Agent Claude Code
Generate or revise ONE MIE (Metadata Interoperability Exchange) YAML file for a single RDF database in TogoMCP, by following the mie-generator skill end to end against the live SPARQL endpoint. Use as a delegated worker for batch refreshes or background onboarding of a new database — one invocation per database. Not…
Settings file Claude Code
Agent settings declaring 3 allowed tools.
Skill Claude CodeCodex
Run a multi-scale disease pathophysiology analysis — molecular defects through to clinical symptoms — using TogoMCP (RDF Portal SPARQL), TogoID ID conversion, OLS4, and PubMed. Use whenever the user asks to "analyze a disease", build a disease mechanism model, find disease-associated proteins/pathways/drugs, map a…
Skill Claude CodeCodex
Update the public TogoMCP intro/landing page at togomcp/data/docs/togomcp-intro.html whenever the catalog of databases, the catalog of MCP tools, or any other surface fact shown on the page changes. Trigger when the user adds/removes/renames a database (MIE file, endpoints.csv row), adds/removes/renames a tool (any…
Skill Claude CodeCodex
Generate or update MIE (Metadata Interoperability Exchange) YAML files that describe RDF databases for TogoMCP. Use this skill whenever the user asks to create, write, regenerate, update, or improve an MIE file for any RDF database (UniProt, ChEMBL, Reactome, Rhea, PubChem, MeSH, PDB, or any new bio/chem database…
Skill Claude CodeCodex
PRISM finds entities (genes, proteins, compounds) at the INTERSECTION of two or more property sets on RDF knowledge graphs via TogoMCP — e.g. "genes common to disease X and druggable pathway Y", "targets both linked to phenotype P and modulated by existing drugs". Use whenever the user asks a set-intersection /…
Skill Claude CodeCodex
Generate, refresh, or replace benchmark questions for the TogoMCP evaluation set (benchmark/questions/questionXXX.yaml). Use whenever the user asks to create, add, extend, refresh, re-validate, replace, redirect, or retire benchmark questions — e.g. "add a few benchmark questions", "extend the QA set", "we need more…
Skill Claude CodeCodex
Systematically validate a research article's claims against TogoMCP RDF databases — molecular formulas, reaction equations, pathways, protein function, GO definitions — instead of trusting the paper's text or keyword-search snippets. Use whenever the user asks to "analyze this paper/article", fact-check or validate a…
Instructions file
Instructions for dbcls/togomcp, covering togomcp, architecture, data layout, parameter conventions and return-shape and error conventions.