openapi: 3.0.1
info:
  title: Pathway Analysis Service database interactors API
  description: Provides an API for pathway over-representation and expression analysis as well as species comparison tool.
  termsOfService: /license
  contact:
    name: Reactome
    url: https://reactome.org
    email: help@reactome.org
  license:
    name: Creative Commons Attribution 3.0 Unsupported License
    url: https://creativecommons.org/licenses/by/3.0/legalcode
  version: '2.0'
servers:
- url: /AnalysisService
tags:
- name: interactors
  description: Molecule interactors
paths:
  /interactors/psicquic/molecule/{resource}/{acc}/details:
    get:
      tags:
      - interactors
      summary: Retrieve clustered interaction, sorted by score, of a given accession by resource.
      operationId: getProteinDetailsByResource
      parameters:
      - name: resource
        in: path
        description: PSICQUIC Resource
        required: true
        schema:
          type: string
        example: MINT
      - name: acc
        in: path
        description: Single Accession
        required: true
        schema:
          type: string
        example: Q13501
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/psicquic/molecule/{resource}/{acc}/summary:
    get:
      tags:
      - interactors
      summary: Retrieve a summary of a given accession by resource
      operationId: getProteinSummaryByResource
      parameters:
      - name: resource
        in: path
        description: PSICQUIC Resource
        required: true
        schema:
          type: string
        example: MINT
      - name: acc
        in: path
        description: Single Accession
        required: true
        schema:
          type: string
        example: Q13501
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/psicquic/molecules/{resource}/details:
    post:
      tags:
      - interactors
      summary: Retrieve clustered interaction, sorted by score, of a given accession(s) by resource.
      operationId: getProteinsDetailsByResource
      parameters:
      - name: resource
        in: path
        description: PSICQUIC Resource
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>Accessions</b>
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/psicquic/molecules/{resource}/summary:
    post:
      tags:
      - interactors
      summary: Retrieve a summary of a given accession list by resource.
      operationId: getProteinsSummaryByResource
      parameters:
      - name: resource
        in: path
        description: PSICQUIC Resource
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>Accessions</b>
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/psicquic/resources:
    get:
      tags:
      - interactors
      summary: Retrieve a list of all Psicquic Registries services
      operationId: getResources
      parameters:
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/PsicquicResource'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/PsicquicResource'
  /interactors/static/molecule/enhanced/{acc}/details:
    get:
      tags:
      - interactors
      summary: Retrieve a custom interaction information of a given accession in Reactome knowledgebase for UI to use, including Reactome entity number
      operationId: getCustomInteractionsByAcc
      parameters:
      - name: acc
        in: path
        description: Interactor accession (or identifier)
        required: true
        schema:
          type: string
        example: Q13501
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/CustomInteraction'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/CustomInteraction'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/CustomInteraction'
  /interactors/static/molecule/{acc}/details:
    get:
      tags:
      - interactors
      summary: Retrieve a detailed interaction information of a given accession
      operationId: getProteinDetailsByAcc
      parameters:
      - name: acc
        in: path
        description: Interactor accession (or identifier)
        required: true
        schema:
          type: string
        example: Q13501
      - name: page
        in: query
        description: For paginating the results
        required: false
        schema:
          type: integer
          format: int32
          default: -1
      - name: pageSize
        in: query
        description: Number of results to be retrieved
        required: false
        schema:
          type: integer
          format: int32
          default: -1
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/static/molecule/{acc}/pathways:
    get:
      tags:
      - interactors
      summary: Retrieve a list of lower level pathways where the interacting molecules can be found
      operationId: getLowerLevelPathways
      parameters:
      - name: acc
        in: path
        description: Accession
        required: true
        schema:
          type: string
        example: Q9BXM7-1
      - name: species
        in: query
        description: The species name for which the pathways are requested  (e.g. 'Homo sapiens')
        required: false
        schema:
          type: string
        example: Homo sapiens
      - name: onlyDiagrammed
        in: query
        description: Specifies whether the pathways has to have an associated diagram or not
        required: false
        schema:
          type: boolean
          default: false
        example: false
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                type: array
                items:
                  type: object
  /interactors/static/molecule/{acc}/summary:
    get:
      tags:
      - interactors
      summary: Retrieve a summary of a given accession
      operationId: getProteinSummaryByAcc
      parameters:
      - name: acc
        in: path
        description: Accession
        required: true
        schema:
          type: string
        example: Q13501
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/static/molecules/details:
    post:
      tags:
      - interactors
      summary: Retrieve a detailed interaction information of a given accession
      operationId: getProteinsDetailsByAccs
      parameters:
      - name: page
        in: query
        description: For paginating the results
        required: false
        schema:
          type: integer
          format: int32
          default: -1
      - name: pageSize
        in: query
        description: Number of results to be retrieved
        required: false
        schema:
          type: integer
          format: int32
          default: -1
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>Interactors</b> Interactor accessions (or identifiers)
        content:
          text/plain:
            schema:
              type: string
              description: Interactor accessions (or identifiers)
            example: O95631, P60484
        required: true
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/static/molecules/summary:
    post:
      tags:
      - interactors
      summary: Retrieve a summary of a given accession list
      operationId: getProteinsSummaryByAccs
      parameters:
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>Interactors</b> Interactor accessions (or identifiers)
        content:
          text/plain:
            schema:
              type: string
            example: O95631, P60484
        required: true
      responses:
        '404':
          description: Could not find the Interactor Resource
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/token/{token}:
    post:
      tags:
      - interactors
      summary: Retrieve custom interactions associated with a token
      operationId: getInteractors
      parameters:
      - name: token
        in: path
        description: A token associated with a data submission
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>Interactors</b> Interactors accessions
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '404':
          description: Could not find the given token
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Interactors'
  /interactors/upload/psicquic/url:
    post:
      tags:
      - interactors
      summary: Registry custom PSICQUIC resource
      operationId: registryPsicquicURL
      parameters:
      - name: name
        in: query
        description: Name which identifies the custom psicquic
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>url</b> A URL pointing to the Custom PSICQUIC Resource
        content:
          text/plain:
            schema:
              type: string
            example: https://reactome.org/download/current/interactors/reactome.homo_sapiens.interactions.psi-mitab.txt
        required: true
      responses:
        '400':
          description: Bad request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CustomPsicquicResource'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CustomPsicquicResource'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/CustomPsicquicResource'
  /interactors/upload/tuple/content:
    post:
      tags:
      - interactors
      summary: Paste file content and get a summary associated with a token
      operationId: postFileContent
      parameters:
      - name: name
        in: query
        description: Name which identifies the sample
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>File Content</b>Paste custom interactors file content
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '400':
          description: Bad request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '413':
          description: Payload too Large
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '415':
          description: Unsupported Media Type ('text/plain' or 'text/csv')
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '422':
          description: Unprocessable Entity
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
  /interactors/upload/tuple/form:
    post:
      tags:
      - interactors
      summary: Parse file and retrieve a summary associated with a token
      operationId: postFile
      parameters:
      - name: name
        in: query
        description: Name which identifies the sample
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        content:
          multipart/form-data:
            schema:
              type: object
              properties:
                file:
                  type: string
                  format: binary
                  description: Upload your custom interactor file
              required:
              - file
      responses:
        '400':
          description: Bad request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '413':
          description: Payload too Large
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '415':
          description: Unsupported Media Type ('text/plain' or 'text/csv')
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '422':
          description: Unprocessable Entity
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
  /interactors/upload/tuple/url:
    post:
      tags:
      - interactors
      summary: Send file via URL and get a summary associated with a token
      operationId: postUrl
      parameters:
      - name: name
        in: query
        description: Name which identifies the sample
        required: true
        schema:
          type: string
      - name: view
        in: query
        description: Global parameter - Customise the view to be more concise and/or aggregate relationships
        required: false
        schema:
          type: string
          default: flatten
          enum:
          - flatten
          - nested
          - nested-aggregated
          example: null
      - name: includeRef
        in: query
        description: Global parameter - If true, replace element ref to dbId by standard JSOG object {@ref}
        required: false
        schema:
          type: boolean
          default: false
          example: null
      requestBody:
        description: <b>url</b> A URL pointing to the Interactors file
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '400':
          description: Bad request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '415':
          description: Unsupported Media Type ('text/plain' or 'text/csv')
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '422':
          description: Unprocessable Entity
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '431':
          description: Request Header Fields Too Large
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
        '500':
          description: Internal Server Error
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TupleResult'
components:
  schemas:
    Interactor:
      type: object
      properties:
        acc:
          type: string
          description: This is the interactor accession (or identifier).
        accURL:
          type: string
          description: This represents the URL for given accession.
        alias:
          type: string
          description: This is the Gene name of the given accession.
        evidences:
          type: integer
          description: This is the Interactions evidences.
          format: int32
        evidencesURL:
          type: string
          description: This represents the URL for the given interactions identifiers.
        id:
          type: integer
          description: This is an auto increment counter which represents an unique number for the interaction.
          format: int64
        score:
          type: number
          description: This represents the confidence value (score) of an interaction.
          format: double
      description: List of Interactors that interacts with the given accession.
    CustomPsicquicResource:
      type: object
      properties:
        summary:
          $ref: '#/components/schemas/Summary'
    Summary:
      type: object
      properties:
        fileName:
          type: string
        interactions:
          type: integer
          format: int32
        interactors:
          type: integer
          format: int32
        name:
          type: string
        token:
          type: string
    CustomInteraction:
      type: object
      properties:
        databaseName:
          type: string
        dbId:
          type: integer
          format: int64
        displayName:
          type: string
        entitiesCount:
          type: integer
          format: int64
        evidenceCount:
          type: integer
          format: int64
        evidenceURL:
          type: string
        geneName:
          type: array
          items:
            type: string
        identifier:
          type: string
        score:
          type: number
          format: double
        speciesName:
          type: string
        url:
          type: string
        variantIdentifier:
          type: string
    PsicquicResource:
      type: object
      properties:
        active:
          type: boolean
        name:
          type: string
        restURL:
          type: string
        soapURL:
          type: string
    Interactors:
      type: object
      properties:
        entities:
          type: array
          description: This is the list of entities which have been requested.
          items:
            $ref: '#/components/schemas/InteractorEntity'
        resource:
          type: string
          description: This is the resource where interactors have been queried.
    InteractorEntity:
      type: object
      properties:
        acc:
          type: string
          description: This is the interactor accession (or identifier).
        count:
          type: integer
          description: This is the number of interactions for the given accession.
          format: int32
        interactors:
          type: array
          description: List of Interactors that interacts with the given accession.
          items:
            $ref: '#/components/schemas/Interactor'
      description: This is the list of entities which have been requested.
    TupleResult:
      type: object
      properties:
        summary:
          $ref: '#/components/schemas/Summary'
        warningMessages:
          type: array
          items:
            type: string