multiomics clinical_trials 2.3.0

[gglusman]

API URL: https://biothings.ncats.io/multiomics_clinicaltrials_kp
Github URL: https://github.com/multiomicsKP/clinical_trials_kp
Git branch/commit: multiomicsKP/clinical_trials_kp@6b673a4
...please note change in location of tsv files, not on google bucket this time
No. Documents (from file_parser.py): 207,683
No. Documents (from annotator_parser.py): 7,378

Changelog:

• Changed: updated code to match new clinicaltrials.gov format as of 20240624
• Changed: modified EPC display accordingly
• Changed: content update to 20240811
• Changed: removed filters on study_type, primary_purpose, intervention_model, overall_status
• Added: rule for special treatment of trials without explicitly stated experimental arms and with just one intervention, recovering 10,000+ trials
• Added: extra 'treats' assertion edges for in_clinical_trials_for edges with phase 4 trials
• Added: using Disease Ontology to map additional conditions
• Added: using NCIT to map additional conditions
• Added: using ORDO (Orphanet) to map additional conditions
• Changed: significant improvements to algorithms for mapping of conditions, relying first on BABEL (Node Normalizer) files, then on rules to supplement
• Added: explanation of supporting evidence for treats edges in per-edge UI
• Fixed: phase and max_research_phase to use allowed values as per https://biolink.github.io/biolink-model/MaxResearchPhaseEnum/
• Fixed: resource roles for clinical_trials_kp, aact, and clinicaltrials
• Added: clinical_approval_status = approved_for_condition, for 'treats' edges
• Removed: 'elevate_to_prediction' attribute
• Fixed: token parsing that led to some false mappings
• Added: annotation of age_range, primary_purpose, intervention_model, and time_perspective for each trial
• Fixed: errors in parser for deployment via Service Provider
• Added: new parser for serving CTKP info via Annotator
• Changed: CTinfo endpoint now provides trial phase information as source_phase (exactly as represented in clinicaltrials.gov), numeric_phase (numbers suitable for comparison/sorting), and phase (using the biolink enumeration)
• Changed: CTKP now includes separate edges for conditions mapping to multiple CURIEs that can’t (yet?) be normalized to one CURIE
• Added: annotation of boxed warnings for subject nodes (active ingredients)

[ctrl-schaff]

Released on CI environment @gglusman