Erica Wood

I suspect the problem is `populate_mysql_db_configured.sh` in the `umls` directory.

I am adding the `verify` tag for `biolink:OrganismalEntity`, not the other two.

This is not fixed as of `KG2.8.4pre`: ``` match (n) where n.category="biolink:OrganismalEntity" return n ``` 

Here are the sources with `biolink:BiologicalEntity` categories: n.provided_by | count(n) -- | -- "['infores:umls']" | 108175 "['infores:loinc-umls']" | 30585 "['infores:reactome']" | 26361 "['infores:foodon']" | 18835 "['infores:mesh']" | 4475 "['infores:chebi']" |...

Here are all the abstract classes in Biolink v3.5.0: (not all are categories) ``` aggregate statistic form or variant qualifier aspect qualifier derivative qualifier part qualifier context qualifier direction qualifier...

Apparently `biolink:BiologicalEntity` has been an abstract class for five years:  This was done as part of https://github.com/biolink/biolink-model/pull/552 (with commit https://github.com/biolink/biolink-model/commit/f40b4a72e6a41fbee9bb856d03f51a608b31b03a#diff-7d3492c4d387de52ea819557b6f2c23f2a79ab9e650f5422777548c3c4acb9a8R294). Given that `abstract entity` [was (around that time) defined](https://github.com/biolink/biolink-model/commit/694109af85f6a8e975b5ede503f06482fc5889c2#diff-7d3492c4d387de52ea819557b6f2c23f2a79ab9e650f5422777548c3c4acb9a8L4251-L4253)...

@saramsey How should we handle that some semantic types are mapped directly to these abstract classes? I feel like this is going to throw the validator in a tricky place.

The biggest problem that I see here is that some semantic types, which we rely on in KG2 pretty heavily, remain mapped to `biological entity`. So, if we change them...

I reached out to Sierra Moxon and we have had a lengthy discussion about how to handle this. @saramsey Do you have any thoughts on the "I will ask Steve"...

I'm concerned about the level of specificity we can reach without `biolink:BiologicalEntity`. Many of the nodes underneath do no fit neatly into a category below `bioink:BiologicalEntity`. However, since the only...