above, we query “/targets” API endpoint to obtain the ‘target_chembl_id’s of these proteins.

    3. From the collection of target_chembl_ids collected from step 2 above, we query “/activities” API endpoint with pChEMBL value >=6, to obtain the ’molecule_chembl_id’s of the molecules that we need.

    4. From the collection of uniprot protein accessions collected from step 1 above, we find out Drug names and ids from the “/drugs” API endpoint that targets our proteins.

    5. From the collection of ’molecule_chembl_id’s obtained in step3, we query “/molecules” endpoint to get the compounds that are interacting with the genes/proteins belonging to the “WNT ligand biogenesis and trafficking” pathway.'
  version: '1.0'
  title: CROssBAR Data PubChem Bioassay Sids API
  contact:
    name: API support
    email: crossbar_dev@ebi.ac.uk
servers:
- url: https://www.ebi.ac.uk/Tools/crossbar
tags:
- name: PubChem Bioassay Sids
  description: Pubchem Bioassay Sids Resource
paths:
  /pubchem/bioassays/sids:
    get:
      tags:
      - PubChem Bioassay Sids
      summary: Get pubchem bioassays associated to particular substance ids (sid) & outcome
      operationId: getBioassaysUsingGET_1
      parameters:
      - name: limit
        in: query
        description: limit
        required: false
        schema:
          type: integer
          format: int32
          default: 10
      - name: outcome
        in: query
        description: outcome
        required: false
        schema:
          type: string
      - name: page
        in: query
        description: page
        required: false
        schema:
          type: integer
          format: int32
          default: 0
      - name: sids
        in: query
        description: sids
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Bioassays'
        '401':
          description: Unauthorized
        '403':
          description: Forbidden
        '404':
          description: Not Found
      deprecated: false
components:
  schemas:
    BioAssay:
      type: object
      properties:
        activity:
          type: integer
          format: int32
        assay_organisms:
          type: array
          items:
            $ref: '#/components/schemas/AssayOrganism'
        assay_pubchem_id:
          type: integer
        assay_type:
          type: string
        chembl_xref:
          type: string
        protein_name:
          type: string
        source:
          type: string
        target_info:
          type: array
          items:
            $ref: '#/components/schemas/TargetInfo'
        target_type_info:
          type: array
          items:
            $ref: '#/components/schemas/TargetType'
      title: BioAssay
    TargetType:
      type: object
      properties:
        molecule_type:
          type: string
        value:
          type: integer
          format: int32
      title: TargetType
    SidRelatedData:
      type: object
      properties:
        assay_data:
          type: array
          items:
            $ref: '#/components/schemas/AssayData'
        assay_pubchem_id:
          type: integer
        outcome:
          type: string
        sid:
          type: integer
        standard_relation:
          type: string
      title: SidRelatedData
    AssayData:
      type: object
      properties:
        standard_type:
          type: string
        standard_units:
          type: string
        standard_value:
          type: number
          format: double
      title: AssayData
    AssayOrganism:
      type: object
      properties:
        db_object_id:
          type: integer
        tax_name:
          type: string
      title: AssayOrganism
    PageMeta:
      type: object
      properties:
        currentElements:
          type: integer
          format: int64
        currentPage:
          type: integer
          format: int32
        limit:
          type: integer
          format: int32
        totalElements:
          type: integer
          format: int64
        totalPages:
          type: integer
          format: int32
      title: PageMeta
    TargetInfo:
      type: object
      properties:
        ncbi_protein_id:
          type: integer
        target_chembl_id:
          type: string
        uniprot_accession:
          type: string
      title: TargetInfo
    Bioassays:
      type: object
      properties:
        bioassays:
          type: array
          items:
            $ref: '#/components/schemas/BioAssayMetaData'
        pageMeta:
          $ref: '#/components/schemas/PageMeta'
      title: Bioassays
    BioAssayMetaData:
      type: object
      properties:
        bioAssay:
          $ref: '#/components/schemas/BioAssay'
        sidRelatedData:
          type: array
          items:
            $ref: '#/components/schemas/SidRelatedData'
      title: BioAssayMetaData
x-provenance:
  method: harvested
  publisher: ChEMBL
  source: https://www.ebi.ac.uk/Tools/crossbar/v2/api-docs
  note: split by refine-openapis from the provider's own published document, verified by fetch (openapi/_original/*.fetch.json);
    stamped by stamp-openapi-provenance.py (roadmap#793)