WormBase MCP Server

#!/usr/bin/env node import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js"; import { z } from "zod"; import { WormBaseClient } from "./client.js"; import { ENTITY_TYPES, EntityType } from "./types.js"; const client = new WormBaseClient(); const server = new McpServer({ name: "wormbase", version: "0.1.0", }); // Tool: Search WormBase server.tool( "search", "Search WormBase for genes, proteins, phenotypes, strains, and other biological entities. Supports natural language queries like 'genes involved in longevity' or specific IDs like 'WBGene00006763'.", { query: z.string().describe("Search query - can be a gene name (e.g., 'daf-2', 'unc-13'), WormBase ID (e.g., 'WBGene00006763'), or natural language description"), type: z.enum(ENTITY_TYPES).optional().describe("Entity type to search for. If not specified, searches all types."), limit: z.number().optional().default(10).describe("Maximum number of results to return"), }, async ({ query, type, limit }) => { try { const results = await client.search(query, type, limit); return { content: [{ type: "text", text: JSON.stringify(results, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error searching WormBase: ${error}` }], isError: true, }; } } ); // Tool: Get Gene Information server.tool( "get_gene", "Get detailed information about a C. elegans gene including description, function, expression, phenotypes, and orthologs.", { id: z.string().describe("Gene identifier - WormBase ID (e.g., 'WBGene00006763') or gene name (e.g., 'daf-2', 'unc-13')"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, expression, phenotype, interactions, homology, sequences, genetics, external_links, references"), }, async ({ id, widgets }) => { try { const data = await client.getGene(id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching gene: ${error}` }], isError: true, }; } } ); // Tool: Get Protein Information server.tool( "get_protein", "Get detailed information about a protein including sequence, domains, motifs, and structure.", { id: z.string().describe("Protein identifier - WormBase protein ID"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, sequences, motif_details, external_links, references"), }, async ({ id, widgets }) => { try { const data = await client.getEntity("protein", id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching protein: ${error}` }], isError: true, }; } } ); // Tool: Get Phenotype Information server.tool( "get_phenotype", "Get detailed information about a phenotype including associated genes, RNAi experiments, and variations.", { id: z.string().describe("Phenotype identifier - WormBase phenotype ID (e.g., 'WBPhenotype:0000643')"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, rnai, variation, transgene, references"), }, async ({ id, widgets }) => { try { const data = await client.getEntity("phenotype", id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching phenotype: ${error}` }], isError: true, }; } } ); // Tool: Get Disease Information server.tool( "get_disease", "Get information about human diseases with C. elegans models, including associated genes and orthologs.", { id: z.string().describe("Disease identifier - DOID or WormBase disease ID"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, genes, references"), }, async ({ id, widgets }) => { try { const data = await client.getEntity("disease", id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching disease: ${error}` }], isError: true, }; } } ); // Tool: Get Strain Information server.tool( "get_strain", "Get information about a C. elegans strain including genotype, available from, and associated phenotypes.", { id: z.string().describe("Strain identifier - strain name (e.g., 'N2', 'CB1370')"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, phenotypes, references"), }, async ({ id, widgets }) => { try { const data = await client.getEntity("strain", id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching strain: ${error}` }], isError: true, }; } } ); // Tool: Get Variation/Allele Information server.tool( "get_variation", "Get information about a genetic variation/allele including molecular details, phenotypes, and strains.", { id: z.string().describe("Variation identifier - allele name (e.g., 'e1370') or WormBase variation ID"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch: overview, molecular_details, phenotypes, references"), }, async ({ id, widgets }) => { try { const data = await client.getEntity("variation", id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching variation: ${error}` }], isError: true, }; } } ); // Tool: Get Interactions server.tool( "get_interactions", "Get protein-protein, genetic, or regulatory interactions for a gene or protein.", { id: z.string().describe("Gene or protein identifier"), interaction_type: z.enum(["genetic", "physical", "regulatory", "all"]).optional().default("all").describe("Type of interactions to retrieve"), }, async ({ id, interaction_type }) => { try { const data = await client.getInteractions(id, interaction_type); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching interactions: ${error}` }], isError: true, }; } } ); // Tool: Get Expression Pattern server.tool( "get_expression", "Get expression pattern information for a gene including tissue/cell expression, life stage expression, and expression images.", { id: z.string().describe("Gene identifier"), }, async ({ id }) => { try { const data = await client.getExpression(id); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching expression: ${error}` }], isError: true, }; } } ); // Tool: Get GO Terms server.tool( "get_ontology", "Get Gene Ontology (GO) terms for a gene including molecular function, biological process, and cellular component annotations.", { id: z.string().describe("Gene identifier"), }, async ({ id }) => { try { const data = await client.getOntology(id); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching ontology: ${error}` }], isError: true, }; } } ); // Tool: Get Generic Entity server.tool( "get_entity", "Get information about any WormBase entity type. Use this for entity types not covered by specific tools.", { type: z.enum(ENTITY_TYPES).describe("Entity type"), id: z.string().describe("Entity identifier"), widgets: z.array(z.string()).optional().describe("Specific widgets to fetch"), }, async ({ type, id, widgets }) => { try { const data = await client.getEntity(type, id, widgets); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching entity: ${error}` }], isError: true, }; } } ); // Tool: Get Paper/Reference server.tool( "get_paper", "Get information about a scientific paper/publication including authors, abstract, and associated genes.", { id: z.string().describe("Paper identifier - WormBase paper ID (e.g., 'WBPaper00000001') or PubMed ID"), }, async ({ id }) => { try { const data = await client.getEntity("paper", id, ["overview", "referenced_genes"]); return { content: [{ type: "text", text: JSON.stringify(data, null, 2) }], }; } catch (error) { return { content: [{ type: "text", text: `Error fetching paper: ${error}` }], isError: true, }; } } ); // Resource: List available entity types server.resource( "entity-types", "wormbase://entity-types", async () => ({ contents: [{ uri: "wormbase://entity-types", mimeType: "application/json", text: JSON.stringify({ description: "Available WormBase entity types that can be queried", types: ENTITY_TYPES.map(t => ({ name: t, description: getEntityDescription(t), })), }, null, 2), }], }) ); function getEntityDescription(type: string): string { const descriptions: Record<string, string> = { gene: "Genes in C. elegans and related nematodes", protein: "Protein sequences and annotations", phenotype: "Observable characteristics and traits", disease: "Human diseases with nematode models", strain: "Laboratory strains and genetic backgrounds", variation: "Genetic variants and alleles", transgene: "Transgenic constructs", rnai: "RNAi experiments and results", anatomy_term: "Anatomical structures and cell types", life_stage: "Developmental stages", go_term: "Gene Ontology terms", interaction: "Molecular and genetic interactions", expression_cluster: "Co-expression clusters", paper: "Scientific publications", person: "Researchers in the field", laboratory: "Research laboratories", }; return descriptions[type] || `${type} entities in WormBase`; } // Start server async function main() { const transport = new StdioServerTransport(); await server.connect(transport); console.error("WormBase MCP server running on stdio"); } main().catch(console.error);