Reconcile facultatively aerobic vs facultatively anaerobic terms

[turbomam]

Problem

METPO has two separate terms for the same biological concept:

• METPO:1000605 facultatively anaerobic - maps to BacDive "facultative anaerobe"
• METPO:1000608 facultatively aerobic - maps to BacDive "facultative aerobe"

Both describe organisms that can grow with OR without oxygen. The standard microbiological term is "facultatively anaerobic" or "facultative anaerobe".

Current State

Both terms:

• Have nearly identical definitions
• Cite similar/overlapping ontology sources (ECOCORE:00000177, OMP:0000087, etc.)
• Share the same synonym "facultative"
• Map to "facultative anaerobe" terms in MICRO, ECOCORE, OMP ontologies

Key difference: They map to different BacDive label variants:

• data/generated/bacdive_oxygen_phenotype_mappings.tsv shows the distinction

Related Terms

This is not unique to oxygen metabolism. Similar patterns exist for:

• Temperature preferences (facultative psychrophilic, etc.)
• Halophily preferences (multiple halophilic terms)
• pH preferences (acidophilic variants)

Options

1. Keep both as distinct synonym mappers - Maintain for ETL/data integration
2. Merge into single term - Add both labels as synonyms, update mappings
3. Mark as exact synonyms - Add skos:exactMatch between them
4. Create parent term - Both as children of "facultative oxygen metabolism"

Recommendation

Given that this pattern exists throughout METPO for pragmatic data integration:

• Keep both terms for now
• Add skos:exactMatch relationship between them
• Document in term definitions that they represent label variants of the same concept
• Consider systematic review of all such pairs across METPO

Related Issues

• Source cleanup identified these terms shared problematic definition sources
• Both now cite appropriate "facultative anaerobe" sources after cleanup