STRING Valuesranks API

openapi: 3.2.0
info:
  title: STRING REST Valuesranks API
  description: 'STRING is a protein-protein interaction network database providing scored associations between proteins across thousands of organisms. The REST API enables programmatic access to interaction scores, network visualizations, functional enrichment analysis, homology data, and protein annotations. STRING integrates data from genomic context, co-expression, text mining, biochemical and genetic experiments, and curated databases.

    '
  version: '12.0'
  contact:
    name: STRING Consortium
    url: https://string-db.org
  license:
    name: Creative Commons Attribution
    url: https://string-db.org/cgi/access?footer_active_subpage=licensing
  termsOfService: https://string-db.org/cgi/info?footer_active_subpage=cookies
servers:
- url: https://string-db.org
  description: STRING Production Server
security: []
tags:
- name: valuesranks
  description: Values/Ranks GSEA-like enrichment (requires API key)
paths:
  /api/json/get_api_key:
    post:
      operationId: getApiKey
      summary: Get API Key
      description: 'Obtain an API key required for the Values/Ranks Enrichment endpoints. The key is tied to the caller_identity you provide.

        '
      tags:
      - valuesranks
      requestBody:
        required: true
        content:
          application/x-www-form-urlencoded:
            schema:
              type: object
              required:
              - caller_identity
              properties:
                caller_identity:
                  type: string
                  description: Unique identifier for your application or organization
                  example: my_lab_pipeline
      responses:
        '200':
          description: API key for Values/Ranks enrichment
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/ApiKey'
        '400':
          $ref: '#/components/responses/BadRequest'
  /api/json/valuesranks_enrichment_submit:
    post:
      operationId: submitValuesRanksEnrichment
      summary: Submit Values/Ranks Enrichment Job
      description: 'Submit a GSEA-like enrichment analysis on a ranked list of proteins with associated numeric values (e.g. fold-change, log p-value). Accepts up to 1000 concurrent jobs per API key. Returns a job_id to poll with the status endpoint.

        '
      tags:
      - valuesranks
      requestBody:
        required: true
        content:
          application/x-www-form-urlencoded:
            schema:
              type: object
              required:
              - api_key
              - identifiers
              - species
              properties:
                api_key:
                  type: string
                  description: API key obtained via the get_api_key endpoint
                identifiers:
                  type: string
                  description: 'Tab-separated protein-value pairs, one per line. Each line: STRING_ID<TAB>numeric_value

                    '
                species:
                  type: integer
                  description: NCBI taxon ID
                  example: 9606
                ge_fdr:
                  type: number
                  description: False discovery rate threshold for significance (default 0.01)
                  default: 0.01
                  minimum: 0
                  maximum: 1
                caller_identity:
                  type: string
                  description: Identifier for your application
      responses:
        '200':
          description: Job submission confirmation with job ID
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/JobSubmission'
        '400':
          $ref: '#/components/responses/BadRequest'
        '401':
          $ref: '#/components/responses/Unauthorized'
  /api/json/valuesranks_enrichment_status:
    get:
      operationId: getValuesRanksEnrichmentStatus
      summary: Check Values/Ranks Enrichment Status
      description: 'Check the status of a submitted Values/Ranks enrichment job. When status is "done", the response also includes the enrichment results.

        '
      tags:
      - valuesranks
      parameters:
      - name: api_key
        in: query
        required: true
        description: API key used to submit the job
        schema:
          type: string
      - name: job_id
        in: query
        required: true
        description: Job ID returned from the submit endpoint
        schema:
          type: string
      responses:
        '200':
          description: Job status and results (when complete)
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/JobStatus'
        '400':
          $ref: '#/components/responses/BadRequest'
        '401':
          $ref: '#/components/responses/Unauthorized'
  /api/json/valuesranks_enrichment_remove:
    get:
      operationId: removeValuesRanksEnrichmentJob
      summary: Remove Values/Ranks Enrichment Job
      description: Remove a submitted or completed Values/Ranks enrichment job to free up the slot.
      tags:
      - valuesranks
      parameters:
      - name: api_key
        in: query
        required: true
        description: API key used to submit the job
        schema:
          type: string
      - name: job_id
        in: query
        required: true
        description: Job ID to remove
        schema:
          type: string
      responses:
        '200':
          description: Job removal confirmation
          content:
            application/json:
              schema:
                type: object
                properties:
                  success:
                    type: boolean
        '400':
          $ref: '#/components/responses/BadRequest'
        '401':
          $ref: '#/components/responses/Unauthorized'
components:
  schemas:
    EnrichmentResult:
      type: object
      description: Functional enrichment result for one term
      properties:
        category:
          type: string
          description: 'Functional annotation category (e.g. Process, KEGG, Pfam, RCTM, Tissue)

            '
          example: Process
        term:
          type: string
          description: Functional term identifier
          example: GO:0006915
        number_of_genes:
          type: integer
          description: Number of input genes annotated to this term
        number_of_genes_in_background:
          type: integer
          description: Number of background genes annotated to this term
        ncbiTaxonId:
          type: integer
          description: NCBI taxon ID
        inputGenes:
          type: string
          description: Comma-separated list of input gene names annotated to this term
        preferredNames:
          type: string
          description: Comma-separated list of preferred gene names
        p_value:
          type: number
          description: Enrichment p-value (hypergeometric test)
          example: 1.23e-10
        fdr:
          type: number
          description: False discovery rate (Benjamini-Hochberg corrected)
          example: 4.56e-08
        description:
          type: string
          description: Human-readable name of the functional term
          example: apoptotic process
    JobStatus:
      type: object
      description: Job status and results
      properties:
        status:
          type: string
          enum:
          - queued
          - running
          - done
          - error
          description: Current job status
        job_id:
          type: string
          description: Job identifier
        results:
          type: array
          description: Enrichment results (only present when status is "done")
          items:
            $ref: '#/components/schemas/EnrichmentResult'
    ApiKey:
      type: object
      description: API key for Values/Ranks enrichment endpoints
      properties:
        api_key:
          type: string
          description: The API key to use in subsequent Values/Ranks requests
    JobSubmission:
      type: object
      description: Job submission response
      properties:
        job_id:
          type: string
          description: Unique job identifier for polling
    Error:
      type: object
      properties:
        status:
          type: integer
        error:
          type: string
        message:
          type: string
  responses:
    BadRequest:
      description: Bad request (invalid parameters)
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
        text/plain:
          schema:
            type: string
    Unauthorized:
      description: Invalid or missing API key
      content:
        application/json:
          schema:
            $ref: '#/components/schemas/Error'
  securitySchemes:
    ApiKeyAuth:
      type: apiKey
      in: query
      name: api_key
      description: 'API key required only for Values/Ranks Enrichment endpoints. Obtain via POST /api/json/get_api_key. All other endpoints are publicly accessible without authentication.

        '
externalDocs:
  description: STRING API Documentation
  url: https://string-db.org/help/api/