bbabbd5d2566d47d923d51dbe350634783455999 mspeir Sun Oct 26 12:14:52 2025 -0700 change soe to gi, refs #35031 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 95bda4c5860..1ec2de5f222 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -32,34 +32,34 @@ data that is available for their analyses. Web APIs, as a technology, were designed for retrieving relatively small pieces of data, often from Javascript. Consequently, Web APIs may not be the best way to get data from the UCSC Genome Browser.

For this reason, we also provide alternative methods to access our data:

The Table Browser for custom exports and reports as tab-separated files and can be joined with other tables.
For tracks that are stored in MySQL, our MySQL/MariaDB server is publicly accessible.
Dumps of SQL-stored tracks, as well as tracks in binary file formats, can be found on our - download server. + download server.
All binary files on the download server (bigBed, bigWig and derivatives like bigPsl, bigChain, - etc) can even be streamed over HTTP.

All these options offer faster bulk downloads and are often easier to parse from scripting languages. If, however, you write Javascript clients or need only a few features within a given range, then the endpoints documented on this page may address your needs. If you require an option or endpoint not listed below for your specific use case, contact us and we can try and implement the feature.

Conditions of use

Avoid excessive or heavy queries that may impact the server performance. Inappropriate query use will result in a restriction of access.
@@ -236,31 +236,31 @@ The hubUrl and genome parameters are required together to specify a unique genome in an assembly or track hub. The genome for a track hub will usually be a UCSC database genome. Assembly hubs will have their own unique genome sequences. Specify genome without a hubUrl to refer to a UCSC Genome Browser assembly.

Using the chrom=<name> parameter will limit the request to the single specified chromosome. To limit the request to a specific position, both start=4321 and end=5678 must be given together. Using the revComp=1 parameter returns the reverse complement.

Use the genome argument with the /list/genarkGenomes function to test for the existence of a specific genome assembly in the -Genark set +Genark set of assembly hubs.

The /list/files endpoint only works for UCSC hosted genome assemblies, not for external hosted assembly hubs.

The /findGenome endpoint can find genome assemblies in the browser or any other assembly available at NCBI even when not in the browser. Note, there are almost 4 million assemblies available at NCBI. All searches are case insensitive. Force inclusion: Use a + sign before +word to ensure it appears in the result. Exclude words: Use a - sign before -word to exclude it from the search result. Wildcard search: Add an * (asterisk) at end of word* to search for all terms starting with that prefix.
@@ -294,31 +294,31 @@
- expRatio (e.g. 'gnfAtlas2' for mm9)
- factorSource (e.g. 'encRegTfbsClustered' for hg38)
- genePred
- gvf (e.g. 'cnvDevDelayCase' for hg19)
- interact/bigInteract
- narrowPeak
- netAlign
- peptideMapping
- pgSnp
- psl
- rmsk - repeat masker
- rmsk - repeat masker
- wiggle/wig
Work is underway to support additional track types
Using the API on mirrors and local installations

In order to access the API from a mirror installation or one of the UCSC official mirrors, the complete URL with the cgi-bin should be used:
- find any genome matching the search string: '+white +rhino* -southern' - api.genome.ucsc.edu/findGenome?q=%2Bwhite%20%2Brhino%2A%20-southern
- find any genome with the accession id: GCF_028858775.2 - api.genome.ucsc.edu/findGenome?q=GCF_028858775.2
- find any genome with the name: GRCh38 - api.genome.ucsc.edu/findGenome?q=GRCh38
- list public hubs - api.genome.ucsc.edu/list/publicHubs
- list UCSC database genomes - api.genome.ucsc.edu/list/ucscGenomes
- list GenArk assembly hub genomes - api.genome.ucsc.edu/list/genarkGenomes?maxItemsOutput=5
- test if genome GCF_028858775.2 exists in the GenArk assembly hub genomes - api.genome.ucsc.edu/list/genarkGenomes?genome=GCF_028858775.2
- list genomes from specified hub - -api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt
- api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hub.txt
- list tracks from specified hub and genome - -api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
- list tracks from UCSC database genome - api.genome.ucsc.edu/list/tracks?genome=hg38
- list chromosomes from UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=hg38
- list chromosomes from specified track in UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold
- list chromosomes from assembly hub genome - -
  api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
- api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.gi.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
- list chromosomes from specified track in assembly hub genome - -
  api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly
- list schema from specified track in UCSC database genome -
  api.genome.ucsc.edu/list/schema?genome=hg38;track=knownGene
- list download files for UCSC GenArk genome 'GCF_000955945.1' in JSON format limit 5 items output -
  api.genome.ucsc.edu/list/files?genome=GCF_000955945.1;maxItemsOutput=5
- list download files for UCSC genome 'hs1' in plain text format limit 5 items output -
  api.genome.ucsc.edu/list/files?genome=hs1;format=text;maxItemsOutput=5

Conditions of use

Using the API on mirrors and local installations

getData functions

Search functions

Error return examples

Practical examples

Looking up the schema of a specific track