Create and maintain a curated species name-to-taxon table - Githubissues

dondi / GRNsight

Web app and service for modeling and visualizing gene regulatory networks.

http://dondi.github.io/GRNsight

BSD 3-Clause "New" or "Revised" License

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Create and maintain a curated species name-to-taxon table #721

Closed dondi closed 4 years ago

kdahlquist commented 5 years ago

@kdahlquist will curate the list of supported species and the corresponding taxon IDs that work with UniProt and JASPAR.

kdahlquist commented 4 years ago

As noted in the meeting, I will add species to this comment as I have time. Starting out with yeast:

Uniprot expects taxon ID 559292 for yeast, while JASPAR expects taxon ID 4932 for yeast.
The reason for the discrepancy is that 4932 refers to Saccharomyces cerevisiae, but 559292 is for Saccharomyces cerevisiae S288c.
Therefore, in our list, we need to have both IDs. They will be interchangeable for users, but the software needs to know which one to use for Uniprot or JASPAR. See issue #723 (which is currently closed).

kdahlquist commented 4 years ago

Homo sapiens, taxon ID 9606 (human)
Drosophila melanogaster, taxon ID 7227 (fruit fly)
Caenorhabditis elegans, taxon ID 6239 (nematode worm)
Mus musculus, taxon ID 10090 (house mouse)
Arabidopsis thaliana, taxon ID 3702 (thale cress)

kdahlquist commented 4 years ago

Rat seems to have the same issue that yeast does

Rattus rattus, taxon ID 10117 (black rat): used by JASPAR
Rattus norvegicus, taxon ID 10116 (rat): used by Uniprot

Let's hold off on Rat until I can do some more investigating. The other ones above seem OK, though

kdahlquist commented 4 years ago

I think this issue can be closed after we do some testing to make sure that gene information retrieval works for the other species besides yeast.

kdahlquist commented 4 years ago

I'm closing this one, test of input workbooks is in issue #720.