update drugs attribute in evidence

README.md

@@ -40,7 +40,7 @@ genotypeAnnotationText | Full annotation string for genotype or allele | `"Patie
 directionality | Allele function annotation (see Table 2 [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5253119/)) | `"Decreased function"`
 haplotypeId | Name of haplotype; can be an allele or a genotype | `"CYP2B6*6"` or `"GSTT1 non-null/non-null"`
 haplotypeFromSourceId | Internal PGKB identifier for the haplotype | `"PA165818762"`
-drugsFromSource | List of drug names (if known to be annotated in combination) | `["succinylcholine"]` or `["ivacaftor", "lumacaftor"]`
+drugs | List of drugs (see [below](#drug-representation)) | `[{"drugFromSource": "ivacaftor"}, {"drugFromSource": "lumacaftor"}]`
 pgxCategory | Pharmacogenomics phenotype category | `"toxicity"`
 phenotypeText | Phenotype name | `"Malignant Hyperthermia"`
 phenotypeFromSourceId | EFO ID of phenotype, mapped through ZOOMA / OXO | `"Orphanet_423"`
@@ -64,8 +64,8 @@ Below is an example of a complete clinical annotation evidence string:
   "targetFromSourceId": "ENSG00000196218",
   "genotype": "del/GAG",
   "genotypeAnnotationText": "Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics (desflurane, enflurane, halothane, isoflurane, methoxyflurane, sevoflurane) and/or succinylcholine as compared to patients with the GAG/GAG genotype. Other genetic or clinical factors may also influence the risk for malignant hyperthermia.",
-  "drugsFromSource": [
-    "succinylcholine"
+  "drugs": [
+    {"drugFromSource": "succinylcholine"}
   ],
   "pgxCategory": "toxicity",
   "phenotypeText": "Malignant Hyperthermia",
@@ -91,3 +91,12 @@ graph TD
     H --> |Reference + context| D
     E --> |Alternate alleles| D
 ```
+
+### Drug representation
+
+The `drugs` property is a list of structs with 2 keys:
+* `drugFromSource`: name of the drug from PGKB
+* `drugId`: CHEMBL ID, left empty in this pipeline but populated by Open Targets 
+
+Lists of drugs are kept together (rather than exploded into separate evidence strings) when they're known to be annotated as a drug combination.
+Currently this is only when they're `/`-separated and associated with a single PGKB chemical ID, as in [ivacaftor / lumacaftor](https://www.pharmgkb.org/chemical/PA166152935).

opentargets_pharmgkb/OT_SCHEMA_VERSION

@@ -1 +1 @@
-2.7.1
+2.7.2

opentargets_pharmgkb/evidence_generation.py

@@ -352,7 +352,7 @@ def generate_clinical_annotation_evidence(so_accession_dict, created_date, row):
         'directionality': row['Allele Function'],
 
         # PHENOTYPE ATTRIBUTES
-        'drugsFromSource': row['split_drug'],
+        'drugs': [{'drugFromSource': d} for d in row['split_drug']],
         'pgxCategory': row['split_pgx_category'].lower(),
         'phenotypeText': row['split_phenotype'],
         'phenotypeFromSourceId': iri_to_code(row['efo'])