Does taxslim contain a class entry for every NCBITaxon purl?

[ddooley]

It isn't quite clear to me the taxonslim subset has every NCBITaxon taxon class term id in it, or whether the following exclude lots of NCBITaxon taxon class term ids? According to README.md it includes:

• Anything used in a taxon constraint in an ontology
• All UniProt Reference Proteomes
• Any taxon that has a non-IEA annotation in GO

I'm looking for a small but complete taxon slim file to use via ODK to import about 4,000 taxa. Wanting a say 7 or 10mb file to give ODK as import source; not wanting a 500mb or 1.5 gig file.

[matentzn]

Hey @ddooley many ontologies use the NCBITaxon taxslim now and everyone is welcome to add terms. We keep adding new ones.

The documentation you cite is a bit old. The list of included taxon ids is specified in here: https://github.com/obophenotype/ncbitaxon/blob/master/subsets/taxon-subset-ids.txt

If you need classes added, you just make a PR and we will add them in the next release!

[ddooley]

I see the question of whether it contains all NCBITaxon ids is answered by the need to add some manually. Thx. I'll see if it contains the 4,000+ we need.

[ddooley]

So we'd have to add over 3,600 new terms to make use of this slim for ODK purposes. Is that ok?

[matentzn]

Yes, its ok!