Reactome token API

openapi: 3.0.1
info:
  title: Pathway Analysis Service database token 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: token
  description: Previous queries filter
paths:
  /token/{token}:
    get:
      tags:
      - token
      summary: Returns the result associated with the token
      description: Use page and pageSize to reduce the amount of data retrieved. Use sortBy and order to sort the result by your preferred option. The resource field will filter the results to show only those corresponding to the preferred molecule type (TOTAL includes all the different molecules type)
      operationId: getToken
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: species
        in: query
        description: list of species to filter the result (accepts taxonomy ids, species names and dbId)
        required: false
        schema:
          type: string
      - name: pageSize
        in: query
        description: pathways per page
        required: false
        schema:
          type: integer
          format: int32
        example: 20
      - name: page
        in: query
        description: page number
        required: false
        schema:
          type: integer
          format: int32
        example: 1
      - name: sortBy
        in: query
        required: false
        schema:
          type: string
          description: how to sort the result
          example: ENTITIES_PVALUE
          enum:
          - NAME
          - TOTAL_ENTITIES
          - TOTAL_INTERACTORS
          - TOTAL_REACTIONS
          - FOUND_ENTITIES
          - FOUND_INTERACTORS
          - FOUND_REACTIONS
          - ENTITIES_RATIO
          - ENTITIES_PVALUE
          - ENTITIES_FDR
          - REACTIONS_RATIO
      - name: order
        in: query
        required: false
        schema:
          type: string
          description: specifies the order
          example: ASC
          enum:
          - ASC
          - DESC
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      - name: min
        in: query
        description: minimum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: max
        in: query
        description: maximum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AnalysisResult'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/AnalysisResult'
  /token/{token}/filter/pathways:
    post:
      tags:
      - token
      summary: Returns the result for the pathway ids sent by post (when they are present in the original result)
      description: For a given list of pathway identifiers it will retrieve a list containing those that are present in the result (with the results for the indicated molecule type)
      operationId: getTokenFilterPathways
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: species
        in: query
        description: list of species to filter the result (accepts taxonomy ids, species names and dbId)
        required: false
        schema:
          type: string
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      - name: min
        in: query
        description: minimum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: max
        in: query
        description: maximum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      requestBody:
        description: '<b>input</b> A comma separated list with the identifiers of the pathways of interest (NOTE: is plain text, not json)'
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/PathwaySummary'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/PathwaySummary'
  /token/{token}/filter/species/{species}:
    get:
      tags:
      - token
      summary: Filters the result by species
      operationId: filterBySpecies
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: species
        in: path
        description: The species to filter the result (accepts the taxonomy id, species names and dbId)
        required: true
        schema:
          type: string
      - name: sortBy
        in: query
        required: false
        schema:
          type: string
          description: how to sort the result
          example: ENTITIES_PVALUE
          enum:
          - NAME
          - TOTAL_ENTITIES
          - TOTAL_INTERACTORS
          - TOTAL_REACTIONS
          - FOUND_ENTITIES
          - FOUND_INTERACTORS
          - FOUND_REACTIONS
          - ENTITIES_RATIO
          - ENTITIES_PVALUE
          - ENTITIES_FDR
          - REACTIONS_RATIO
      - name: order
        in: query
        required: false
        schema:
          type: string
          description: specifies the order
          example: ASC
          enum:
          - ASC
          - DESC
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SpeciesFilteredResult'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/SpeciesFilteredResult'
  /token/{token}/found/all:
    post:
      tags:
      - token
      summary: Returns a summary of the contained identifiers and interactors for each requested pathway and a given token
      description: The identifiers submitted by the user that have a match in Reactome database. It also retrieves the mapping to the main identifiers for those that have been found.
      operationId: getTokenHitEntitiesPathways
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      requestBody:
        description: '<b>input</b> A comma separated list with the identifiers of the pathways of interest (NOTE: is plain text, not json)'
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/FoundElements'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/FoundElements'
  /token/{token}/found/all/{pathway}:
    get:
      tags:
      - token
      summary: Returns a summary of the contained identifiers and interactors for a given pathway and token
      description: The identifiers submitted by the user that have a match in Reactome database. It also retrieves the mapping to the main identifiers for those that have been found.
      operationId: getTokenHitEntitiesPathway
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pathway
        in: path
        description: The identifier of the pathway of interest
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundElements'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundElements'
  /token/{token}/found/entities/{pathway}:
    get:
      tags:
      - token
      summary: Returns a summary of the found curated identifiers for a given pathway and token
      description: The identifiers submitted by the user that have a match in Reactome database. It also retrieves the mapping to the main identifiers for those that have been found.
      operationId: getTokenIdentifiersPathway
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pathway
        in: path
        description: The identifier of the pathway of interest
        required: true
        schema:
          type: string
      - name: page
        in: query
        description: page number
        required: false
        schema:
          type: integer
          format: int32
        example: 1
      - name: pageSize
        in: query
        description: identifiers per page
        required: false
        schema:
          type: integer
          format: int32
        example: 20
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundEntities'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundEntities'
  /token/{token}/found/interactors/{pathway}:
    get:
      tags:
      - token
      summary: Returns a summary of the found interactors for a given pathway and token
      description: The identifiers submitted by the user that have a match with an interactor in Reactome database. It also retrieves the mapping to the main identifiers (the one interacting with) for those that have been found.
      operationId: getTokenInteractorsPathway
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pathway
        in: path
        description: The identifier of the pathway of interest
        required: true
        schema:
          type: string
      - name: page
        in: query
        description: page number
        required: false
        schema:
          type: integer
          format: int32
        example: 1
      - name: pageSize
        in: query
        description: identifiers per page
        required: false
        schema:
          type: integer
          format: int32
        example: 20
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundInteractors'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FoundInteractors'
  /token/{token}/notFound:
    get:
      tags:
      - token
      summary: Returns a list of the identifiers not found for a given token
      description: Those identifiers that have not been found in the Reactome database
      operationId: getNotFoundIdentifiers
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pageSize
        in: query
        description: identifiers per page
        required: false
        schema:
          type: integer
          format: int32
        example: 40
      - name: page
        in: query
        description: page number
        required: false
        schema:
          type: integer
          format: int32
        example: 1
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/IdentifierSummary'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/IdentifierSummary'
  /token/{token}/page/{pathway}:
    get:
      tags:
      - token
      summary: Returns the page where the corresponding pathway is taking into account the passed parameters
      description: Useful when implementing UI with tables showing the results in a page way and the user needs to know in which page a certain pathway is present for a given set of sorting and filtering options.
      operationId: getPageOfPathway
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pathway
        in: path
        description: The database identifier of the pathway of interest
        required: true
        schema:
          type: string
      - name: pageSize
        in: query
        description: pathways per page
        required: false
        schema:
          type: integer
          format: int32
        example: 20
      - name: sortBy
        in: query
        required: false
        schema:
          type: string
          description: how to sort the result
          example: ENTITIES_PVALUE
          enum:
          - NAME
          - TOTAL_ENTITIES
          - TOTAL_INTERACTORS
          - TOTAL_REACTIONS
          - FOUND_ENTITIES
          - FOUND_INTERACTORS
          - FOUND_REACTIONS
          - ENTITIES_RATIO
          - ENTITIES_PVALUE
          - ENTITIES_FDR
          - REACTIONS_RATIO
      - name: order
        in: query
        required: false
        schema:
          type: string
          description: specifies the order
          example: ASC
          enum:
          - ASC
          - DESC
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      - name: min
        in: query
        description: minimum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: max
        in: query
        description: maximum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: integer
                format: int32
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: integer
                format: int32
  /token/{token}/pathways/binned:
    get:
      tags:
      - token
      summary: Returns a list of binned hit pathway sizes associated with the token
      description: 'Each bin has a key that determines the range by multiplying it by the binSize: [key x binSize - key+1 x binSize). For example, for a binSize of 100 and the range for the bin with key equals 8 is [800 - 900)'
      operationId: getPathwaysBinnedBySize
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: binSize
        in: query
        required: false
        schema:
          type: string
          description: 'defines the size of each bin for the classification (min: 100)'
          example: 100
      - name: species
        in: query
        description: list of species to filter the result (accepts taxonomy ids, species names and dbId)
        required: false
        schema:
          type: string
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Bin'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Bin'
  /token/{token}/reactions/pathways:
    post:
      tags:
      - token
      summary: Returns the reaction ids of the pathway ids sent by post that are present in the original result
      description: It filters the submitted list and retrieves back only those that at least one of the participating molecules has been hit with the user submitted data.
      operationId: getTokenFilterPathwaysReactions
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      - name: min
        in: query
        description: minimum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: max
        in: query
        description: maximum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      requestBody:
        description: '<b>input</b> A comma separated list with the identifiers of the pathways of interest (NOTE: is plain text, not json)'
        content:
          text/plain:
            schema:
              type: string
        required: true
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                uniqueItems: true
                type: array
                items:
                  type: integer
                  format: int64
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                uniqueItems: true
                type: array
                items:
                  type: integer
                  format: int64
  /token/{token}/reactions/{pathway}:
    get:
      tags:
      - token
      summary: Returns the reaction ids of the provided pathway id that are present in the original result
      description: For a given pathway it returns the identifiers (dbId) of the reactions in the pathway that have been hit with the sample taking into account their participating molecules.
      operationId: getTokenFilterPathwayReactions
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      - name: pathway
        in: path
        description: The database identifier of the pathway of interest
        required: true
        schema:
          type: string
      - name: resource
        in: query
        required: false
        schema:
          type: string
          description: the resource to sort
          example: TOTAL
          enum:
          - TOTAL
          - UNIPROT
          - ENSEMBL
          - CHEBI
          - IUPHAR
          - MIRBASE
          - NCBI_PROTEIN
          - EMBL
          - COMPOUND
          - PUBCHEM_COMPOUND
      - name: pValue
        in: query
        description: defines the pValue threshold. Only hit pathway with pValue equals or below the threshold will be returned
        required: false
        schema:
          type: number
          format: double
          default: 1.0
        example: 1
      - name: includeDisease
        in: query
        description: set to 'false' to exclude the disease pathways from the result (it does not alter the statistics)
        required: false
        schema:
          type: boolean
      - name: min
        in: query
        description: minimum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: max
        in: query
        description: maximum number of contained entities per pathway (takes into account the resource)
        required: false
        schema:
          type: integer
          format: int32
      - name: importableOnly
        in: query
        description: Filters resources to only includes importable ones
        required: false
        schema:
          type: boolean
          default: false
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                uniqueItems: true
                type: array
                items:
                  type: integer
                  format: int64
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                uniqueItems: true
                type: array
                items:
                  type: integer
                  format: int64
  /token/{token}/resources:
    get:
      tags:
      - token
      summary: Returns the resources summary associated with the token
      description: A summary of the molecules type associated to the submitted data.
      operationId: getResources
      parameters:
      - name: token
        in: path
        description: The token associated with the data to query
        required: true
        schema:
          type: string
      responses:
        '404':
          description: No result corresponding to the token was found
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/ResourceSummary'
        '410':
          description: Result deleted due to a new data release
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/ResourceSummary'
components:
  schemas:
    PathwayBase:
      type: object
      properties:
        dbId:
          type: integer
          format: int64
        disease:
          type: boolean
        entities:
          $ref: '#/components/schemas/EntityStatistics'
        stId:
          type: string
    FoundInteractors:
      type: object
      properties:
        expNames:
          type: array
          items:
            type: string
        found:
          type: integer
          format: int32
        identifiers:
          type: array
          items:
            $ref: '#/components/schemas/FoundInteractor'
        resources:
          uniqueItems: true
          type: array
          items:
            type: string
    FoundElements:
      type: object
      properties:
        entities:
  

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# Full source: https://raw.githubusercontent.com/api-evangelist/reactome/refs/heads/main/openapi/reactome-token-api-openapi.yml