Terms are not completely removed by --make-species-subset

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
java
Domain
bioinformatics, tooling

Research direction

Start by running the reported owltools go-plus.obo command with --make-species-subset for NCBITaxon:4896 and inspect the generated OBO stanza for GO:0000795. Trace how never_in_taxon relationships are handled during subset generation; done means terms excluded by that relationship do not remain as identifier-only stanzas.

Written by the indexing model from the issue text.

Description

I'd like to get an OBO file of GO terms that make sense for pombe. I've
tried:

owltools go-plus.obo --reasoner elk --make-species-subset -t NCBITaxon:4896 -o -f obo go-pombe-subset.obo

That nearly does what I need but the output OBO file has some stanzas
that I didn't expect.

As an example, in go-plus.obo, GO:0000795 ("synaptonemal complex") has
this relationship:

relationship: never_in_taxon NCBITaxon:4896 {id="GOTAX:0010058"} ! Schizosaccharomyces pombe

so I was expecting that GO:0000795 wouldn't appear in the output.
Instead it was there but with just "id:" and "alt_id:" lines:

[Term]
id: GO:0000795
alt_id: GO:0005716

CC @ValWood @mah11

Dominant language
Java
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Forks
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