Biolink 3.0 Compliance

[acevedol]

Biolink 3.0 will be released on 7/22. In order to get a head start in implementing compliance, I will reference the tag v2.4.2-alpha-qualifiers on the biolink repo.

• [x] Update predicate-remap.yaml
• [x] Update filter_kg_and_remap_predicates.py
• [x] Update run_simplify.sh
• [x] Update Rule Simplify in Post-ETL
• [x] Update validate_predicate_remap_yaml.py

[acevedol]

Keep in mind, Sierra mentioned that qualifiers are in their own file, qualifiers.yaml

[acevedol]

The Biolink team thoughtfully produced this document to assist in migrating existing predicates

[acevedol]

I am clearing out the buildkg2 instance for a full build because we also are updating sources.

[acevedol]

Running build on branch issue-221 on buildkg2.rtx.ai

[acevedol]

[Mon Aug 22 16:46:17 2022] Error in rule UMLS: jobid: 27 output: /home/ubuntu/kg2-build/umls_cuis.tsv log: /home/ubuntu/kg2-build/extract-umls.log (check log file(s) for error message) shell: bash -x /home/ubuntu/kg2-code/extract-umls.sh /home/ubuntu/kg2-build /home/ubuntu/kg2-build/umls_cuis.tsv > /home/ubuntu/kg2-build/extract-umls.log 2>&1 (exited with non-zero exit code)

[acevedol]

Error in rule KEGG:
    jobid: 47
    output: /home/ubuntu/kg2-build/kegg.json
    log: /home/ubuntu/kg2-build/extract-kegg.log (check log file(s) for error message)
    shell:
        bash -x /home/ubuntu/kg2-code/extract-kegg.sh /home/ubuntu/kg2-build/kegg.json > /home/ubuntu/kg2-build/extract-kegg.log 2>&1
        (exited with non-zero exit code)

[acevedol]

[Mon Aug 22 16:45:31 2022]
Error in rule DrugCentral:
    jobid: 44
    output: /home/ubuntu/kg2-build/drugcentral/drugcentral_psql_json.json
    log: /home/ubuntu/kg2-build/extract-drugcentral.log (check log file(s) for error message)
    shell:
        bash -x /home/ubuntu/kg2-code/extract-drugcentral.sh /home/ubuntu/kg2-build/drugcentral/drugcentral_psql_json.json /home/ubuntu/kg2-build/drugcentral > /home/ubuntu/kg2-build/extract-drugcentral.log 2>&1
        (exited with non-zero exit code)