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obophenotype / ncbitaxon

Build for NCBITaxon
BSD 3-Clause "New" or "Revised" License
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Missing several rank annotations #89

Closed cthoyt closed 8 months ago

cthoyt commented 9 months ago

I tried running the converter locally and got many logging messages for ranks that are not handled:

rank count
strain 45990
isolate 1333
serotype 1237
clade 956
forma specialis 750
serogroup 151
genotype 22
biotype 17
morph 12
pathogroup 5

I think these can be addressed by appending these strings to https://github.com/obophenotype/ncbitaxon/blob/aae8b65a7b98a7bdf231f255d744ee4aa508e44a/src/ncbitaxon.py#L45-L79. Is there any reason this hasn't been done already?

jamesaoverton commented 9 months ago

I think it's fine to update this list.

IIRC, I just kept the list of ranks from the previous version of the codebase, which kept the list from the previous version, and so on.