Jim Balhoff

I agree that a standard ordering would make sense. I'm not sure how quickly I can get to that—PRs are definitely welcome.

> @balhoff, should I open an issue against https://github.com/balhoff/owl-diff to track this request? @jclerman that sounds good. Looking at it, I think the lines are "mostly sorted". It looks like...

Hi! "Perplexity" refers to a data structure in the application which is a clump of mappings that it's an attempting to resolve exhaustively. So it likely means there is no...

@OliverHex I think what might be going on is that the ontology is incoherent (i.e., contains unsatisfiable classes) even without adding any of the mappings. I loaded it into Protege...

Hi @OliverHex I think the issue is with boomer's expectations of the prefixes file. This is not really explained in the readme. In our typical inputs, the ptable TSV uses...

@OliverHex I think the issue is the probabilities you're using for those lines. `0 0 1 0` makes the equivalence a certainty rather than probabilistic. You could try something like...

Hi @OliverHex, sorry for the delay. I suggest trying without any `0` entries in your table (e.g. `0.1 0.1 0.75 0.05`. You may need to allow that there could be...

Hi @OliverHex, sorry — I was busy last week then was out sick. Doing a really large mapping like this will take some experimentation. I suspect you may have to...

Discussion with @matentzn: implement output of cliques in order of increasing confidence (joint posterior prop most likely of clique / prop next most).

We can leave it open for now. I'm in the middle of a big overhaul of boomer, which may or may not pan out. It would impact how the output...