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Augmented-NatureMCP SERVER

Unofficial Reactome MCP Server

Search Reactome pathways and read their participants, reactions, hierarchy and protein interactions — gene-first or disease-first.

by Augmented-Nature ↗Biomedical: Genomics & Clinical DataCommunity

LABSCO SUMMARY

Enter by gene or by disease, then walk the pathway down.

The two entry tools are what make this useful in a conversation: you rarely know a Reactome stable id, you know a gene symbol or a disease name. From there the hierarchy, participants, reactions and interaction tools let the model descend without you translating identifiers by hand. It is unofficial — a community wrapper over Reactome's public service, not a Reactome product.

What it is

An unofficial MCP server over the Reactome Content Service, the curated pathway and systems-biology database. It answers the questions a researcher actually starts from — which pathways contain this gene, which pathways relate to this disease — and then lets you descend into a pathway's molecules, reactions and interaction network by its stable identifier.

What you get

  • Pathways found by name, description or keyword, optionally narrowed to pathway, reaction, protein, complex or disease — search_pathways
  • One pathway's full record by its Reactome stable identifier — get_pathway_details
  • Every pathway containing a gene symbol or UniProt ID, with species selectable and human as the default — find_pathways_by_gene
  • Disease-associated pathways by disease name or DOID identifier — find_pathways_by_disease
  • A pathway's parent and child structure, so you can see where it sits — get_pathway_hierarchy
  • All molecules participating in a pathway, and all biochemical reactions within it — get_pathway_participants, get_pathway_reactions
  • Protein-protein interactions within a pathway, filterable to protein-protein, regulatory, catalysis or all — get_protein_interactions
  • Resource templates for direct addressing: reactome://pathway/{id}, reactome://reaction/{id}, reactome://protein/{id}, reactome://disease/{id}, reactome://search/{query}

Requirements

No account and no key — the Reactome Content Service at https://reactome.org/ContentService requires no authentication and its limits are described as generous for research use. Build it yourself: npm install, npm run build, then point your client at build/index.js. Calls carry a 30s timeout.

Setup effort

Build from source

See installation options