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

Noah Dukler ndukler at gmail.com
Fri Jul 17 18:41:44 BST 2020

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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