dustine32

Awesome thanks @cmungall ! This is exactly what I'm looking for. I'll give it a shot. Last Friday I wrote something that seemed to do the trick using ontobio, but...

@cmungall Yeah we discussed this a bit in issue #179 and I really liked your [comment](https://github.com/biolink/ontobio/issues/179#issuecomment-393733239) explaining the justification for the ontobio object-subject reversal. Perhaps we can add this same...

@kltm Oh yeah, I forgot to update the [datasets.schema.yaml](https://github.com/geneontology/go-site/blob/master/metadata/datasets.schema.yaml), thanks! I'll make a ticket and PR in `go-site` for this. Existing `filter_out` defines annotation values that would trigger a line...

Linking schema PR: https://github.com/geneontology/go-site/pull/1554

Thinking about changing `filter_for` to `only_allow` as @dougli1sqrd suggested. Still brainstorming though.

I hooked in the obonet parser for handling .obo files. However, the result totals seem to differ from how ontobio was previously parsing the owltools JSON output. **Using go_1.0.obo file**:...

@cmungall thanks for the pointer! Would examples of testing for semantic sense be calling .search(), .traverse_nodes(), and .label() on the resulting ontology as in test_wd_ontol.py?

OK, lifting test_graph for nucleus.obo causes it to fail on the first assert checking for correct ID. Looks like the label checks will also fail since none of the labels...

@dhimmel That would be awesome, thanks! Looking at the obonet code, it seems to be saving the term's properties in the node attributes, but I'm having trouble getting the attributes...

OK @dhimmel , I'm able to get the labels/names out of the obonet-supplied nodes now. Simply an issue with my networkx knowledge. So I don't think you'll need to do...