7 jed metpo curation assignment #1 llm ontology definition review and editing#19
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realmarcin merged 11 commits intomainfrom Nov 3, 2025
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Generated 26 OBO-compliant definitions for METPO terms with improved prompt template including batch processing, domain guidelines, and validation checklist. Organized outputs in raw/reviewed workflow.
…-#1---LLM-ontology-definition-review-and-editing Add curator5 definitions and improved v2.0 prompt template
…SV converter - Added definition-generation v2.1 prompt with batch processing (5-10 terms) - Executed v2.1 prompt on all 33 curator5 terms in 4 batches - Enhanced json_to_robot_tsv.py to support v2.1 format: - Structured sources with URLs - Parent class IDs - Quantitative values with measurement sources - Enhanced comments field with reasoning - Generated 4 JSON outputs with ontology-verified definitions - Generated 4 ROBOT template TSV files ready for ontology integration - All definitions include OBO Foundry compliance with genus-differentia form
…ology-definition-review-and-editing
Removed detailed comments and version info from the script.
Add missing type annotations to satisfy mypy strict mode: - Add type annotation for 'data' variable (line 35) - Add type annotation for 'sources' parameter (line 40) - Add type annotation for 'quant_values' parameter (line 70) - Add return type annotation for main() function (line 283) - Remove invalid comparison between dict and string literal (line 80) All mypy checks now pass for this script.
…ology-definition-review-and-editing
…spell Auto-fixes applied by pre-commit hooks: - Remove trailing whitespace from 10 files - Fix ruff linting errors (15 issues auto-fixed) - Reformat code with ruff-format (1 file) Manual fixes: - Add 'formate' to codespell ignore list (it's a chemical compound, not a typo) Formate (HCOO⁻) is a legitimate term in microbiology/biochemistry Files modified: - pyproject.toml: Add 'formate' to ignore-words-list - scripts/json_to_robot_tsv.py: Code formatting - Multiple TSV, MD files: Trailing whitespace removed
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nice work, merging ahead
realmarcin
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In the outputs - reviewed folder is my up-to-date JSON and TSV file for curator5 terms. In the prompts - executed folder are the different versions of prompts I have created (version 3 is the most updated one currently). Not so sure as to why the JSON and TSV files formatting is rough on here compared to when I view them in my branch.