G2P

Scope

This project tracks how Gene2Phenotype (G2P) disease rows map onto dismech's disease-centric knowledge model, with the goal of turning comparison output into curation triage rather than a one-off research exercise.

Canonical Locations

• Project note: docs/research/g2p_database_alignment.md
• Full-release audit snapshot: docs/research/g2p_all_genes_audit_2026_03_28.md
• Row-level triage TSV: docs/research/g2p_all_genes_row_triage_2026_03_28.tsv
• Gene-level summary TSV: docs/research/g2p_all_genes_gene_summary_2026_03_28.tsv

Code Organization

Comparison code now lives under src/dismech/compare/ instead of the package top level:

• src/dismech/compare/d2p.py: disease-to-phenotype comparison flow
• src/dismech/compare/g2p.py: G2P-to-dismech comparison flow
• src/dismech/compare/g2p_audit.py: compatibility wrapper for the initial G2P audit CLI
• src/dismech/compare/support.py: shared comparison helpers

This keeps the G2P work aligned with the earlier D2P comparison architecture instead of adding another top-level framework.

Practical Commands

just g2p-compare PTEN
just g2p-compare-all PTEN FLNB PIK3CA FGFR2
just g2p-compare-release
just g2p-compare-release-triage
uv run python -m dismech.compare.g2p compare PTEN --format json

Current Focus

• make row-status output actionable for curation
• identify genes where dismech has rooted disease coverage vs embedded-only coverage
• separate disease-identity alignment, PMID overlap, and mechanism-model alignment in the audit output