Reactome search API

openapi: 3.0.1
info:
  title: Pathway Analysis Service database search 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: search
  description: Reactome Search
paths:
  /search/diagram/{diagram}:
    get:
      tags:
      - search
      summary: Performs a Solr query (diagram widget scoped) for a given QueryObject
      operationId: getDiagramResult
      parameters:
      - name: diagram
        in: path
        required: true
        schema:
          type: string
        example: R-HSA-8848021
      - name: query
        in: query
        required: true
        schema:
          type: string
        example: MAD
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: start
        in: query
        description: Start row
        required: false
        schema:
          type: integer
          format: int32
      - name: rows
        in: query
        description: Number of rows to include
        required: false
        schema:
          type: integer
          format: int32
      - name: scope
        in: query
        description: Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types
        required: false
        schema:
          type: string
          default: PHYSICAL_ENTITY
          enum:
          - REFERENCE_ENTITY
          - PHYSICAL_ENTITY
          - BOTH
      - name: includeInteractors
        in: query
        description: Whether the result should consider interactors as part of a diagram
        required: false
        schema:
          type: boolean
          default: 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DiagramResult'
  /search/diagram/{diagram}/occurrences/{instance}:
    get:
      tags:
      - search
      summary: Performs a Solr query (diagram widget scoped) for a given QueryObject
      operationId: getDiagramOccurrences
      parameters:
      - name: diagram
        in: path
        required: true
        schema:
          type: string
        example: R-HSA-68886
      - name: instance
        in: path
        required: true
        schema:
          type: string
        example: R-HSA-141433
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: includeInteractors
        in: query
        description: Whether the result should consider interactors as part of a diagram
        required: false
        schema:
          type: boolean
          default: 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DiagramOccurrencesResult'
  /search/diagram/{pathwayId}/flag:
    get:
      tags:
      - search
      summary: A list of diagram entities plus pathways from the provided list containing the specified identifier
      description: This method traverses the content and checks not only for the main identifier but also for all the cross-references to find the flag targets
      operationId: getEntitiesInDiagramForIdentifier
      parameters:
      - name: pathwayId
        in: path
        description: The pathway to find items to flag
        required: true
        schema:
          type: string
        example: R-HSA-446203
      - name: query
        in: query
        description: The identifier for the elements to be flagged
        required: true
        schema:
          type: string
        example: CTSA
      - name: includeInteractors
        in: query
        description: Whether the result should consider interactors as part of a diagram
        required: false
        schema:
          type: boolean
          default: 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DiagramOccurrencesResult'
  /search/facet:
    get:
      tags:
      - search
      summary: A list of facets corresponding to the whole Reactome search data
      description: This method retrieves faceting information on the whole Reactome search data.
      operationId: facet
      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:
                $ref: '#/components/schemas/FacetMapping'
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FacetMapping'
  /search/facet_query:
    get:
      tags:
      - search
      summary: A list of facets corresponding to a specific query
      description: This method retrieves faceting information on a specific query
      operationId: facet_type
      parameters:
      - name: query
        in: query
        description: Search term
        required: true
        schema:
          type: string
        example: TP53
      - name: species
        in: query
        description: Species name
        required: false
        schema:
          type: array
          items:
            type: string
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: compartments
        in: query
        description: Compartments to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: keywords
        in: query
        description: Keywords
        required: false
        schema:
          type: array
          items:
            type: string
      - name: scope
        in: query
        description: Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types
        required: false
        schema:
          type: string
          default: PHYSICAL_ENTITY
          enum:
          - REFERENCE_ENTITY
          - PHYSICAL_ENTITY
          - BOTH
      - name: Force filters
        in: query
        description: Force filters<br>In case where applied filters yield to no results, filters are removed by default to grant results as much as possible. Set <b>Force filters</b> to true to avoid this behaviour
        required: false
        schema:
          type: boolean
          default: 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:
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FacetMapping'
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FacetMapping'
  /search/fireworks:
    get:
      tags:
      - search
      summary: Performs a Solr query (fireworks widget scoped) for a given QueryObject
      operationId: getFireworksResult
      parameters:
      - name: query
        in: query
        required: true
        schema:
          type: string
        example: BRAF
      - name: species
        in: query
        description: Species name
        required: false
        schema:
          type: string
          default: Homo sapiens
        example: Homo sapiens
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: start
        in: query
        description: Start row
        required: false
        schema:
          type: integer
          format: int32
      - name: scope
        in: query
        description: Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types
        required: false
        schema:
          type: string
          default: PHYSICAL_ENTITY
          enum:
          - REFERENCE_ENTITY
          - PHYSICAL_ENTITY
          - BOTH
      - name: includeInteractors
        in: query
        description: Whether the result should consider interactors as part of a diagram
        required: false
        schema:
          type: boolean
          default: false
      - name: rows
        in: query
        description: Number of rows to include
        required: false
        schema:
          type: integer
          format: int32
      - 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FireworksResult'
  /search/fireworks/flag:
    get:
      tags:
      - search
      summary: Performs a Solr query (fireworks widget scoped) for a given QueryObject
      operationId: fireworksFlagging
      parameters:
      - name: query
        in: query
        required: true
        schema:
          type: string
        example: KNTC1
      - name: species
        in: query
        required: false
        schema:
          type: string
          default: Homo sapiens
      - 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/FireworksOccurrencesResult'
  /search/pathways/of/{dbId}:
    get:
      tags:
      - search
      summary: Find the different pathways containing a specific entity determined by its dbId. Can customise the output using fields
      operationId: getContainingPathwaysOf
      parameters:
      - name: dbId
        in: path
        required: true
        schema:
          type: integer
          format: int64
        example: 227785
      - name: includeInteractors
        in: query
        description: Whether the result should consider interactors as part of a diagram
        required: false
        schema:
          type: boolean
          default: false
      - name: directlyInDiagram
        in: query
        description: Whether the result should exclude higher level diagrams containing pathways, themselves containing the targeted entity
        required: false
        schema:
          type: boolean
          default: false
      - name: species
        in: query
        description: Species name to filter results for
        required: false
        schema:
          type: string
        example: Homo sapiens
      - name: fields
        in: query
        description: Fields to include in the response. If empty, retrieves all field available (not recommended)
        required: false
        schema:
          type: array
          items:
            type: string
            enum:
            - DB_ID
            - ST_ID
            - PHYSICAL_ENTITIES_DB_ID
            - NAME
            - SPECIES
            - SPECIES_FACET
            - TYPES
            - KEYWORDS
            - COMPARTMENT_FACET
            - ICON_CATEGORIES_FACET
            - SUMMATION
            - INFERRED_SUMMATION
            - REFERENCE_URL
            - REFERENCE_NAME
            - REFERENCE_IDENTIFIERS
            - IS_DISEASE
            - TYPE
            - IS_REFERENCE_SUMMARY
            - HAS_REFERENCE_ENTITY
            - HAS_EHLD
            - EXACT_TYPE
            - DATABASE_NAME
            - REGULATOR
            - REGULATOR_ID
            - REGULATED_ENTITY
            - REGULATED_ENTITY_ID
            - COMPARTMENT_NAME
            - COMPARTMENT_ACCESSION
            - FIREWORKS_SPECIES
            - OCCURRENCES
            - OCCURRENCES_INTERACTOR
            - DIAGRAMS
            - DIAGRAMS_INTERACTOR
            - LLPS
            - AUTHORED_PATHWAYS
            - AUTHORED_REACTIONS
            - REVIEWED_PATHWAYS
            - REVIEWED_REACTIONS
            - ORCIDID
            - TARGET_IDENTIFIER
            - TARGET_ACCESSIONS
            - TARGET_GENENAMES
            - TARGET_SYNONYMS
            - TARGET_RESOURCE
            - ICON_NAME
            - ICON_CATEGORIES
            - ICON_CURATOR_NAME
            - ICON_CURATOR_ORCIDID
            - ICON_CURATOR_URL
            - ICON_DESIGNER_NAME
            - ICON_DESIGNER_URL
            - ICON_DESIGNER_ORCIDID
            - ICON_REFERENCES
            - ICON_PHYSICAL_ENTITIES
            - ICON_EHLDS
            - DELETED
            - DELETED_REASON
            - DELETED_EXPLANATION
            - DELETED_DATE
            - DELETED_REPLACEMENT_DB_IDS
            - DELETED_REPLACEMENT_ST_IDS
      - 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:
        '200':
          description: OK
          content:
            application/json:
              schema:
                type: array
                items:
                  $ref: '#/components/schemas/Entry'
  /search/query:
    get:
      tags:
      - search
      summary: Queries Solr against the Reactome knowledgebase
      description: This method performs a Solr query on the Reactome knowledgebase. Results can be provided in a paginated format.
      operationId: getSearchResult
      parameters:
      - name: query
        in: query
        description: Search term
        required: true
        schema:
          type: string
        example: Biological oxidations
      - name: species
        in: query
        description: Species name
        required: false
        schema:
          type: array
          items:
            type: string
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: compartments
        in: query
        description: Compartments to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: keywords
        in: query
        description: Keywords
        required: false
        schema:
          type: array
          items:
            type: string
      - name: cluster
        in: query
        description: Cluster results
        required: false
        schema:
          type: boolean
          default: true
        example: true
      - name: parserType
        in: query
        description: Query parser to use
        required: false
        schema:
          type: string
          default: STD
          enum:
          - DISMAX
          - EDISMAX
          - STD
        example: STD
      - name: Start row
        in: query
        description: Start row
        required: false
        schema:
          type: integer
          format: int32
          default: 0
        example: 0
      - name: rows
        in: query
        description: Number of rows to include
        required: false
        schema:
          type: integer
          format: int32
          default: 10
        example: 10
      - name: scope
        in: query
        description: Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types
        required: false
        schema:
          type: string
          default: PHYSICAL_ENTITY
          enum:
          - REFERENCE_ENTITY
          - PHYSICAL_ENTITY
          - BOTH
      - name: Force filters
        in: query
        description: Force filters<br>In case where applied filters yield to no results, filters are removed by default to grant results as much as possible. Set <b>Force filters</b> to true to avoid this behaviour
        required: false
        schema:
          type: boolean
          default: 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: Entry not found. Targets inform if the term is our scope of annotation
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
  /search/query/paginated:
    get:
      tags:
      - search
      summary: Queries Solr against the Reactome knowledgebase
      description: This method performs a Solr query on the Reactome knowledgebase. Results are in a paginated format, pages count starting from 1.
      operationId: getResult
      parameters:
      - name: query
        in: query
        description: Search term
        required: true
        schema:
          type: string
        example: Biological oxidations
      - name: page
        in: query
        description: Page, should be strictly positive
        required: true
        schema:
          type: integer
          format: int32
        example: 1
      - name: rowCount
        in: query
        description: Rows per page
        required: true
        schema:
          type: integer
          format: int32
        example: 10
      - name: species
        in: query
        description: Species name
        required: false
        schema:
          type: array
          items:
            type: string
      - name: types
        in: query
        description: Types to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: compartments
        in: query
        description: Compartments to filter
        required: false
        schema:
          type: array
          items:
            type: string
      - name: keywords
        in: query
        description: Keywords
        required: false
        schema:
          type: array
          items:
            type: string
      - name: cluster
        in: query
        description: Cluster results
        required: false
        schema:
          type: boolean
          default: true
        example: true
      - name: scope
        in: query
        description: Scope of the query. Can be either REFERENCE_ENTITY to group Physical Entities having a reference entity (Proteins, Genes, etc.) into a single ReferenceEntity, and keep those which don't (Complexes, Sets, etc.) as Physical Entity. PHYSICAL_ENTITY to remove the grouping by reference entity. BOTH to include both types
        required: false
        schema:
          type: string
          default: PHYSICAL_ENTITY
          enum:
          - REFERENCE_ENTITY
          - PHYSICAL_ENTITY
          - BOTH
      - name: parserType
        in: query
        description: Query parser to use
        required: false
        schema:
          type: string
          default: STD
          enum:
          - DISMAX
          - EDISMAX
          - STD
        example: STD
      - 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:
        '400':
          description: One or more parameter is illegal
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
        '404':
          description: Entry not found. Targets inform if the term is our scope of annotation
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
        '406':
          description: Not acceptable according to the accept headers sent in the request
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/GroupedResult'
  /search/spellcheck:
    get:
      tags:
      - search
      summary: Spell-check suggestions for a given query
      description: This method retrieves a list of spell-check suggestions for a given search term.
      operationId: spellcheckerSuggestions
      parameters:
      - name: query
        in: query
        description: Search term
        required: true
        schema:
          type: string
        example: repoduction
      - 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:
                  type: string
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                type: array
                items:
                  type: string
  /search/suggest:
    get:
      tags:
      - search
      summary: Auto-suggestions for a given query
      description: This method retrieves a list of suggestions for a given search term.
      operationId: suggesterSuggestions
      parameters:
      - name: query
        in: query
        description: Search term
        required: true
        schema:
          type: string
        example: platele
      - 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:
                  type: string
        '500':
          description: Internal Error in SolR
          content:
            application/json:
              schema:
                type: array
                items:
                  type: string
components:
  schemas:
    DiagramResult:
      type: object
      properties:
        entries:
          type: array
          items:
            $ref: '#/components/schemas/Entry'
        facets:
          type: array
          items:
            $ref: '#/components/schemas/FacetContainer'
        found:
          type: integer
          format: int64
    FacetList:
      type: object
      properties:
        available:
          type: array
          items:
            $ref: '#/components/schemas/FacetContainer'
        selected:
          type: array
          items:
            $ref: '#/components/schemas/FacetContainer'
    GroupedResult:
      type: object
      properties:
        numberOfGroups:
          type: integer
          format: int32
        numberOfMatches:
          type: integer
          format: int32
        results:
          type: array
          items:
            $ref: '#/components/schemas/Result'
        rowCount:
          type: integer
          format: int32
        targetResults:
          uniqueItems: true
          type: array
          items:
            $ref: '#/components/schemas/TargetResult'
    TargetResult:
      type: object
      properties:
        resource:
          type: string
        target:
          type: boolean
        term:
          type: string
    FacetContainer:
      type: object
      properties:
        count:
          type: integer
          format: int64
        name:
          type: string
    FireworksOccurrencesResult:
      type: object
      properties:
        interactsWith:
          type: array
          items:
            type: string
        llps:
          type: array
          items:
            type: string
    DiagramOccurrencesResult:
      type: object
      properties:
        diagramEntity:
          type: string
        inDiagram:
          type: boolean
        interactsWith:
          type: array
          items:
            type: string
        occurrences:
          type: array
          items:
            type: string
    Result:
      type: object
      properties:
        entries:
          type: array
          items:
            $ref: '#/components/schemas/Entry'
        entriesCount:
          type: integer
          format: int64
        rowCount:
          type: integer
          format: int32
        typeName:
          type:

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