update field name

EBIvariation · Jan 30, 2024 · aab59d4 · aab59d4
1 parent 2ca5c0f
commit aab59d4
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Showing 3 changed files with 38 additions and 38 deletions.
diff --git a/README.md b/README.md
@@ -41,7 +41,7 @@ genotype | Genotype or allele string | SNP `"TA"`, indel `"del/GAG"`, repeat `"(
 genotypeAnnotationText | Full annotation string for genotype or allele | `"Patients with the rs121918596 del/GAG genotype may develop malignant hyperthermia when treated with volatile anesthetics [...]"`
 alleleFunction | 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"`
-internalHaplotypeId | Internal PGKB identifier for the haplotype | `"PA165818762"`
+haplotypeFromSourceId | Internal PGKB identifier for the haplotype | `"PA165818762"`
 drugFromSource | Drug name | `"succinylcholine"`
 drugId | CHEBI ID of drug, mapped through OLS | `"CHEBI_45652"`
 pgxCategory | Pharmacogenomics phenotype category | `"toxicity"`

diff --git a/opentargets_pharmgkb/evidence_generation.py b/opentargets_pharmgkb/evidence_generation.py
@@ -406,7 +406,7 @@ def add_variant_haplotype_attributes(so_accession_dict, row, evidence_string):
     else:
         evidence_string.update({
             'haplotypeId': row['haplotype_id'],
-            'internalHaplotypeId': row['pgkb_haplotype_id'],
+            'haplotypeFromSourceId': row['pgkb_haplotype_id'],
             'targetFromSourceId': row['gene_from_pgkb']
         })
     return evidence_string