Jim Balhoff
Jim Balhoff
I was trying to clean things up for this reason, but not sure what to do with the failing check: #1526
@nicolevasilevsky FYI (in case you do add the taxon restriction), use `only_in_taxon` rather than its parent `in_taxon`.
@paulmillar can you provide sample input that shows the issue?
Thanks @paulmillar, the example is helpful since I wanted to make sure you were dealing with an anonymous individual, and not blank nodes related to the RDF representation of class...
@ate47 thank you! Your suggestion worked perfectly.
This is better than the one in the Uberon PR: https://github.com/geneontology/go-ontology/pull/28186/files#diff-2df631a546eac0a6b1aed7315dae51f10781001eebf4d0a7815a0595414c1e73 The first version has a flaw that gets into infinite paths when terms have mutual cycles.
@dosumis you will need to use whelk to get the Self inferences. It is in ROBOT, and here is a Protege plugin: https://github.com/INCATools/whelk/releases/tag/v1.1.1 The plugin is not quite up-to-date; I...
> @balhoff - any reason we shouldn't switch the CL pipeline to use Whelk`? It should be fine. Whelk is just a little slower for pipeline use.
I see that these kinds of problems are in many (maybe all) of the models created from yeast pathways. This one is here: https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=PWY3O-4107 and the problem IRI stems from...
@dosumis I refreshed Ubergraph; want to check MBA?