Releases: berkeleybop/metpo
2026-03-24
Ontology Content Changes (since 2025-11-17)
Entity counts: 376 → 416 (+40 net; 26 new classes + 37 new properties − 23 removed properties)
New classes (26)
Biochemical tests (6) — indole, methyl red, Voges-Proskauer (each with positive/negative subclasses)
Flagellum arrangements (7) — peritrichous, polar, amphitrichous, lophotrichous, monotrichous, lateral, subpolar
Nitrogen cycle processes (3) — nitrification, denitrification, nitrogen fixation
Hemolysis (3) — hemolysis (parent), hemolytic, non-hemolytic
Other (7) — capnophilic (oxygen preference), generalist (ecology), enzyme, growth medium, plus the above parent classes
New object properties (11)
- Enzyme activity: `enzyme activity analyzed`, `shows activity of`, `does not show activity of`
- Growth medium: `grows in`, `does not grow in`
- Nitrogen cycle: `denitrifies`/`does not denitrify`, `ammonifies`/`does not ammonify`
- Redox: `oxidizes in darkness`/`does not oxidize in darkness`
New data properties (26)
Numeric measurement properties for:
- Temperature, pH, salinity (growth/min/max — 9 properties)
- Genome size, gene count (actual/estimated — 4 properties)
- GC percentage, coding density (2 properties)
- Cell length, cell width (value/min/max — 6 properties)
- Ecology metrics: generalism score, habitat count, pangenome openness, nucleotide diversity (5 properties including parent)
Removed properties (23)
Speculative placeholders removed in PR #317 (2025-11-24): lyses, fixes, catabolizes, mineralizes, conjugates, binds, chelates, precipitates, solubilizes, volatilizes, crystallizes, adsorbs (and their negations). These had no synonyms, assay outcomes, or data backing. See #370 for deprecation discussion.
Other changes
- Label change: METPO:2000202 `synthesizes` → `produces`
- MetaTraits synonym column added to classes template (38 of 281 classes = 13% coverage)
- Assay outcome column (+/−) populated for all existing object properties
- Column alignment fix: GC, temperature, NaCl, pH bin classes had values shifted into wrong columns; corrected
Infrastructure
- `diff-templates` CLI for structured template comparison across Google Sheets, git refs, and files
- pytest test suite (17 tests)
- `litellm` removed from dependencies (PyPI supply chain compromise)
- Google Sheets tabs promoted: classes (gid=1569766102), properties (gid=681401984)
Build
ODK v1.6 / ROBOT 1.9.8. All SPARQL checks (0 violations), ELK reasoning, OWL2 DL profile validation, and LightRDF checks passed.
2025-12-12
Contributors
Assets 2
2025-11-24
Contributors
Assets 2
2025-11-21
Contributors
Assets 2
2025-11-17
What's Changed
- Updates to definitions, definition sources, and term editor credit
- Enhance non-OLS ontology pipeline with analysis tools and ChromaDB integration by @turbomam in #275
- OntoGPT template optimization: Fix annotator paths and improve signal-to-noise ratio by @turbomam in #276
- Finalize ChromaDB as vector DB and remove Qdrant migration scripts by @turbomam in #278
- ICBO 2025 Preparation: Documentation reorganization and ontology cross-reference analysis by @turbomam in #282
- Icbo prep docs reorg by @turbomam in #283
- Add ICBO 2025 infrastructure documentation and reference papers by @turbomam in #289
- Reorganize project root directories and documentation by @turbomam in #291
- Add comprehensive data provenance documentation and fix README by @turbomam in #293
- Fix ontology build and complete repository cleanup by @turbomam in #302
- slides-marp-md-make-pdf by @turbomam in #303
- Slides marp md make pdf by @turbomam in #310
- 2025 11 17 by @turbomam in #308
Full Changelog: 2025-10-31...2025-11-17
Contributors
Assets 2
METPO October 2025 Release
METPO October 2025 Release
This release includes ontology updates, literature mining pipeline improvements, and enhanced documentation.
What's New
Ontology Updates:
- Updated ontology templates with 256 terms in main sheet and 378 stub definitions
- Improved ontology validation and quality control processes
- Enhanced coverage analysis for term alignment
Literature Mining Enhancements:
- OntoGPT template optimization for improved extraction accuracy (#272, #266)
- Fixed annotator paths and improved signal-to-noise ratio in extractions
- Completed abstract collection, categorization, and template analysis (#261)
- Added artl-mcp integration for literature mining workflows (#262)
Documentation & Integration:
- Added SSSOM integration guide for mapping and alignment workflows (#260)
- Added BacDive keywords documentation with analysis notebooks (#250)
- Improved ontology validation documentation and examples
Infrastructure:
- Enhanced Python code quality with standardized notebook guidelines
- Improved .gitignore patterns for cleaner repository management
- Better ontology filtering with --include and --exclude options in migration tools
Release Files
This release includes three editions of METPO in OWL, OBO, and JSON formats:
- metpo.owl/obo/json - Standard release with imported terms
- metpo-base.owl/obo/json - Base ontology without imports
- metpo-full.owl/obo/json - Full ontology with all reasoning and imports merged
For More Information
- Repository: https://github.com/berkeleybop/metpo
- OBO Foundry: http://obofoundry.org/ontology/metpo
- License: CC-BY 4.0
2025-10-15
What's Changed
- Round-trip assessment documentation for issue #223 by @turbomam in #224
- Add comprehensive Madin-METPO reconciliation tooling by @turbomam in #225
- feat(bacdive): Add OntoGPT pipeline for chemical utilization by @turbomam in #229
- 223 round trip assessment of source data synonyms by @turbomam in #230
- feat(ontology): Add pigment classes and fix reconciliation by @turbomam in #232
- feat: Add cell length and width classes from BactoTraits by @turbomam in #238
- dynamic generation of inter-template stubs by @turbomam in #240
- grouping and cleanup of phenotypes with min/max by @turbomam in #242
Full Changelog: 2025-10-03...2025-10-15
Contributors
Assets 2
2025-10-03
What's Changed
- 2025-10-03 build by @turbomam in #216
- helpers for loading source data into MongoDB and checking results by @turbomam in #220
- more OLS prep by @turbomam in #217
- root cleanup by @turbomam in #221
- download all google sheets, bioportal versioned ontologies, and assess id and label reuse by @turbomam in #206
Full Changelog: 2025-09-23...2025-10-03
Contributors
Assets 2
2025-09-23
What's Changed
- Prepare repo for release
2025-09-23by @sujaypatil96 in #201
Full Changelog: 2025-09-22...2025-09-23
Contributors
Assets 2
2025-09-22
What's Changed
- Update ROBOT templates and generated OWL files by @sujaypatil96 in #193
- 2025-09-22 release for GH and BP with TSVs from GSheets by @turbomam in #199
New Contributors
- @sujaypatil96 made their first contribution in #193
Full Changelog: 2025-08-26...2025-09-22