[ensembl-dev] FEATURE REQUEST: Improving annotation of chromosome synonyms

jose miguel mut jmmut at ebi.ac.uk
Mon Jul 20 12:20:18 BST 2020

Hi Noah,

Let me pop in the conversation. I work at EBI-EVA 
(https://www.ebi.ac.uk/eva/) 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.

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.

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.


On 17/07/2020 , Noah Dukle wrote:

Subject: 	[ensembl-dev] FEATURE REQUEST: Improving annotation of 
chromosome synonyms
Date: 	Fri, 17 Jul 2020 13:41:44 -0400
From: 	Noah Dukler <ndukler at gmail.com>
Reply-To: 	Ensembl developers list <dev at ensembl.org>
To: 	dev at ensembl.org

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 
Thank you for your time.

Noah Dukler


Siepel Lab

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