brenda-enzyme-datalisted

Life sciences / Enzymology — Parameterized BRENDA ingestion from a caller-supplied licensed bulk JSON release. Subset extractor and deterministic canonical-record builder where organism substring, EC number, and file path are all parameters. Includes a BRENDA numeric-value-string parser covering ranges, the -999 {more} sentinel, and ligand-in-braces labels, plus a schema validator that surfaces a genuine publisher-side EC-key regex defect instead of hiding it behind a false "0 errors". You must supply your own licensed BRENDA download: this skill never bundles, caches, downloads, or accepts the license for any BRENDA dump. WHEN: "BRENDA", "brenda-enzymes.org", "BRENDA bulk JSON", "km_value", "turnover_number", "kcat_km_value", "specific_activity", "BRENDA -999 sentinel", "BRENDA schema validation", "BRENDA license", "ingest enzyme kinetic parameters from BRENDA".
timothymeyers/discovery-tools · ★ 1 · Data & Documents · score 70

Install: claude install-skill timothymeyers/discovery-tools

# brenda-enzyme-data — Parameterized BRENDA Bulk-JSON Ingestion Reusable, project-agnostic adapter for extracting and canonicalizing enzyme/kinetic-parameter data from BRENDA's licensed bulk JSON release, generalized from two independent extraction passes (disjoint EC numbers and organisms) over release `2026.1`. Every EC number, organism substring, and file path here is a caller-supplied parameter — this skill is not scoped to any single project's target enzymes. ## Dependencies The extractor and canonical-record builder are standard-library only. Only `scripts/validate_schema.py` needs a third-party package, and `gh skill install` does not install it: ```bash python3 -m pip install -r requirements.txt # jsonschema ``` Without it the validator raises a clear error; everything else still runs. **Access-route status is owned by the `scientific-database-access` hub skill** (`references/sources/brenda.md` there records the last-verified route status: the bulk JSON route is `reachable_documented_auth` — a click-through license acceptance, no account needed; SOAP is `gated_credentialed`; SPARQL is `reachable_public` but not a fully validated recipe). This skill does not duplicate that; it assumes the bulk-JSON route has already been confirmed and focuses on extraction/parsing/validation logic over a file **you** have already licensed and downloaded. ## Hard requirement: bring your own licensed bulk file This skill **never** bundles, caches, auto-downloads, or reads any f