STRING Valuesranks API
Values/Ranks GSEA-like enrichment (requires API key)
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OpenAPI Specification
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:
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'
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
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
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
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/