ChEMBL Proteins 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 Proteins API
  contact:
    name: API support
    email: crossbar_dev@ebi.ac.uk
servers:
- url: https://www.ebi.ac.uk/Tools/crossbar
tags:
- name: Proteins
  description: Protein Resource
paths:
  /proteins:
    get:
      tags:
      - Proteins
      summary: Proteins collected from Uniprot for selective tax ids HUMAN(9606)…
      operationId: getProteinsUsingGET
      parameters:
      - name: accession
        in: query
        description: accession
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: ec
        in: query
        description: ec
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: fullName
        in: query
        description: fullName
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: gene
        in: query
        description: gene
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: go
        in: query
        description: go
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: interpro
        in: query
        description: interpro
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: limit
        in: query
        description: limit
        required: false
        schema:
          type: integer
          format: int32
          default: 10
      - name: omim
        in: query
        description: omim
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: orphanet
        in: query
        description: orphanet
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: page
        in: query
        description: page
        required: false
        schema:
          type: integer
          format: int32
          default: 0
      - name: pfam
        in: query
        description: pfam
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: reactome
        in: query
        description: reactome
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: string
      - name: taxId
        in: query
        description: taxId
        required: false
        style: form
        explode: true
        schema:
          type: array
          items:
            type: integer
            format: int32
      responses:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Proteins'
        '401':
          description: Unauthorized
        '403':
          description: Forbidden
        '404':
          description: Not Found
      deprecated: false
components:
  schemas:
    Kegg:
      type: object
      properties:
        id:
          type: string
      title: Kegg
    Features:
      type: object
      properties:
        active_site:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        binding_site:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        chain:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        domain:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        mutagen:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        region:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        top_dom:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
        variant:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarFeature'
      title: Features
    OpenTargets:
      type: object
      properties:
        id:
          type: string
      title: OpenTargets
    PDBe:
      type: object
      properties:
        chains:
          type: string
        id:
          type: string
        method:
          type: string
        resolution:
          type: string
      title: PDBe
    VariationEvidenceSource:
      type: object
      properties:
        id:
          type: string
        name:
          type: string
      title: VariationEvidenceSource
    Omim:
      type: object
      properties:
        _id:
          type: string
        type:
          type: string
      title: Omim
    VariationAssociation:
      type: object
      properties:
        description:
          type: string
        evidences:
          type: array
          items:
            $ref: '#/components/schemas/VariationEvidence'
        name:
          type: string
        xrefs:
          type: array
          items:
            $ref: '#/components/schemas/VariationXref'
      title: VariationAssociation
    Orphanet:
      type: object
      properties:
        disease:
          type: string
        id:
          type: string
      title: Orphanet
    Interpro:
      type: object
      properties:
        entry_id:
          type: string
        entry_name:
          type: string
        entry_type:
          type: string
        fragments:
          type: array
          items:
            $ref: '#/components/schemas/Fragment'
        hit_position:
          $ref: '#/components/schemas/HitPosition'
      title: Interpro
    Go:
      type: object
      properties:
        evidences:
          type: array
          items:
            $ref: '#/components/schemas/GoEvidence'
        id:
          type: string
        term:
          type: string
      title: Go
    FeaturePosition:
      type: object
      properties:
        ceil:
          type: integer
          format: int32
        floor:
          type: integer
          format: int32
        uncertain:
          type: boolean
        unparsed:
          type: string
      title: FeaturePosition
    CrossbarFeature:
      type: object
      properties:
        begin:
          $ref: '#/components/schemas/FeaturePosition'
        category:
          type: string
        description:
          type: string
        end:
          $ref: '#/components/schemas/FeaturePosition'
        ftId:
          type: string
        type:
          type: string
      title: CrossbarFeature
    CrossReferences:
      type: object
      properties:
        ensembl:
          type: array
          items:
            $ref: '#/components/schemas/Ensembl'
        go:
          type: array
          items:
            $ref: '#/components/schemas/Go'
        interpro:
          type: array
          items:
            $ref: '#/components/schemas/Interpro'
        kegg:
          type: array
          items:
            $ref: '#/components/schemas/Kegg'
        omim:
          type: array
          items:
            $ref: '#/components/schemas/Omim'
        openTargets:
          type: array
          items:
            $ref: '#/components/schemas/OpenTargets'
        orphanet:
          type: array
          items:
            $ref: '#/components/schemas/Orphanet'
        pdBe:
          type: array
          items:
            $ref: '#/components/schemas/PDBe'
        pfam:
          type: array
          items:
            $ref: '#/components/schemas/Pfam'
        reactome:
          type: array
          items:
            $ref: '#/components/schemas/Reactome'
      title: CrossReferences
    VariationXref:
      type: object
      properties:
        id:
          type: string
        name:
          type: string
      title: VariationXref
    Fragment:
      type: object
      properties:
        from:
          type: integer
          format: int32
        to:
          type: integer
          format: int32
        type:
          type: string
      title: Fragment
    Protein:
      type: object
      properties:
        accession:
          type: string
        chromosome:
          type: string
        crossreferences:
          $ref: '#/components/schemas/CrossReferences'
        ec_numbers:
          type: array
          items:
            type: string
        features:
          $ref: '#/components/schemas/Features'
        full_name:
          type: string
        genes:
          type: array
          items:
            type: string
        interactions:
          type: array
          items:
            $ref: '#/components/schemas/ProteinInteraction'
        length:
          type: number
          format: double
        mass:
          type: number
          format: double
        tax_id:
          type: integer
          format: int32
        variations:
          type: array
          items:
            $ref: '#/components/schemas/CrossbarProteinVariation'
      title: Protein
    Ensembl:
      type: object
      properties:
        geneId:
          type: string
        id:
          type: string
        isoform:
          type: string
        proteinSequenceId:
          type: string
      title: Ensembl
    Reactome:
      type: object
      properties:
        id:
          type: string
        pathwayName:
          type: string
      title: Reactome
    ProteinInteraction:
      type: object
      properties:
        id:
          type: string
        interaction_type:
          type: string
        interactors:
          type: array
          items:
            type: string
      title: ProteinInteraction
    CrossbarProteinVariation:
      type: object
      properties:
        alternativeSequence:
          type: string
        association:
          type: array
          items:
            $ref: '#/components/schemas/VariationAssociation'
        begin:
          $ref: '#/components/schemas/FeaturePosition'
        clinicalSignificances:
          type: string
        description:
          type: string
        end:
          $ref: '#/components/schemas/FeaturePosition'
        evidences:
          type: array
          items:
            $ref: '#/components/schemas/VariationEvidence'
        ftId:
          type: string
        somaticStatus:
          type: integer
          format: int64
        sourceType:
          type: string
        wildType:
          type: string
        xrefs:
          type: array
          items:
            $ref: '#/components/schemas/VariationXref'
      title: CrossbarProteinVariation
    GoEvidence:
      type: object
      properties:
        source_id:
          type: string
        source_name:
          type: string
      title: GoEvidence
    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
    Proteins:
      type: object
      properties:
        pageMeta:
          $ref: '#/components/schemas/PageMeta'
        proteins:
          type: array
          items:
            $ref: '#/components/schemas/Protein'
      title: Proteins
    Pfam:
      type: object
      properties:
        entryName:
          type: string
        id:
          type: string
      title: Pfam
    HitPosition:
      type: object
      properties:
        from:
          type: integer
          format: int32
        to:
          type: integer
          format: int32
      title: HitPosition
    VariationEvidence:
      type: object
      properties:
        source:
          $ref: '#/components/schemas/VariationEvidenceSource'
      title: VariationEvidence
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)