122b566fdaf3a4bcb26835deaa0b537f1c7cc39a chmalee Thu Jan 30 08:22:01 2020 -0800 Committing a stub of a track hub metadata help page I wrote a long time ago, refs #21641 diff --git src/hg/htdocs/goldenPath/help/metadata.html src/hg/htdocs/goldenPath/help/metadata.html new file mode 100755 index 0000000..30c664f --- /dev/null +++ src/hg/htdocs/goldenPath/help/metadata.html @@ -0,0 +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="#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> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->