<div dir="ltr">Thanks Jose, that sounds perfect! I'd be happy to beta test at some point. Here's a link to the catalog where we document the species we are currently supporting (
<a href="https://stdpopsim.readthedocs.io/en/latest/catalog.html">https://stdpopsim.readthedocs.io/en/latest/catalog.html</a> ). We will also be adding the Bos Taurus genome sometime in the near future. This really sounds fantastic and I appreciate you taking the time to help me here.<div><br></div><div>Noah</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jul 20, 2020 at 7:21 AM jose miguel mut <<a href="mailto:jmmut@ebi.ac.uk">jmmut@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
Hi Noah,<br>
<br>
<p>Let me pop in the conversation. I work at EBI-EVA
(<a href="https://www.ebi.ac.uk/eva/" target="_blank">https://www.ebi.ac.uk/eva/</a>) and we are working on a REST
webservice called contig-alias that matches your use case. Given a
chromosome name or accession, you will get back its synonyms.<br>
</p>
<p>It's in early stages and we don't have anything usable yet, but
we plan to support GenBank and RefSeq chromosome accessions, as
well as chromosome names (like "chr1"), and possibly UCSC names
and GA4GH refget checksums. Some information about the assemblies
will be available too.</p>
<p>Let me know if you are willing to beta-test the system some time
during next months and provide any feedback you find. Also, you
can tell us which species/assemblies would you be interested in,
so that we can support them early and have some extra focus on
them.</p>
<p>Regards<br>
Jose<br>
</p>
<pre></pre>
<br>
<div>On 17/07/2020 , Noah Dukle wrote:</div>
<div><br>
<table cellspacing="0" cellpadding="0" border="0">
<tbody>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">Subject:
</th>
<td>[ensembl-dev] FEATURE REQUEST: Improving annotation of
chromosome synonyms</td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">Date: </th>
<td>Fri, 17 Jul 2020 13:41:44 -0400</td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">From: </th>
<td>Noah Dukler <a href="mailto:ndukler@gmail.com" target="_blank"><ndukler@gmail.com></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">Reply-To:
</th>
<td>Ensembl developers list <a href="mailto:dev@ensembl.org" target="_blank"><dev@ensembl.org></a></td>
</tr>
<tr>
<th valign="BASELINE" nowrap align="RIGHT">To: </th>
<td><a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a></td>
</tr>
</tbody>
</table>
<br>
<br>
<div dir="ltr">
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Would
it be possible for you to make alternative chromosome
nomenclatures available under the `xrefs` endpoint? Such a
feature would be immensely useful to a group I work with
(stdpopsim) that is working to standardize population genetic
simulations and improve the ease of realistic simulations. As
of now there are relatively few resources for converting
between different nomeclatures (eg. UCSC <--> Ensembl
<--> NCBI <--> others). We are working on
automating species specific annotations using the Ensembl REST
API but one of our issues is that most chromosome synonyms are
not available. The best resource I have found for converting
IDs in in the R Bioconductor package GenomeInfoDb (<a href="https://github.com/terminiter/GenomeInfoDb/tree/release-3.3/inst/extdata/dataFiles" style="color:rgb(5,99,193)" target="_blank">https://github.com/terminiter/GenomeInfoDb/tree/release-3.3/inst/extdata/dataFiles</a>).
Thank you for your time.</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"> </p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Noah
Dukler</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Post-Doc</p>
<p class="MsoNormal" style="margin:0in 0in 0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">Siepel
Lab</p>
</div>
</div>
<blockquote type="cite"> </blockquote>
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