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ropensci / biomartr

Genomic Data Retrieval with R
https://docs.ropensci.org/biomartr
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Support species synonyms #21

Open lutteropp opened 6 years ago

lutteropp commented 6 years ago

Hi,

currently, species genomes are not found by the biomartr package if I search for a species synonym. For example: is.genome.available("Kluyveromyces thermotolerans", db="refseq") returns FALSE, but is.genome.available("Lachancea thermotolerans", db="refseq") returns TRUE.

I have written a tiny R script for retrieving the list of synonyms for a species name using the "Catalogue of Life" web interface, maybe this is helpful: https://github.com/lutteropp/SpeciesSynonymFinder

There is also a more comprehensive solution out there: https://github.com/ropensci/taxize

Best, Sarah

HajkD commented 6 years ago

Hi Sarah,

This is a great idea!

Many thanks for sharing it with me! :-)

I will definitely put this one on my TODO list and will start working on this in the new year.

Kind regards, Hajk

johanneswerner commented 3 years ago

Maybe this can be solved in concurrence with https://github.com/ropensci/biomartr/issues/6#issuecomment-788771908 (taxonkit).