biocyc-network-contextlisted

Life sciences / Systems biology — Parameterized bounded BioCyc, EcoCyc, and CyanoCyc network-context traversal: reaction -> enzyme/complex -> gene -> pathway. Preserves every catalyst for a reaction rather than collapsing isoenzymes, expands multi-subunit complexes to each subunit's own gene, and verifies organism identity from the PGDB's own NCBI-TAXONOMY-DB cross-reference rather than assuming it from the orgid string. Distinguishes missing_frame (the frame genuinely does not exist) from gated (a bot or subscription challenge blocked the page) instead of conflating both as "access failed". Rate-limited getxml client, never a bulk endpoint. Every identifier is a parameter. WHEN: "query BioCyc", "query EcoCyc", "query CyanoCyc", "getxml traversal", "BioCyc network context", "reaction to gene to pathway", "BioCyc isoenzyme", "protein complex subunits", "missing frame vs gated", "BioCyc rate limit", "BioCyc Limited Use License".
timothymeyers/discovery-tools · ★ 1 · AI & Automation · score 70

Install: claude install-skill timothymeyers/discovery-tools

# biocyc-network-context — Parameterized BioCyc/EcoCyc/CyanoCyc Network-Context Traversal Reusable, project-agnostic adapter for walking a BioCyc-family PGDB's `getxml` REST API from a single reaction frame out to its catalyzing enzyme(s)/complex(es), their gene(s), and pathway membership -- generalized from two prior, independently validated ingestion passes: DX-30 (3 Calvin-Benson-cycle reactions against *Prochlorococcus marinus* MED4 / CyanoCyc) and DX-53 (3 central-metabolism reactions -- pgi/EC 5.3.1.9, pfk/EC 2.7.1.11, zwf/EC 1.1.1.49 -- against *E. coli* K-12 MG1655 / EcoCyc). Every organism, orgid, frame ID, EC number, and taxid used in this skill's scripts/fixtures is illustrative; nothing is hardcoded as a default inside `scripts/traversal.py` itself. **Access-route status and general database-access procedure are owned by the `scientific-database-access` hub skill** (`references/sources/biocyc.md` there records the last-verified route status and rate-limit contract) -- this skill does not duplicate that; see `references/access-routes-and-terms.md` for a summary from already- committed evidence and focuses on the traversal/classification/outcome logic for actually walking a PGDB's object graph. ## When to use - Walk a BioCyc/EcoCyc/CyanoCyc reaction frame out to its catalyzing enzyme(s), the gene(s) encoding them, and pathway membership, with every step individually rate-limited and every outcome (success/missing/gated/ failure) explicit (`scripts/traversa