d7b4748a91dc6442607af5c9a3c0c9a96282dd53
hiram
Wed Apr 3 14:13:00 2019 -0700
add link to trackDb definition document help refs #18869
diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html
index 3e43bf4..65231a9 100755
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JSON API data interface
Contents
-
-
-Additional resources
-
What is JSON data ?
JSON data is a data transfer syntax from a data provider to a data consumer.
See also: JSON Introduction
What is the access URL ?
The gateway html page to the interface is available at
api-test.gi.ucsc.edu. This page can be used
to explore track hubs, assembly hubs, and UCSC browser data resources.
Example URL links for JSON output are provided on that page for track
types that are currently supported for data output. Work is underway
to provide access to additional data track types.
This access url: https://api-test.gi.ucsc.edu/ is used to access
the endpoint functions. For example:
wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs'
What type of data can be accessed ?
The following data sets can be accessed at this time:
- Listing of available public hubs
- Listing of available UCSC browser genome assemblies
- List genomes from a specified assembly or track hub
-- List available data tracks from a specified hub or UCSC browser genome assembly
+- List available data tracks from a specified hub or UCSC browser genome assembly (see also: track definition help)
- List of chromosomes contained in an assembly hub or UCSC browser genome assembly.
- List of chromosomes contained in a specific track of an assembly or track hub or UCSC browser genome assembly.
- Return DNA sequence from an assembly hub 2bit file, or UCSC genome browser assembly
- Return track data from a specified assembly or track hub or UCSC genome browser assembly
Endpoint functions to return data
Use the url: https://api-test.gi.ucsc.edu/ is access
the endpoint functions. For example:
wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs'
- /list/publicHubs - list public hubs
- /list/ucscGenomes - list UCSC database genomes
- /list/hubGenomes - list genomes from specified hub
-- /list/tracks - list data tracks available in specified hub or database genome
+- /list/tracks - list data tracks available in specified hub or database genome (see also: track definition help)
- /list/chromosomes - list chromosomes from a data track in specified hub or database genome
- /getData/sequence - return sequence from specified hub or database genome
- /getData/track - return data from specified track in hub or database genome
Parameters to endpoint functions
- hubUrl=<url> - specify track hub or assembly hub URL
- genome=<name> - specify genome assemby in track or assembly hub (only used with hubUrl)
- db=<ucscDb> - specify database (aka genome assembly) in UCSC genome browser (either hubUrl or db specified, not both)
- track=<trackName> - specify data track in hub or UCSC database genome assembly
- chrom=<chrN> - specify chromosome name for sequence or track data
- start=<123> - specify start coordinate (0 relative) for data from track or sequence retrieval (start and end required together)
- end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together)
- (see also: UCSC browser coordinate counting systems)
- maxItemsOutput=1000 - limit number of items to output, default: 1,000, maximum limit: 1,000,000
The parameters are added to the endpoint URL beginning with a
question mark ?, and multiple parameters are separated with
the semi-colon ;. For example:
https://api-test.gi.ucsc.edu/getData/sequence?db=ce11;chrom=chrM
Required and optional parameters
| Endpoint function | Required | Optional |
|---|
| /list/publicHubs | (none) | (none) |
|---|
| /list/ucscGenomes | (none) | (none) |
|---|
| /list/hubGenomes | hubUrl | (none) |
|---|
| /list/tracks | (hubUrl and genome) or db | (none) |
|---|
| /list/chromosomes | ((hubUrl and genome) or db) and track | (none) |
|---|
| /getData/sequence | ((hubUrl and genome) or db) and chrom | start and end |
|---|
| /getData/track | ((hubUrl and genome) or db) and track | chrom, (start and end), maxItemsOutput |
|---|
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.
When not an assembly or track hub, to access UCSC database assemblies,
the parameter db=<name> is required.
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.
Supported track types, at this time (April 2019), for getData functions
Example data access
Listing functions
- list public hubs - api.genome.ucsc.edu/list/publicHubs
- list UCSC database genomes - api.genome.ucsc.edu/list/ucscGenomes
- list genomes from specified hub - api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt
- list tracks from specified hub and genome - api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1
- list tracks from UCSC database genome - api.genome.ucsc.edu/list/tracks?db=ce11
- list chromosomes from UCSC database genome - api.genome.ucsc.edu/list/chromosomes?db=ce11
- list chromosomes from specified track in UCSC database genome - api.genome.ucsc.edu/list/chromosomes?db=ce11;track=gold
- list chromosomes from assembly hub genome -
api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1
- list chromosomes from specified track in assembly hub genome -
api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_
getData functions
- Get DNA sequence from specified chromosome in UCSC database genome -
api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM
- Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome -
api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM;start=4321;end=5678
- Get DNA sequence from a track hub where 'genome' is a UCSC database -
api.genome.ucsc.edu/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678
- Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome -
api.genome.ucsc.edu/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678
- Get track data for specified track in UCSC database genome -
api.genome.ucsc.edu/getData/track?db=ce11;track=gold;maxItemsOutput=100
- Get track data for specified track and chromosome in UCSC database genome -
api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrM
- Get track data for specified track, chromosome and start,end coordinates in UCSC database genome -
api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrI;start=47000;end=48000
- Get track data for specified track in an assembly hub genome -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_
- Get track data for specified track and chromosome in an assembly hub genome -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp
- Get track data for specified track in a track hub -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved
- Get track data for specified track and chromosome in a track hub -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8
- Wiggle track data for specified track, chromosome with start and end limits in an assembly hub genome -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp;start=4321;end=5678
- Wiggle track data for specified track in a UCSC database genome -
api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100
- bigBed data from a UCSC database, chrom and start,end limits -
api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000
Error return examples
- Request track data for non-existent chromosome in an assembly hub genome -
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrI;start=43521;end=54321