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<p>Hello Julie,</p>
<p>The REST API for Xrefs were conceived for mainly query EnsEMBL
using non-EnsEMBL identifiers/accession numbers: thus, I am not
sure they may be fit for your purpose.</p>
<p>Also, I am not sure I can understand your use case: a gene may
come with many Xrefs. Please, see for instance<br>
<a class="moz-txt-link-freetext" href="https://www.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000038219;r=4:13568738-13627725;t=ENST00000040738">https://www.ensembl.org/Homo_sapiens/Gene/Matches?db=core;g=ENSG00000038219;r=4:13568738-13627725;t=ENST00000040738</a></p>
<p>Assuming - because of your Perl snippet - you have EnsEMBL gene
stable IDs, you are happy with using REST API, and <u>you are
interested in the "gene description" only</u>, I might suggest
to look at the <b>/lookup </b>end point<br>
</p>
<p>For instance,
<a class="moz-txt-link-freetext" href="https://rest.ensembl.org/lookup/id/ENSG00000038219?content-type=application/json">https://rest.ensembl.org/lookup/id/ENSG00000038219?content-type=application/json</a><br>
</p>
<p>If REST does not work for you, you may want to download the
"gene" table dump to find the same information<br>
</p>
<p><a class="moz-txt-link-freetext" href="https://ftp.ensembl.org/pub/release-108/mysql/homo_sapiens_core_108_38/gene.txt.gz">https://ftp.ensembl.org/pub/release-108/mysql/homo_sapiens_core_108_38/gene.txt.gz</a></p>
<p>Hope it helps</p>
<p>Any further questions, please do not hesitate to reach out</p>
<p>Best wishes,</p>
<p>Stefano <br>
</p>
<div class="moz-cite-prefix">On 14/10/2022 13:22, Julie Sullivan
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20221014122458.E9DEE11803A_349551AB@hh-mx4.ebi.ac.uk">
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<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">Is there a flat file I can download that
contains gene xrefs and descriptions?<br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">I see the end point in the REST API for
xrefs but I don't see descriptions.</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><a href="https://rest.ensembl.org/"
moz-do-not-send="true" class="moz-txt-link-freetext">https://rest.ensembl.org/</a></div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">And I see the Perl API has these data so
I can do this:</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">$gene->stable_id."\t".$gene->description."\n";</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">But the environment I'm running these
scripts in doesn't allow for me to install the mysql client,
so I haven't be able to successfully run that except on my
laptop (where it times out).</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default"><br>
</div>
<div style="font-family:trebuchet ms,sans-serif;font-size:small"
class="gmail_default">Any suggestions? Thank you!! <br>
</div>
<div class="gmail_default" style="font-family:trebuchet
ms,sans-serif;font-size:small"><br>
</div>
</div>
<br>
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