PathwayMech

PathwayMech curates pathway-level microbial mechanisms as small YAML records with explicit participants, reactions, causal edges, and reference-backed evidence.

The repository follows the current Mech layout:

• data/pathways/ contains curated pathway mechanism records.
• conf/ declares source inventories and import configuration.
• curation/ tracks curator decisions that are separate from generated data.
• scripts/ contains entry points for validation, rendering, seeding, and QC.
• src/pathwaymech/ contains reusable schema and IO code.
• tests/ protects the curation contract.
• pages/ contains the generated static browser.

The first PathwayMech contract ports the DisMech pattern of evidence modules into a pathway-specific schema:

• every mechanistic edge must cite a local references entry;
• every evidence quote must be short enough for review;
• graph edge endpoints must resolve to the pathway itself, a participant, or a reaction in the same record;
• record identifiers must use explicit CURIE-style prefixes;
• static pages are generated from the same YAML records that feed QC.

Quickstart

uv run pathwaymech-validate
uv run pathwaymech-check-provenance
uv run pathwaymech-render-pages
uv run pytest

Run the complete local gate with:

just validate