<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div>Hi Sarah,</div>
<div><br>
</div>
<div><br>
</div>
<div>Thank you very much for the quick reply and for fixing this issue!</div>
<div><br>
</div>
<div>Best,</div>
<div>Daniel</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Sarah Hunt <<a href="mailto:seh@ebi.ac.uk">seh@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, January 24, 2017 at 1:41 PM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>" <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] REST API - overlap endpoint with variant_set option<br>
</div>
<div><br>
</div>
<div>
<div bgcolor="#FFFFFF" text="#000000">
<p><br>
</p>
<p>Hi Daniel,</p>
<p>Thanks for reporting this one. There is a data problem in the GRCh37 database and GWAS catalog variants are not associated with the 'NHGRI-EBI GWAS catalog' or 'ph_variants' set. Until we can fix the data in our March release, this would have to be a two
step process, extracting all variants by region then looking up by id to filter the for those with phenotype information.<br>
</p>
Best wishes,<br>
<br>
Sarah<br>
<br>
<div class="moz-cite-prefix">On 24/01/2017 12:39, Daniel Suveges wrote:<br>
</div>
<blockquote cite="mid:D4ACFB86.3DB1A%25ds26@sanger.ac.uk" type="cite">
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Hi Guys,</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div><font face="Calibri,sans-serif">I'm planning to use the overlap endpoint of the REST API to get a list of variants which have phenotype annotations using the '</font><font face="Calibri,sans-serif">variant_set=</font><span style="font-family: Calibri, sans-serif;">ph_variants'
option. However it does not work as I expected. </span><span style="font-family: Calibri, sans-serif; font-size: 14px;">Let's take a GWAS hit rs1314913, a variant with phenotype annotation:</span></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q --header='Content-type:application/json' --header='Accept:application/json' --post-data='{ "ids" : ["rs1314913" ] }' '<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1">http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<div><br>
</div>
<div>The output looks alright, the variant has the expected phenotype annotation. But when querying the same region, the variant is not listed:</div>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q '<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants">http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
If the variant_set option is removed, the variant is there:</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i>wget -q '<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json">http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json</a>'
-O -</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<i><br>
</i></div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
This example works well on the newer genome build, so this issue is probably GRCh37 specific.</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Thanks for your help!</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Best,</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
Daniel</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<div style="color: rgb(0, 0, 0); font-family: Calibri, sans-serif;
font-size: 14px;">
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset> <br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a></pre>
</blockquote>
<br>
</div>
</div>
</span>
</body>
</html>