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 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -1,212 +1,209 @@ <!DOCTYPE html> <!--#set var="TITLE" value="JSON API data interface" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>JSON API data interface</h1> <h2>Contents</h2> <h6><a href="#Intro">What is JSON data ?</a></h6> <h6><a href="#Access">What is the access URL ?</a></h6> <h6><a href="#Return">What type of data can be accessed ?</a></h6> <h6><a href="#Endpoint">Endpoint functions</a></h6> <h6><a href="#Parameters">Parameters to endpoint functions</a></h6> <h6><a href="#Parameter use">Required and optional parameters</a></h6> <h6><a href="#Track types">Supported track types</a></h6> <h6><a href="#list examples">Example data access, list functions</a></h6> <h6><a href="#getData examples">Example data access, getData functions</a></h6> <h6><a href="#Error examples">Error return examples</a></h6> -<hr> -<p> -<strong>Additional resources</strong></p> -<ul> -</ul> <!-- ========== What is JSON data ? ============================== --> <a name="Intro"></a> <h2>What is JSON data ?</h2> <p> JSON data is a data transfer syntax from a data provider to a data consumer. See also: <a href="https://www.w3schools.com/js/js_json_intro.asp" target=_blank>JSON Introduction</a> </p> <!-- ========== What is the access URL ? ============================== --> <a name="Access"></a> <h2>What is the access URL ?</h2> <p> The gateway html page to the interface is available at <a href="https://api-test.gi.ucsc.edu/" target=_blank>api-test.gi.ucsc.edu</a>. 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. </p> <p> This access url: <b>https://api-test.gi.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs' </pre> <!-- ========== What type of data can be accessed ? ===================== --> <a name="Return"></a> <h2>What type of data can be accessed ?</h2> <p> The following data sets can be accessed at this time: <ul> <li>Listing of available public hubs</li> <li>Listing of available UCSC browser genome assemblies</li> <li>List genomes from a specified assembly or track hub</li> -<li>List available data tracks from a specified hub or UCSC browser genome assembly</li> +<li>List available data tracks from a specified hub or UCSC browser genome assembly (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li> <li>List of chromosomes contained in an assembly hub or UCSC browser genome assembly. <li>List of chromosomes contained in a specific track of an assembly or track hub or UCSC browser genome assembly. <li>Return DNA sequence from an assembly hub 2bit file, or UCSC genome browser assembly</li> <li>Return track data from a specified assembly or track hub or UCSC genome browser assembly</li> </ul> </p> <!-- ========== Endpoint functions ======================= --> <a name="Endpoint"></a> <h2>Endpoint functions to return data</h2> <p> Use the url: <b>https://api-test.gi.ucsc.edu/</b> is access the endpoint functions. For example: <pre> wget -O- 'https://api-test.gi.ucsc.edu/list/publicHubs' </pre> </p> <p> <ul> <li><b>/list/publicHubs</b> - list public hubs</li> <li><b>/list/ucscGenomes</b> - list UCSC database genomes</li> <li><b>/list/hubGenomes</b> - list genomes from specified hub</li> -<li><b>/list/tracks</b> - list data tracks available in specified hub or database genome</li> +<li><b>/list/tracks</b> - list data tracks available in specified hub or database genome (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li> <li><b>/list/chromosomes</b> - list chromosomes from a data track in specified hub or database genome</li> <li><b>/getData/sequence</b> - return sequence from specified hub or database genome</li> <li><b>/getData/track</b> - return data from specified track in hub or database genome</li> </ul> </p> <!-- ========== Parameters to endpoint functions ======================= --> <a name="Parameters"></a> <h2>Parameters to endpoint functions</h2> <p> <ul> <li>hubUrl=<url> - specify track hub or assembly hub URL</li> <li>genome=<name> - specify genome assemby in track or assembly hub (only used with hubUrl)</li> <li>db=<ucscDb> - specify database (aka genome assembly) in UCSC genome browser (either hubUrl or db specified, not both)</li> <li>track=<trackName> - specify data track in hub or UCSC database genome assembly</li> <li>chrom=<chrN> - specify chromosome name for sequence or track data</li> <li>start=<123> - specify start coordinate (0 relative) for data from track or sequence retrieval (start and end required together)</li> <li>end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together)</li> <li>(see also: <a href='http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems)</a></li> <li>maxItemsOutput=1000 - limit number of items to output, default: 1,000, maximum limit: 1,000,000</li> </ul> </p> <p> The parameters are added to the endpoint URL beginning with a question mark <b>?</b>, and multiple parameters are separated with the semi-colon <b>;</b>. For example: <pre> https://api-test.gi.ucsc.edu/getData/sequence?db=ce11;chrom=chrM </pre> </p> <!-- ========== Required and optional parameters ======================= --> <a name="Parameter use"></a> <h2>Required and optional parameters</h2> <p> <table border=1> <tr><th>Endpoint function</th><th>Required</th><th>Optional</th></tr> <tr><th>/list/publicHubs</th><td>(none)</td><td>(none)</td></tr> <tr><th>/list/ucscGenomes</th><td>(none)</td><td>(none)</td></tr> <tr><th>/list/hubGenomes</th><td>hubUrl</td><td>(none)</td></tr> <tr><th>/list/tracks</th><td>(hubUrl and genome) or db</td><td>(none)</td></tr> <tr><th>/list/chromosomes</th><td>((hubUrl and genome) or db) and track</td><td>(none)</td></tr> <tr><th>/getData/sequence</th><td>((hubUrl and genome) or db) and chrom</td><td>start and end</td></tr> <tr><th>/getData/track</th><td>((hubUrl and genome) or db) and track</td><td>chrom, (start and end), maxItemsOutput</td></tr> </table> </p> <p> The <b>hubUrl</b> and <b>genome</b> parameters are required together to specify a unique genome in an assembly or track hub. The <b>genome</b> for a track hub will usually be a UCSC database genome. Assembly hubs will have their own unique <b>genome</b> sequences. </p> <p> When not an assembly or track hub, to access UCSC database assemblies, the parameter <b>db=<name></b> is required. </p> <p> Using the <b>chrom=<name></b> parameter will limit the request to the single specified chromosome. To limit the request to a specific position, both <b>start=4321</b> and <b>end=5678</b> must be given together. </p> <!-- ========== Supported track types ======================= --> <a name="Track types"></a> <h2>Supported track types, at this time (April 2019), for getData functions</h2> <p> <ul> <li><a href='/FAQ/FAQformat.html#format1' target=_blank>bed</a></li> <li><a href='/FAQ/FAQformat.html#format1.5' target=_blank>bigBed</a></li> +<!-- not yet <li><a href='/FAQ/FAQformat.html#format9.1' target=_blank>bigGenePred</a></li> +--> <li><a href='/FAQ/FAQformat.html#format9.5' target=_blank>bigNarrowPeak</a></li> <li><a href='/FAQ/FAQformat.html#format6.1' target=_blank>bigWig</a></li> -<li>broadPeak</li> +<li><a href='/FAQ/FAQformat.html#format9' target=_blank>genePred</a></li> <li><a href='/FAQ/FAQformat.html#format9.5' target=_blank>narrowPeak</a></li> <li><a href='/FAQ/FAQformat.html#format6' target=_blank>wig</a></li> <li>(Work is under way to support additional track types)</li> </ul> </p> <!-- ========== Example data access ======================= --> <a name="list examples"></a> <h2>Example data access</h2> <h3>Listing functions</h3> <ol> <li><a href='/list/publicHubs' target=_blank>list public hubs</a> - <b>api.genome.ucsc.edu/list/publicHubs</b></li> <li><a href='/list/ucscGenomes' target=_blank>list UCSC database genomes</a> - <b>api.genome.ucsc.edu/list/ucscGenomes</b></li> <li><a href='/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt' target=_blank>list genomes from specified hub</a> - <b>api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt</b></li> <li><a href='/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list tracks from specified hub and genome</a> - <b>api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li> <li><a href='/list/tracks?db=ce11' target=_blank>list tracks from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/tracks?db=ce11</b></li> <li><a href='/list/chromosomes?db=ce11' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11</b></li> <li><a href='/list/chromosomes?db=ce11;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11;track=gold</b></li> <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list chromosomes from assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li> <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>list chromosomes from specified track in assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li> </ol> <a name="getData examples"></a> <h3>getData functions</h3> <ol> <li><a href='/getData/sequence?db=ce11;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM</b></li> <li><a href='/getData/sequence?db=ce11;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM;start=4321;end=5678</b></li> <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from a track hub where 'genome' is a UCSC database</a> -<br><b>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</b></li> <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678' target=_blank><b></b> Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome</a> -<br><b>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</b></li> <li><a href='/getData/track?db=ce11;track=gold;maxItemsOutput=100' target=_blank>Get track data for specified track in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;maxItemsOutput=100</b></li> <li><a href='/getData/track?db=ce11;track=gold;chrom=chrM' target=_blank>Get track data for specified track and chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrM</b></li> <li><a href='/getData/track?db=ce11;track=gold;chrom=chrI;start=47000;end=48000' target=_blank>Get track data for specified track, chromosome and start,end coordinates in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?db=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>Get track data for specified track in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp' target=_blank>Get track data for specified track and chromosome in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved' target=_blank>Get track data for specified track in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8' target=_blank>Get track data for specified track and chromosome in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrCp;start=4321;end=5678' target=_blank>Wiggle track data for specified track, chromosome with start and end limits in an assembly hub genome</a> -<br><b>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</b></li> <li><a href='/getData/track?db=galGal6;track=gc5BaseBw;maxItemsOutput=100' target=_blank>Wiggle track data for specified track in a UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100</b></li> <li><a href='/getData/track?db=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000' target=_blank>bigBed data from a UCSC database, chrom and start,end limits</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000</b></li> </ol> <p> </p> <a name="Error examples"></a> <h3>Error return examples</h3> <p> <ol> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrI;start=4321;end=5678' target=_blank>Request track data for non-existent chromosome in an assembly hub genome</a> -<br><b>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</b></li> </ol> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->