PTS drug processing steps and remove ETL drug steps#160
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- Add new PTS steps: pts_drug_warning, pts_chembl_molecule, pts_drug_mechanism_of_action, pts_drug_molecule, pts_target_prioritisation - Remove ETL steps: etl_drug, etl_pharmacogenomics, etl_known_drug, etl_target_engine - Update dependencies to use new PTS drug steps instead of removed ETL steps
76 tasks
…teps Add three new PTS transformer steps for clinical data processing: - clinical_report: generates clinical reports from chembl_molecule and disease - clinical_indication: generates clinical indications from clinical_report - clinical_target: generates clinical targets from clinical_report and drug_mechanism_of_action
Aligns the config with the transformer's updated signature that expects named keys (disease_path, phenotype_path, mondo_path) instead of a list.
- drug_molecule: use clinical_report instead of indication - evidence_chembl: use clinical_report and drug_mechanism_of_action instead of chembl_evidence and drug_indications - Update dependency graph accordingly
pis_target is already an implicit dependency through pts_pharmacogenetics
…chembl pts_disease is already an implicit dependency through pts_evidence_chembl
…et_prioritisation pts_drug_mechanism_of_action is already an implicit dependency through pts_drug_molecule
…ence_postprocess_chembl pts_drug_mechanism_of_action is already an implicit dependency through pts_evidence_chembl
Rename pts_evidence_chembl and pts_evidence_postprocess_chembl steps. Remove pis_evidence_chembl from pis.yaml and unified_pipeline.yaml. Update score expression with string-based clinicalStage map and raw stop reason category names.
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Related to #4247