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

[kevinschaper]

Summary

Swap the clean_and_normalize_graph contexts argument from [\"obo\", \"bioregistry.upper\"] to a single [\"merged.monarch\"]. Fixes a CURIE-casing bug where OBO mixed-case anatomy prefixes (FBbt, WBbt) were being emitted as all-uppercase (FBBT, WBBT) in merged-kg_nodes.tsv.

Why the existing code produces uppercase

The two-context combination of \"obo\" + \"bioregistry.upper\" is fed to universalizer.norm.clean_and_normalize_graph, which builds reverse-IRI maps in make_id_maps:

all_reverse_contexts = {val: key for key, val in all_contexts.items()}
all_reverse_contexts_lc = {val.lower(): key for key, val in all_contexts.items()}
all_reverse_contexts.update(all_reverse_contexts_lc)
iri_converter = Converter.from_reverse_prefix_map(all_reverse_contexts)

That lowercased-reverse-IRI key, merged on top of the canonical map, plus the two-context overlap, leaves room for non-canonical CURIEs to win on round-trips for OBO prefixes that have non-default casing — specifically FBbt: and WBbt:.

Why a single "merged.monarch" context fixes it

merged.monarch is a single-context prefixmap (16,972 entries, same data as merged with a Monarch-specific label) that has one canonical IRI prefix per CURIE. With only one entry per IRI in the reverse map, the lowercased synonym can't override anything; the canonical case wins.

Verified locally — http://purl.obolibrary.org/obo/FBbt_00000001 compresses to FBbt:00000001 and http://purl.obolibrary.org/obo/WBbt_0000001 compresses to WBbt:0000001 under merged.monarch, as do all the other prefixes monarch-app exercises.

Why this matters in practice

The 2026-06-03 monarch-kg release lost 504,820 alliance gene-expression edges to the dangling pile — essentially the entire shortfall observed on alliance_gene_to_expression_edges (1.45M vs 1.9M expected). Investigation showed 99.7% are anatomy-side missing, and 100% of those (503,187) are FBbt + WBbt — exactly the two prefixes affected by this casing bug.

missing namespace	dangling edges	species
FBbt	397,914	Drosophila melanogaster
WBbt	105,273	C. elegans

After this PR ships and monarch-ingest picks up the next kg-phenio release, those edges resolve natively without any monarch-ingest-side workaround.

Related

• kg-phenio uppercases FBbt/WBbt prefixes; upstream fix needed (currently worked around in monarch-ingest) monarch-initiative/monarch-app#1319 — tracking issue with the full investigation.
• curie_service: switch to merged.monarch context monarch-initiative/monarch-app#1320 — companion PR aligning monarch-app's curie_service.py on merged.monarch so the whole Monarch stack uses one curated CURIE convention.