acevedol

Validation completed, starting partial build

Error in rule DGIdb: jobid: 36 output: /home/ubuntu/kg2-build/dgidb/interactions.tsv log: /home/ubuntu/kg2-build/extract-dgidb.log (check log file(s) for error m essage) shell: bash -x /home/ubuntu/kg2-code/extract-dgidb.sh /home/ubuntu/kg2-build/dg idb > /home/ubuntu/kg2-build/extract-dgidb.log 2>&1 [Fri Apr 12 19:59:49...

Error in rule ChEMBL_Conversion: jobid: 11 output: /home/ubuntu/kg2-build/kg2-chembl-nodes.jsonl, /home/ubuntu/kg2-build/kg2-chembl-edges.jsonl log: /home/ubuntu/kg2-build/chembl_mysql_to_kg_jsonl.log (check log file(s) for error message) shell: /home/ubuntu/kg2-venv/bin/python3 -u /home/ubuntu/kg2-code/chembl_mysql_to_kg_jsonl.py /home/ubuntu/kg2-build/mysql-config.conf chembl /home/ubuntu/kg2-build/kg2-chembl-nodes.jsonl /home/ubuntu/kg2-build/kg2-chembl-edges.jsonl > /home/ubuntu/kg2-build/chembl_mysql_to_kg_jsonl.log 2>&1

Build completed, now I am uploading to Neo4J, testing, and reviewing the reports.

loaded into neo4j on kg2endpoint4.rtx.ai

Switched SEMMEDDB:TREATS to biolink:treats_or_applied_or_studied to treat and rebuilding from Simplify

On KG2.8.6pre I don't see this edge. I ran the query `match (n {id:"MONDO:0008491"})-[r]->(m {id:"MONDO:0005015"}) return *` and returned no results, as shown below.  No results were...

I checked the edges with subject `UMLS:C0267167` between KG2.8.6 and KG2.8.4 and found that most of the edges match, except for 2.8.4's `UMLS:C0267167---SEMMEDDB:augments---biolink:causes---activity_or_abundance---None---UMLS:C0013299---SEMMEDDB:` does not match 2.8.6's 'UMLS:C0013299---SEMMEDDB:coexists_with---None---None---None---UMLS:C0267167---SEMMEDDB:' and 'UMLS:C0013299---SEMMEDDB:causes---None---None---None---UMLS:C0267167---SEMMEDDB:'

@saramsey Do you mind reviewing my reasoning here? In `umls_mysql_to_list_jsonl.py`, the relations seems to be extracted using ` relations_sql_statement = "SELECT DISTINCT CUI1, REL, RELA, DIR, CUI2, SAB FROM MRREL...

On test build of KG2.9.0, I did not find the problematic edge `"UMLS:C0013395---NCIT:disease_may_have_finding---None---None---None---UMLS:C0278701---umls_source:NCI"`  The reversed edge is present ``` {"domain_range_exclusion": false, "id": "UMLS:C0278701---NCIT:disease_may_have_finding---None---None---None---UMLS:C0013395---umls_source:NCI", "negated":...