Erica Wood

Here's this from `KG2.8.3c` (`kg2canonicalized.rtx.ai`):  The edges in question are: ``` CHEBI:28915---rdfs:subClassOf---None---None---None---CHEBI:32955---OBO:chebi.owl CHEBI:28915---rdfs:subClassOf---None---None---None---CHEBI:32955---OBO:go/extensions/go-plus.owl CHEBI:28915---rdfs:subClassOf---None---None---None---CHEBI:32955---OBO:genepio.owl ```

In `KG2.8.0c` (`kg2canonicalized2.rtx.ai`), this was an issue:  ``` { "predicate": "biolink:subclass_of", "primary_knowledge_source": "infores:chebi; infores:genepio; infores:go-plus", "publications_info": "{}", "kg2_ids": [ "CHEBI:28915---rdfs:subClassOf---None---None---None---CHEBI:32955---OBO:chebi.owl" ], "subject": "PUBCHEM.COMPOUND:446987", "id": "9271251", "object": "MESH:D004852" } ```...

I'm marking this for verification, so that we can remember to check this query when `KG2.8.3` is rolled out shortly.

Further, they have the same name. UniProt:  ChEMBL: 

This error occurred during the build: ``` [Thu Jul 20 19:34:20 2023] Error in rule SemMedDB: jobid: 30 output: /home/ubuntu/kg2-build/semmeddb/kg2-semmeddb-tuplelist.json, /home/ubuntu/kg2-build/semmed-exclude-list.yaml log: /home/ubuntu/kg2-build/extract-semmeddb.log (check log file(s) for error message) shell:...

There was an error with SMPDB, which doesn't make sense since it was recently tested and worked the first time around: ``` [Thu Jul 20 21:02:58 2023] Error in rule...

An error occurred in Ontologies and TTL, due to #303: ``` Traceback (most recent call last): File "/home/ubuntu/kg2-code/multi_ont_to_json_kg.py", line 1391, in save_pickle) File "/home/ubuntu/kg2-code/multi_ont_to_json_kg.py", line 142, in make_kg2 assert os.path.exists(ont_source_info_dict['file']),...

Here were the major report changes: ``` There was a significant drop in edges from infores:fma-umls in this build. The count dropped from 368827 to 290475 There was a significant...

Some of the UMLS nodes do not have English names. I ran a query on those: ``` ["UMLS:C0005475", "UMLS:C0005521", "UMLS:C0012245", "UMLS:C0013320", "UMLS:C0013458", "UMLS:C0023099", "UMLS:C0026862", "UMLS:C0036894", "UMLS:C0085309", "UMLS:C0085310", "UMLS:C0085312", "UMLS:C0085352", "UMLS:C0085357",...

Sometimes, the current model conflates nodes that shouldn't be conflated. While they aren't necessarily assigned `biolink:close_match`, they do absorb each other's definition. Ex. ``` a owl:Class ; skos:prefLabel """Phospholipid Ethers"""@en...