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normalize.py: use merged.monarch context (fixes FBbt/WBbt prefix uppercasing) #201

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Merged
kevinschaper merged 1 commit into from
Jun 4, 2026
Merged

normalize.py: use merged.monarch context (fixes FBbt/WBbt prefix uppercasing) #201

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12 changes: 11 additions & 1 deletion kg_phenio/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
)
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