Support species synonyms

[lutteropp]

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]

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]

Maybe this can be solved in concurrence with #6 (comment) (taxonkit).

[Roleren]

Did this ever go anywhere?

I think it is a good idea, and very easy to implement something basic that will work for the users.

[HajkD]

Hi @Roleren ,

Nope, was never implemented. So please feel free to send an PR if you have some time :)

Happy to merge right away.

With many thanks and very best wishes,
Hajk