医学公开数据库查询与登记

references/ucsc-genome.md

Overview

Provides programmatic access to genome annotations, gene tracks, sequence data, and other resources from the UCSC Genome Browser database.

Base URL

https://api.genome.ucsc.edu

Auth

None required (public, unauthenticated).

Response Format

JSON for all endpoints.

Key Endpoints

List available genomes

GET /list/ucscGenomes

Returns all genome assemblies (hg38, mm39, etc.) with descriptions.

List tracks for a genome

GET /list/tracks?genome=hg38

Returns all annotation tracks available for the specified assembly.

List chromosomes/contigs

GET /list/chromosomes?genome=hg38

Optional: add &track=<trackName> to limit to chroms with data in that track.

List tables in a track

GET /list/schema?genome=hg38&track=knownGene

Returns table schema including field names, types, and SQL create statement.

Get track data (annotations)

GET /getData/track?genome=hg38&track=knownGene&chrom=chr1&start=11873&end=14409

Parameters:

• genome -- assembly name (required)
• track -- track name (required)
• chrom -- chromosome (optional, limits to one chrom)
• start, end -- 0-based half-open coordinates (optional, requires chrom)
• maxItemsOutput -- limit number of items returned (default and maximum 1,000,000; still request a smaller bounded result)

Get sequence

GET /getData/sequence?genome=hg38&chrom=chr1&start=11873&end=11893

Returns DNA sequence for the specified region. Coordinates are 0-based half-open.

Search for a term

GET /search?search=BRCA1&genome=hg38

Returns matching positions across tracks (gene names, accessions, etc.).

Get hub genome data

GET /list/hubGenomes?hubUrl=<hubURL>

Lists genomes available in a track hub.

Example calls

Get RefSeq gene annotations in a region

GET https://api.genome.ucsc.edu/getData/track?genome=hg38&track=ncbiRefSeq&chrom=chr17&start=43044295&end=43125483

Get DNA sequence

GET https://api.genome.ucsc.edu/getData/sequence?genome=hg38&chrom=chr7&start=117119148&end=117119178

Response example (sequence)

{
  "genome": "hg38",
  "chrom": "chr7",
  "start": 117119148,
  "end": 117119178,
  "dna": "atgcagatatcagcgatgcagatcgatcg..."
}

Response example (track data)

{
  "genome": "hg38",
  "track": "ncbiRefSeq",
  "chrom": "chr17",
  "start": 43044295,
  "end": 43125483,
  "ncbiRefSeq": [
    {
      "chrom": "chr17",
      "chromStart": 43044295,
      "chromEnd": 43125483,
      "name": "NM_007294.4",
      "strand": "-",
      "name2": "BRCA1",
      "exonCount": 23,
      "exonStarts": "43044295,43047642,...",
      "exonEnds": "43045802,43047703,..."
    }
  ]
}

Coordinate system

All coordinates are 0-based, half-open (standard BED format). This means start is inclusive and end is exclusive.

Rate Limits

• No published hard rate limits
• The API is intended for moderate programmatic use; bulk downloads should use the MySQL public server (genome-mysql.soe.ucsc.edu) or BigBed/BigWig file downloads
• Requests returning very large result sets may be truncated via maxItemsOutput

Common genome values

• hg38 -- Human GRCh38 (current)
• hg19 -- Human GRCh37
• mm39 -- Mouse GRCm39
• mm10 -- Mouse GRCm38
• dm6 -- Drosophila
• danRer11 -- Zebrafish
• sacCer3 -- Yeast