Proliferation of `http://purl.oboInOwllibrary.org/oboInOwl` URLs

Question

Proliferation of `http://purl.oboInOwllibrary.org/oboInOwl` URLs

cthoyt opened this issue 2 years ago · 5 comments

there are tons of ontologies that have http://purl.oboInOwllibrary.org/oboInOwl URLs that appear to have originated from PATO. these should be bulk fixed to match the proper OBO PURL

You can see the impact across many ontologies this search https://github.com/search?q=oboInOwllibrary&type=code

Interestingly, I can't seem to find if/where this is getting introduced in PATO itself

Answer 1 · 2022-08-17T16:28:11.000Z

I don't see any URIs like that in PATO. Do you mean http://www.geneontology.org/formats/oboInOwl#? This is part of the OBO spec and comes from the OWLAPI OBO parser.

Answer 2 · 2022-08-17T16:29:26.000Z

Now I see your github search. That's really weird; it seems like someone's tool is introducing that.

Answer 3 · 2022-08-17T16:32:23.000Z

Somewhere somebody did a find and replace for obo with oboInOWL, so that http://purl.obolibrary.org/obo became http://purl.oboInOwllibrary.org/oboInOwl.

Answer 4 · 2022-08-17T16:41:03.000Z

Every project I looked at in your search results made use of OntoFox to extract imports. I wonder if it has or had a bug.

Answer 5 · 2022-08-17T20:45:45.000Z

That's an interesting thought, but I just searched the OntoFox codebase for mentions of oboInOwl with https://github.com/OntoZoo/ontofox/search?q=oboinowl and nothing looked fishy (other than it being in PHP)