Verify BacDive enzyme activities use correct edge type (not metabolite utilization)

[turbomam]

Context

PR #174 (opened 2024-06-04 by @realmarcin, now closed) removed NCBI_TO_ENZYME_EDGE and routed all enzyme activity data through NCBI_TO_METABOLITE_UTILIZATION_EDGE. Copilot review (Aug 2025) flagged this as a bug — enzyme activities and metabolite utilization are semantically different and should have distinct edge types.

The original problem

The BacDive transform was conflating two types of edges:

• Enzyme activities (organism has enzyme capability, e.g. catalase) — should use biolink:capable_of / CAPABLE_OF relation
• Metabolite utilization (organism uses/produces a metabolite) — should use biolink:has_phenotype or biolink:produces

PR #174 made this worse by merging them into one edge type.

Current state

The current bacdive.py has been heavily rewritten with a richer data model including METPO predicates and CAPABLE_OF relations. This issue may already be resolved, but it should be verified.

What needs to happen

1. Check current bacdive.py enzyme activity edge handling — confirm enzyme activities get CAPABLE_OF or equivalent, not metabolite utilization predicates
2. Verify edge predicates match the patterns established in the metatraits transform (PR Add metatraits data source transform and mappings (isolated) #502): biolink:capable_of for enzymes, biolink:produces for products, biolink:has_phenotype for phenotypes

Original PR

#174 by @realmarcin — closed 2026-03-18, see closing comment for full analysis.