TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context...

Querying the RDF Portal knowledge graph maintained by DBCLS-which aggregates ~60 life-science databases-requires proficiency in both SPARQL and database-specific RDF schemas, placing this resource beyond the reach of most researchers. Large Language Models (LLMs) can, in principle, translate natural-language questions into executable SPARQL, but without schema-level context, they frequently fabricate non-existent predicates or fail to resolve entity names to database-specific identifiers. We present TogoMCP, a system that recasts the LLM as a protocol-driven inference engine orchestrating specialized tools via the Model Context Protocol (MCP). Two mechanisms are essential to its design: (i) the MIE (Metadata-Interoperability-Exchange) file, a concise YAML document that dynamically supplies the LLM with each target database's structural and semantic context at query time; and (ii) a two-stage workflow separating entity resolution via external REST APIs from schema-guided SPARQL generation. On a benchmark of 50 biologically grounded questions spanning five types and 23 databases, TogoMCP achieved a large improvement over an unaided baseline (Cohen's $d = 1.82$, Wilcoxon $P \lt .001$), with win rates exceeding 80% for question types with precise, verifiable answers. An ablation study shows that all component configurations deliver significant improvements, with MIE schema files providing the largest marginal contribution on mean per-question score ($\Delta = +0.50$ relative to a no-MIE condition, two-sided Wilcoxon $P = .067$; 90% bootstrap CI $[+0.04,\,\,+0.94]$ excludes zero); a one-line instruction to load the relevant MIE file recovers the same mean improvement as a full procedural protocol, while the protocol additionally reduces downside risk (loss rate 1.6% vs. 4.8%, Fisher $P = .036$). These results suggest a general design principle: concise, dynamically delivered schema context is more valuable than complex orchestration logic for mean score performance, while procedural guidance plays a complementary role in narrowing variance. Database URL:  https://togomcp.rdfportal.org/.