rpgoldman

Unfortunately, OWLAPI does not seem to use content negotiation. If content negotiation worked properly, I should be able to just use an unqualified IRI like `http://purl.obolibrary.org/obo/so` and OWLAPI and the...

> I think this may have more to do with the OBO PURL system, which just redirects based on patterns. Any content negotiation would be handled by the ultimate URL...

@matentzn Am I correct in thinking that any terms in the term list _will_ be included, despite the value of the `--individuals` option to `robot extract`? Is it also true...

> The purpose of the `--individuals` parameter is simply to allow people to ignore individuals before extracting the module.. So if you include an individual in the term list, then...

@matentzn -- I don't think I have a good mental model of how `extract` is working.... Here are two files, first with `--individuals minimal` and the second with no `--individuals`...

@matentzn That was very clear, thank you! Does this make sense as an approach? Let *S* be the set of IRIs, including individuals. 1. Classify all *s ∈ S* where...

@matentzn > 1. Use ROBOT remove to delete all individuals from the ontology except the ones you care about (`robot remove ... -T signature.txt --select complement --select individuals`) Doesn't the...

Shouldn't I do the materialize before the extraction, in order to avoid having inferred superclasses of an individual be stripped out before the individual is classified? Also, do I want...

`find-plans-stack` could use the same improvement. Checking the code, `sb-texinfo` claims to handle itemized lists if lines begin with a `*`. So that is worth a try. Feel free to...

Good catch! Thanks.