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

Noah Dukler ndukler at gmail.com
Mon Jul 20 17:35:06 BST 2020

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 ( https://stdpopsim.readthedocs.io/en/latest/catalog.html ). 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


On Mon, Jul 20, 2020 at 7:21 AM jose miguel mut <jmmut at ebi.ac.uk> wrote:

> 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> <ndukler at gmail.com>
> Reply-To: Ensembl developers list <dev at ensembl.org> <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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