Microbial ecophysiological trait and phenotype ontology

More information can be found at http://obofoundry.org/ontology/metpo

The latest version of the ontology can always be found at:

http://purl.obolibrary.org/obo/metpo.owl

(note this will not show up until the request has been approved by obofoundry.org)

Editors of this ontology should use the edit version, src/ontology/metpo-edit.owl

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

This ontology repository was created using the Ontology Development Kit (ODK).

• https://docs.google.com/spreadsheets/d/1_Lr-9_5QHi8QLvRyTZFSciUhzGKD4DbUObyTpJ16_RU/edit?gid=0#gid=0

• https://github.com/berkeleybop/group-meetings/issues/155#issuecomment-2715444097

METPO is intended to drive mining knowldge out of papers form journals like IJSEM and expressing the findings with classes and predicates from METPO or the Biolink model, which would then become part of KG-Microbe.

We strive to keep our class heirachies pure. Reuse of terms from OBO foundry ontologies and the use of logical axioms are hihg but secondary priorities.

This repository contains two main components:

The core METPO ontology is built using the Ontology Development Kit (ODK). The root Python code and Makefiles are not involved in ontology releases.

To rebuild the ontology from source (requires Docker):

cd src/ontology
make squeaky-clean          # Clean all generated files
./run.sh make all          # Full build with Docker wrapper

The build process:

• Fetches the latest CSV data from Google Sheets
• Generates robot template output
• Builds all ontology format files (OWL, OBO, JSON)

To prepare a new release:

cd src/ontology
./run.sh prepare_release   # Copies files to project root

Manual steps after prepare_release:

• Review generated files in project root
• Git add, commit, and push changes
• Create GitHub release
• Monitor third-party systems (Bioportal, etc.)

After releases, monitor integration with:

• OBO Foundry
• Bioportal
• Other ontology repositories

Documentation needed: Detailed monitoring procedures and third-party system integration.

The literature mining component uses OntoGPT to extract knowledge from research papers (especially IJSEM) and annotates the extracted data using METPO ontology files. This pipeline is separate from ontology maintenance and its outputs are intended for integration into KG-Microbe.

The literature mining workflow uses:

• METPO ontology files as knowledge annotators
• OntoGPT for information extraction from abstracts
• Custom templates for structured data extraction

Final destination: KG-Microbe knowledge graph