06d7be056190c14b85e71bc12523f18ea6815b5e markd Mon Dec 7 00:50:29 2020 -0800 BLAT mmap index support merge with master diff --git src/hg/htdocs/goldenPath/help/metadata.html src/hg/htdocs/goldenPath/help/metadata.html index 30c664f..939e371 100755 --- src/hg/htdocs/goldenPath/help/metadata.html +++ src/hg/htdocs/goldenPath/help/metadata.html @@ -1,117 +1,117 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Adding Track Metadata" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Adding metadata to tracks</h1> <h2>Contents</h2> <h6><a href="#intro">Adding metadata to tracks</a></h6> -<h6><a href="#tagstom">Tagstorm metadata</a></h6> +<h6><a href="#tagstorm">Tagstorm metadata</a></h6> <h6><a href="#tabsep">Tab Sep metadata</a></h6> <h6><a href="#metadata">Previous metadata versions</a></h6> <a name="intro"></a> <h2>Adding metadata to tracks</h2> <p> Adding metadata to your tracks about cell lines, experimental protocols, or assays can be accomplished in a number of ways, via the newly supported <em>metadb</em> or <em>metatab</em> trackDb fields, or via the older style <em>metadata</em> trackDb field. The <em>metadb</em> and <em>metatab</em> fields link external tagStorm or tabSep metadata files to the data in the hub. The new formats are preferred over the older <em>metadata</em> field, although the <em>metadata</em> lines will continue to be supported for track hubs, but no new features will be added as they will for tagStorm and tabSep files.</p> <a name="metadata"></a> <h2>Previous metadata versions</h2> <p> Currently, in order to add metadata to your tracks, you must specify all of the metadata key-value pairs in each stanza of a track that includes metadata, like the last line of the following example:<br> <pre> track oneA-1 bigDataUrl http://genome-test.soe.ucsc.edu/~chmalee/tagStormHubs/test2/bbi/one-a1.bb parent oneA off type bigBed 3 shortLabel oneA-1 longLabel oneA-1 color 250,108,0 visilibility dense metadata differentiation=10hour treatment=X donor=A lab=UCSC data_set_id=ucscTest1 access=group assay=long-RNA-seq enriched_in=exon life_stage=postpartum species="Homo sapiens" ucsc_db=hg38 </pre> Each track must have a separate <em>metadata</em> field and its own list of key-values, which can become cumbersome when each track in a group all share a common subset of metadata. For instance, if there are 10 tracks in a composite or multiWig, where each subtrack only differs in the "differentiation" tag, it would be more convenient to have a shared set of metadata and then specify the differences for each track. This is the motivation behind the tagStorm format, described below. </p> <a name="tagstorm"></a> <h2>Tagstorm metadata</h2> <p> The tagStorm format is a plaintext file similar to the <em>trackDb.txt</em> file that describes all of the tracks in a <a href="hgTrackHubHelp.html">track hub</a>, in that both are files where the first word in a line is the tag and the rest of the line is the value, and different stanza's are line delimited. TagStorm's are also similar to a spreadsheet, where a tag corresponds to a column and a stanza to an entire row. Here is a canonical tagStorm example:<br> <pre> lab UCSC data_set_id ucscTest1 access group assay long-RNA-seq enriched_in exon life_stage postpartum species Homo sapiens ucsc_db hg38 treatment X donor A differentiation 10 hour meta ucsc1_1 differentiation 1 day meta ucsc1_4 differentiation 5 days meta ucsc1_7 treatment Y donor B differentiation 10 hour meta ucsc1_2 differentiation 1 day meta ucsc1_5 differentiation 5 days meta ucsc1_8 donor C differentiation 10 hour meta ucsc1_3 differentiation 1 day meta ucsc1_6 differentiation 5 days meta ucsc1_9 </pre> <p> Each stanza, such as "donor B", inherits from any stanzas above it at the right indentation level, and is a parent to stanzas beneath.</p> <a name="tabsep"></a> <h2>Tab sep metadata</h2> <p> </p> <a name="License"></a> <h2>Licensing information</h2> <p> GBiB is free for non-profit academic research and for personal use. Corporate use requires a license, setup fee and annual payment. To purchase a license or download the GBiB, visit the -<a href="//genome-store.ucsc.edu/" target="_blank">Genome Browser store</a>.</p> +<a href="http://genome-store.ucsc.edu/" target="_blank">Genome Browser store</a>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->