biochemical-identifier-crosswalklisted

Life sciences / Biochemistry — Reconcile reactions, compounds, proteins, and taxa across Rhea, ChEBI (via EBI OLS4), MetaNetX, and UniProt into one one-to-many identifier crosswalk without collapsing chemical or mapping ambiguity. Config-driven: entities are declarative YAML records, so adding a reaction, compound, or enzyme means adding a record rather than editing code. Resolves reaction direction from the retrieved equation text rather than the Rhea LR/RL label, verifies mass and net-charge balance against an independently retrieved ChEBI formula and charge table, and never treats name similarity or a shared EC number alone as proof of identity. WHEN: "map Rhea to ChEBI, UniProt, or MetaNetX", "identifier crosswalk", "reaction identifier reconciliation", "resolve reaction direction", "preserve isoenzyme ambiguity", "is this the same reaction or compound", "mass and charge balance check", "currency metabolite vs generic compound".
timothymeyers/discovery-tools · ★ 1 · AI & Automation · score 70

Install: claude install-skill timothymeyers/discovery-tools

# biochemical-identifier-crosswalk Reconcile a reaction/compound/protein/taxon across model-native, Rhea, ChEBI, EC, UniProt, NCBI Taxonomy, BioCyc/CyanoCyc, SABIO-RK, BRENDA ligand, KEGG, and MetaNetX namespaces into one `identifier-crosswalk.schema.json`-conformant record — while deliberately preserving every ambiguity that a naive "one canonical ID per entity" crosswalk would silently destroy. ## Dependencies This skill is **not** standard-library only. `gh skill install` and plugin install do not install Python packages, so install these before first use: ```bash python3 -m pip install -r requirements.txt # PyYAML, jsonschema ``` `scripts/build_crosswalk.py` needs `PyYAML` to read the declarative entity configs; `scripts/validate_crosswalk.py` needs `jsonschema`. `scripts/formula_parser.py` is standard-library only and works without either. ## When to use Trigger when the user asks anything like: - "Map this Rhea/ChEBI ID to UniProt / MetaNetX / KEGG" - "Is this really the same reaction/compound as that one?" - "Build an identifier crosswalk for these reactions" - "Resolve which direction this reaction actually runs" - "This reaction has isoenzymes / paralogs — keep them separate" - "Check mass and charge balance for this reaction" - "Is a locus tag the same thing as a reaction ID?" (no) Do NOT trigger for: - Retrieving raw kinetic parameters (`sabio-rk-kinetics`, `brenda-enzyme-data`) or gene→pathway network context (`biocyc-network-context`) — this skill