David Osumi-Sutherland

Results 451 comments of David Osumi-Sutherland

> We can use date string as versionInfo. But some common terms are redefined in multiple ontologies. For example, http://purl.obolibrary.org/obo/BFO_0000002 defined in both cl, pato and ubero It's actually just...

> Note that the old "base" file should still be exportable, but renamed to "editors release". should -> will I agree that the new file is useful & important, but...

We discussed this on a strategy call with @cmungall & @matentzn. Agreed that this is a high priority and that @cmungall's [suggested solution](https://github.com/ontodev/robot/issues/497#issuecomment-975873714) would work well (In fact, we've successfully...

> I trust @balhoff and his code. Two concerns: > > Specific: backwards compatibility of existing ROBOT options and commands. I'm not clear on what is being proposed in this...

Hi @jamesaoverton - did you get a chance to give this more thought? I'm happy to assign @hkir-dev to do this work if you're happy to give it the thumbs...

> Unless permission explicitly granted, on a per-term, per-branch, or per-ontology basis. This is critical. PCL defines subclasses of CL terms. Single species AOs subclass Uberon and CL... Big ask...

And why are we folding COB into this issue? Isn't point 1 above more aspiration than reality for many ontology branches? (e.g. see issues around anatomical entities)

@cmungall - your graph strategy looks reasonable to me. @balhoff good point on how aggressive trimming is with the current strategy. It would be good to see a side-by-side comparison....

Would be good to have more control over what browsers consume. e.g. there have been various confusing and hard to explain changes to display of CL on OLS over the...

Current implementation should be modified to take taxon into account (as specified in ontology metadata). It is currently incorrectly flagging ontologies as having overlapping scope where they apply to non-overlapping...