diff --git a/kg_phenio/normalize.py b/kg_phenio/normalize.py index 71cf5dc..fdf26a4 100644 --- a/kg_phenio/normalize.py +++ b/kg_phenio/normalize.py @@ -12,13 +12,23 @@ def normalize() -> None: None """ + # Use the Monarch-specific `merged.monarch` context from prefixmaps as + # the single source of CURIE↔IRI conventions. The previous + # `["obo", "bioregistry.upper"]` pair interacted with universalizer's + # lowercased-reverse-IRI logic in `make_id_maps` and was producing + # all-uppercase prefix casings for OBO mixed-case anatomies (FBbt → + # FBBT, WBbt → WBBT). That dropped ~503k Drosophila + C. elegans + # gene-expression edges to dangling in the 2026-06-03 monarch-kg build + # (the entire shortfall on `alliance_gene_to_expression_edges`). + # `merged.monarch` is also what monarch-app's `curie_service.py` uses, + # so the whole stack is now aligned. print("Normalizing nodes and categories...") clean_and_normalize_graph( filepath="data/merged/", compressed=False, maps=[], update_categories=True, - contexts=["obo", "bioregistry.upper"], + contexts=["merged.monarch"], namespace_cat_map="", oak_lookup=False, )