sabio-rk-kineticslisted

Life sciences / Enzymology — Parameterized SABIO-RK kinetic-law ingestion. Organism, genus, and EC-number query tiering (exact organism -> genus wildcard -> higher-taxon lineage -> any organism) driven by taxid ancestry rather than lineage-name string matching. Explicit outcome and failure_kind semantics that never conflate a confirmed-empty result with a transport, authorization, or parser failure. Sample-vs-exhaustive pagination with honest truncation reporting, and Retry-After-aware handling of the documented 60-requests/60-seconds rate limit. Nothing is scoped to an organism, project, or EC number — every identifier is a parameter. WHEN: "query SABIO-RK", "SABIO-RK kinetic law", "SABIO-RK Export API", "ingest kinetic parameters", "kcat", "Km", "enzyme kinetics for an organism", "EC number query tiers", "organism lineage fallback", "taxid ancestry", "SABIO-RK pagination", "SABIO-RK 429", "SABIO-RK rate limit".
timothymeyers/discovery-tools · ★ 1 · Data & Documents · score 70

Install: claude install-skill timothymeyers/discovery-tools

# sabio-rk-kinetics — Parameterized SABIO-RK Kinetic-Law Ingestion Reusable, project-agnostic adapter for querying the SABIO-RK Export API (`/export-api/sabio/...`) for kinetic-law entries, generalized from a prior ingestion pass that (1) built a stable-identifier-first, controlled-fallback query strategy and (2) fixed a real production bug where a lineage-name *string* match silently rejected genuinely matching organisms whose lineage used a different (but current) NCBI taxon name than the one hardcoded in the filter. Every organism/genus/EC-number/higher-taxon value here is a parameter — this skill is not scoped to any single organism or project. **Access-route status and general database-access procedure are owned by the `scientific-database-access` hub skill** (`references/sources/sabio-rk.md` there records the last-verified route status and rate-limit contract) — this skill does not duplicate that; it assumes the Export API route has already been confirmed reachable and focuses on the query/pagination/taxonomy/ outcome logic for actually pulling and post-filtering kinetic-law entries. ## When to use - Query SABIO-RK for kinetic-law entries for a given EC number and target organism, with a documented, auditable fallback strategy when the exact organism has no direct SABIO-RK coverage. - Debug or extend a lineage/taxonomy-based organism filter and want to avoid the "hardcoded lineage-name string never matches the API's actual current name" class of bug (see `re