acecde132ebb9310c523d1a204bfbd72836f5c94
brianlee
Thu Sep 19 13:34:44 2019 -0700
Adding a note about the API on a retired page that describes how to find schema information.
diff --git src/hg/htdocs/goldenPath/gbdDescriptions.html src/hg/htdocs/goldenPath/gbdDescriptions.html
index eb558fc..398e213 100755
--- src/hg/htdocs/goldenPath/gbdDescriptions.html
+++ src/hg/htdocs/goldenPath/gbdDescriptions.html
@@ -1,81 +1,93 @@
<!DOCTYPE html>
<!-- Page header -->
<!--#set var="TITLE" value="UCSC Genome Browser: Document Styles" -->
<!--#set var="ROOT" value="../" -->
<!-- Relative paths to support mirror sites with non-standard GB docs install -->
<!--#include virtual="$ROOT/inc/gbPageStart.html" -->
<!-- Page content -->
<h1>This page is no longer maintained.</h1>
<p>
<span class="gbsWarnText">This page was retired long ago when the table descriptions
for the annotation database stopped being updated.</span> To retrieve the schemas
for tables underlying the Genome Browser annotation tracks one can use the Table Browser
-using the "describe table schema" button.</p>
+using the "describe table schema" button or the JSON API.</p>
<h2>refFlat example</h2>
<p>
<ol>
<p>
Gene Predictions and RefSeq Genes with Gene Names</p>
<p>
A version of genePred that associates the gene name with the gene prediction information.
In alternative splicing situations each transcript has a row in this table.</p>
<pre>
table refFlat
"A gene prediction with additional geneName field."
(
string geneName; "Name of gene as it appears in Genome Browser."
string name; "Name of gene"
string chrom; "Chromosome name"
char[1] strand; "+ or - for strand"
uint txStart; "Transcription start position"
uint txEnd; "Transcription end position"
uint cdsStart; "Coding region start"
uint cdsEnd; "Coding region end"
uint exonCount; "Number of exons"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
)</pre>
</ol>
<p>
The text for this entry is deprecated. Please use the below
Table Browser method to access this information.</p>
-<h2>Current method to use Table Browser with refFlat example</h2>
+<h2>Current method to use Table Browser or API with refFlat example</h2>
<p>
-<span class="gbsWarnText">Here is the current way to retrieve table descriptions.</span></p>
+<h3>Table Browser</h3>
+<span class="gbsWarnText">Here is the current way to retrieve table descriptions with the Table Browser.</span></p>
<ol>
<li>
Navigate to the Table Browser for the specific assembly you are interested in that has the
data you are seeking. For example, if you are working with the hg19 assembly,
you would make that selection:
<a href="/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19</a>
</li>
<li>
Select the table from the appropriate group. Or set the group to "All Tables"
and find the table you are interested in finding the description of, in this case the
refFlat table:
<a href="/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=allTables&hgta_track=hg19&hgta_table=refFlat"
target="_blank">http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=allTables&hgta_track=hg19&hgta_table=refFlat</a>
</li>
<li>
Click the "describe table schema" button and find the table description along
with example data displayed and the related Track Description if available.
</li>
</ol>
<p>
For more information on using the Table Browser, see the <a href="help/hgTablesHelp.html"
target="_blank">Table Browser User's Guide</a>.</p>
+
+<h3>API</h3>
+<span class="gbsWarnText">Here is the current way to retrieve table descriptions with the API.</span></p>
+<p>
+You can also access table schema information in JSON notation using our
+<a href="help/api.html#Practical_examples" target="_blank">API</a>
+with a query such as the following:</p>
+<p>
+<a href="http://api.genome.ucsc.edu/list/schema?genome=hg38;track=refFlat">http://api.genome.ucsc.edu/list/schema?genome=hg38;track=refFlat</a></p>
+<p>
+Please note the response will be in JSON notation and may need parsing to interpret.</p>
<p>
There are also links to our source code in <a href="http://genome-source.soe.ucsc.edu/gitlist/kent.git/tree/master/src/hg/lib"
target="_blank">src/hg/lib</a> to discover the autoSql files (.as) that define our tables.
Here is an example link to the refFlat.as file: <a href=" http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/refFlat.as"
target="_blank">http://genome-source.soe.ucsc.edu/gitlist/kent.git/raw/master/src/hg/lib/refFlat.as</a></p>
<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->