[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.
Regards
Jose
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
(https://github.com/terminiter/GenomeInfoDb/tree/release-3.3/inst/extdata/dataFiles).
Thank you for your time.
Noah Dukler
Post-Doc
Siepel Lab
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