UCSC Genomic Data Tracks API

openapi: 3.0.0
info:
  title: UCSC Genome Browser REST Genomes Tracks API
  description: The UCSC Genome Browser REST API provides programmatic access to genomic data, sequences, annotation tracks, genome assemblies, and track hubs. All endpoints return JSON and require no authentication. Rate limiting of one request per second is recommended to avoid the botDelay system.
  version: 1.0.0
  contact:
    name: UCSC Genome Browser
    url: https://genome.ucsc.edu
servers:
- url: https://api.genome.ucsc.edu
  description: UCSC Primary API Server
- url: https://genome-euro.ucsc.edu/cgi-bin/hubApi
  description: UCSC Europe Mirror
- url: https://genome-asia.ucsc.edu/cgi-bin/hubApi
  description: UCSC Asia Mirror
tags:
- name: Tracks
  description: Annotation track listings and data retrieval
paths:
  /list/tracks:
    get:
      operationId: listTracks
      summary: List Tracks
      description: Returns all data tracks available for a given genome assembly or hub.
      tags:
      - Tracks
      parameters:
      - name: genome
        in: query
        required: true
        schema:
          type: string
        description: Genome assembly identifier (e.g., hg38, mm39). Required unless hubUrl is provided.
      - name: hubUrl
        in: query
        required: false
        schema:
          type: string
          format: uri
        description: URL of the hub.txt file for a track hub.
      - name: trackLeavesOnly
        in: query
        required: false
        schema:
          type: integer
          enum:
          - 0
          - 1
          default: 0
        description: Set to 1 to return only leaf tracks (hide composite containers).
      responses:
        '200':
          description: List of tracks for the genome.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TrackListResult'
  /list/schema:
    get:
      operationId: getTrackSchema
      summary: Get Track Schema
      description: Returns the schema and field definitions for a specific annotation track.
      tags:
      - Tracks
      parameters:
      - name: genome
        in: query
        required: true
        schema:
          type: string
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: track
        in: query
        required: true
        schema:
          type: string
        description: Track name to return schema for.
      - name: hubUrl
        in: query
        required: false
        schema:
          type: string
          format: uri
        description: URL of the hub.txt file for a track hub.
      responses:
        '200':
          description: Track schema definition.
          content:
            application/json:
              schema:
                type: object
  /getData/track:
    get:
      operationId: getTrackData
      summary: Get Track Data
      description: Retrieves annotation data from a specific track for a genomic region.
      tags:
      - Tracks
      parameters:
      - name: genome
        in: query
        required: true
        schema:
          type: string
        description: Genome assembly identifier (e.g., hg38, mm39).
      - name: track
        in: query
        required: true
        schema:
          type: string
        description: Track name to retrieve data from.
      - name: chrom
        in: query
        required: false
        schema:
          type: string
        description: Chromosome to retrieve data for.
      - name: start
        in: query
        required: false
        schema:
          type: integer
        description: Start position (0-based).
      - name: end
        in: query
        required: false
        schema:
          type: integer
        description: End position (1-based).
      - name: hubUrl
        in: query
        required: false
        schema:
          type: string
          format: uri
        description: URL of the hub.txt file for a track hub.
      - name: maxItemsOutput
        in: query
        required: false
        schema:
          type: integer
          default: 1000000
        description: Maximum number of annotation items to return.
      - name: jsonOutputArrays
        in: query
        required: false
        schema:
          type: integer
          enum:
          - 0
          - 1
        description: Set to 1 to format output as JSON arrays instead of objects.
      responses:
        '200':
          description: Track annotation data.
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/TrackDataResult'
components:
  schemas:
    TrackListResult:
      type: object
      properties:
        genome:
          type: string
          description: Genome assembly identifier.
        tracks:
          type: object
          additionalProperties:
            $ref: '#/components/schemas/Track'
    TrackDataResult:
      type: object
      properties:
        genome:
          type: string
          description: Genome assembly identifier.
        track:
          type: string
          description: Track name.
        chrom:
          type: string
          description: Chromosome identifier.
        start:
          type: integer
          description: Start position.
        end:
          type: integer
          description: End position.
        itemsReturned:
          type: integer
          description: Number of annotation items returned.
    Track:
      type: object
      properties:
        track:
          type: string
          description: Track name identifier.
        shortLabel:
          type: string
          description: Short display label.
        longLabel:
          type: string
          description: Long description label.
        type:
          type: string
          description: Track data type (e.g., bed, bigBed, bigWig).
        visibility:
          type: string
          description: Default visibility setting.
        html:
          type: string
          description: Track description HTML path.