METPO

Microbial ecophysiological trait and phenotype ontology

Versions

Stable release versions

METPO releases are available from multiple sources:

BioPortal (Recommended for browsing and search):

• https://bioportal.bioontology.org/ontologies/METPO
• Browse classes, search terms, and visualize the hierarchy
• API access available

GitHub Releases:

• See Releases
• Download OWL, OBO, and JSON formats

Direct OWL file:

• Latest release: metpo.owl in this repository

Editors' version

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

Contact

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

Installation

Requirements

• Python: 3.11 or higher
• Package Manager: uv (recommended)
• ROBOT: For ontology processing (see ROBOT installation)
• MongoDB: For database workflows (optional)

Environment Setup

# Check your environment
make check-env

# Install core dependencies only
make install

# Install for specific workflows
make install-dev           # Development tools (oaklib, rdflib, semsql)
make install-literature    # Literature mining (ontogpt, artl-mcp)
make install-databases     # BactoTraits/Madin workflows (pandas, pymongo)
make install-notebooks     # Jupyter notebooks (chromadb, matplotlib)

# Install everything
make install-all

Acknowledgements

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

METPO research relies on numerous external data sources and ontologies. See ACKNOWLEDGMENTS.md for complete citations and attributions for:

• BactoTraits, Madin et al., and BacDive microbial trait databases
• 24+ ontologies from OBO Foundry and BioPortal
• Semsql databases, embedding infrastructure, and software tools

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Input:

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

Development Notes

• Historical development discussion: berkeleybop/group-meetings #155 (Note: May require repository access)

---

METPO is intended to drive mining knowledge out of papers from 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 hierarchies pure. Reuse of terms from OBO Foundry ontologies and the use of logical axioms are high but secondary priorities.

Repository Structure and Workflows

This repository supports multiple research workflows beyond ontology development:

1. Ontology Development (src/ontology/)

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

Building the ontology (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, and builds all ontology format files (OWL, OBO, JSON).

Creating a release:

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

See src/ontology/README-editors.md for detailed instructions.

2. Literature Mining Pipeline (literature_mining/)

Extract structured microbial trait data from research papers using OntoGPT with METPO grounding.

Quick start:

make install-literature

# Fetch abstracts and run extraction
make -C literature_mining pmids SOURCE=ijsem
make -C literature_mining abstracts SOURCE=ijsem N_ABSTRACTS=10
make -C literature_mining extract TEMPLATE=growth_conditions

Key features:

• OntoGPT-based extraction with custom templates
• METPO-grounded entity recognition
• Cost/performance benchmarking
• Multiple extraction templates (growth conditions, chemical utilization, morphology, etc.)

See literature_mining/README.md for full documentation.

3. ICBO Example Extractions (literature_mining/)

Example extractions demonstrating METPO's grounding strengths and weaknesses, used in ICBO 2025 presentation.

make install-literature

# Extract phenotypes and chemical utilizations from example abstracts
make -C literature_mining icbo-phenotypes
make -C literature_mining icbo-chemicals

# Analyze METPO grounding quality
make -C literature_mining icbo-analyze

Example inputs, templates, and outputs are in literature_mining/abstracts/icbo_examples/ and literature_mining/outputs/icbo_examples/.

Presentation materials: See docs/presentations/icbo_2025/ for slides and analysis from ICBO 2025.

4. Database Reconciliation (metpo/scripts/)

Import and reconcile microbial trait databases (BactoTraits, Madin et al.) with METPO terminology.

make install-databases

# Import datasets to MongoDB
make import-bactotraits
make import-madin

# Generate reconciliation reports
make all-reports

Outputs:

• reports/bactotraits-metpo-reconciliation.yaml
• reports/madin-metpo-reconciliation.yaml
• reports/synonym-sources.tsv

5. Historical ID Tracking (metadata/historical_usage_analysis/)

Track METPO entity stability and IRI evolution across BioPortal submissions.

# Download historical submissions
make download-all-bioportal-submissions

# Extract entities from each version
make extract-all-metpo-entities

Analyzes IRI numbering scheme changes, entity additions/removals, and ID reuse violations. See metadata/historical_usage_analysis/README.md for comprehensive findings.

6. Ontology Alignment Pipeline (notebooks/)

Semantic matching between METPO and other microbial ontologies using ChromaDB embeddings.

make install-notebooks

# Run alignment pipeline
make alignment-run-all

# Or run individual steps
make alignment-fetch-ontology-names
make alignment-categorize-ontologies
make alignment-analyze-matches

Identifies high-quality alignment candidates from OLS4 and non-OLS ontologies.

7. External Ontology Integration (external/)

Centralized storage for all external ontology files and derived databases.

make install-dev

# Download microbial ontologies from BioPortal
make download-external-bioportal-ontologies

# Extract terms for embeddings
make notebooks/non-ols-terms/MPO.tsv
make notebooks/non-ols-terms/D3O.tsv

Structure:

• external/ontologies/bioportal/ - Downloaded from BioPortal (13+ ontologies: MPO, OMP, D3O, GMO, MISO, etc.)
• external/ontologies/manual/ - Manually added files (e.g., n4l_merged.owl)
• external/databases/ - Derived semsql databases
• external/metpo_historical/ - Historical METPO BioPortal submissions

Key Documentation

• Ontology editing: src/ontology/README-editors.md
• CLI reference: docs/cli-reference.md - Complete guide to all 30+ command-line tools
• Literature mining: literature_mining/README.md
• Historical analysis: metadata/ontology/historical_submissions/README.md
• Database metadata: metadata/databases/README.md
• Development guide: CLAUDE.md
• Analysis reports: reports/

Common Tasks

# Check environment setup
make check-env

# Generate all analysis reports
make all-reports

# Test complete workflow reproducibility
make test-workflow

# Clean generated data
make clean-data

License

METPO is released under the Creative Commons Attribution 4.0 International License (CC-BY-4.0).

You are free to:

• Share — copy and redistribute the material in any medium or format
• Adapt — remix, transform, and build upon the material for any purpose, even commercially

Under the following terms:

• Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made

See LICENSE for full details.