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Add missing taxranks that appear in NCBI Taxonomy Database #5

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@cthoyt cthoyt commented Nov 27, 2024

Closes #4

This PR adds the ranks that appear in the NCBI Taxonomy Database to TAXRANK. Here's a table that shows the impact of each of these terms, where the count is how many distinct NCBI Taxa have this rank. I then ran make and make prepare_release after.

Note: I also did a bit of housekeeping in this PR too to add the license and contributor list.

NCBI Rank CURIE Count Example Example Name
strain NCBITaxon:strain 46478 NCBITaxon:355 Azotobacter chroococcum (strain mcd 1)
isolate NCBITaxon:isolate 1305 NCBITaxon:5838 Plasmodium falciparum FCR-3/Gambia
serotype NCBITaxon:serotype 1229 NCBITaxon:10510 Bovine adenovirus 3
clade NCBITaxon:clade 963 NCBITaxon:3193 Embryophyta
forma specialis NCBITaxon:forma_specialis 785 NCBITaxon:5508 Fusarium oxysporum f. sp. cucumerinum
serogroup NCBITaxon:serogroup 154 NCBITaxon:491 Neisseria meningitidis serogroup B
genotype NCBITaxon:genotype 22 NCBITaxon:33745 Hepatitis C virus genotype 4
biotype NCBITaxon:biotype 17 NCBITaxon:725 Haemophilus influenzae biotype aegyptius
morph NCBITaxon:morph 11 NCBITaxon:304407 Acontias orientalis morph lineacauda
cohort NCBITaxon:cohort 5 NCBITaxon:33341 Polyneoptera
pathogroup NCBITaxon:pathogroup 5 NCBITaxon:1982676 Xanthomonas axonopodis subcluster 9.1
subcohort NCBITaxon:subcohort 3 NCBITaxon:32519 Ostariophysi

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LGTM

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@hlapp hlapp left a comment

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Nice 👍

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hlapp commented Nov 28, 2024

@cthoyt any chance you can add the OWL conversion?

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cthoyt commented Nov 28, 2024

@hlapp I ran make and make_release as instructed in the README-editors file and committed the two updated files in 0527d24. Since this repository doesn't have contributing guidelines, I wasn't sure if this was something I should do or not

@hlapp hlapp self-requested a review November 28, 2024 16:13
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Awesome, thanks so much @cthoyt. I agree there should be a contributors template. I'll make that an issue so it can be tracked.

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hlapp commented Nov 28, 2024

@balhoff are you handling new release etc?

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Add a term for "strain"
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