Export Proposed Terms

Use this skill when the user asks for a TSV or tabular extract of ontology term requests recorded in gene review YAML files.

Run the helper from the repository root:

uv run python src/ai_gene_review/tools/export_proposed_terms.py -o reports/proposed_new_terms.tsv

Pass files or directories after the options to restrict the export. With no inputs, the helper scans genes/**/*-ai-review.yaml.

The TSV defaults to reports/proposed_new_terms.tsv. It has one row per top-level proposed_new_terms entry and skips reviews where proposed_new_terms is empty. It includes:

• source review fields: source_path, organism, gene_directory, review_id, gene_symbol, taxon_id, taxon_label
• proposal fields: term_index, proposed_name, proposed_definition, justification, proposed_parent_id, proposed_parent_label
• structured evidence fields serialized as JSON: proposed_mappings, supported_by

The exporter intentionally ignores knowledge_gaps[].proposed_terms; those are nested gap-specific proposals, not the review's top-level ontology request list. If the user explicitly asks for gap proposals too, write a separate ad hoc extract with a column that distinguishes top-level terms from gap terms.

For custom column order, filtering, or aggregation, treat the generated TSV as a staging table and post-process it with Python's csv module or pandas. Preserve TSV safety by keeping embedded tabs and newlines out of scalar cells.

Treat the TSV as a read-only reporting view, not a round-trip editing source. Scalar columns are whitespace-normalized for tabular readability; nested proposed_mappings and supported_by values are compact JSON for inspection. When updating a review, copy exact supporting_text from the source YAML or publication cache, not from a TSV extract.