#!/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 { AllianceClient } from "./client.js";
import { ENTITY_TYPES, EntityType, SPECIES } from "./types.js";
const client = new AllianceClient();
const server = new McpServer({
name: "agr-genomics",
version: "4.0.0",
});
// Tool: Search genes
server.tool(
"search_genes",
"Search for genes across all Alliance of Genome Resources model organisms. Supports species filtering.",
{
query: z
.string()
.describe(
"Search query - gene symbol (e.g., 'BRCA1', 'daf-2'), name, or keyword"
),
species: z
.string()
.optional()
.describe(
"Filter by species: human, mouse, rat, zebrafish, fly, worm, yeast, frog, or full name like 'Homo sapiens'"
),
limit: z
.number()
.optional()
.default(20)
.describe("Maximum number of results to return"),
},
async ({ query, species, limit }) => {
try {
const results = await client.search(query, "gene", species, limit);
return {
content: [{ type: "text", text: JSON.stringify(results, null, 2) }],
};
} catch (error) {
return {
content: [{ type: "text", text: `Error searching genes: ${error}` }],
isError: true,
};
}
}
);
// Tool: Get Gene Info
server.tool(
"get_gene_info",
"Get detailed information about a specific gene including symbol, name, location, species, and cross-references.",
{
gene_id: z
.string()
.describe(
"Gene identifier - e.g., 'HGNC:1100' (human BRCA1), 'MGI:95892' (mouse), 'ZFIN:ZDB-GENE-990415-72'"
),
},
async ({ gene_id }) => {
try {
const data = await client.getGene(gene_id);
if (!data) {
return {
content: [{ type: "text", text: `Gene not found: ${gene_id}` }],
isError: true,
};
}
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 Gene Diseases
server.tool(
"get_gene_diseases",
"Get disease associations for a gene, including human disease models and annotations.",
{
gene_id: z.string().describe("Gene identifier"),
limit: z.number().optional().default(100).describe("Maximum results"),
},
async ({ gene_id, limit }) => {
try {
const data = await client.getGeneDiseases(gene_id, limit);
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [{ type: "text", text: `Error fetching diseases: ${error}` }],
isError: true,
};
}
}
);
// Tool: Search Diseases
server.tool(
"search_diseases",
"Search for diseases in the Alliance database.",
{
query: z
.string()
.describe("Disease name or keyword (e.g., 'breast cancer', 'diabetes')"),
limit: z.number().optional().default(20).describe("Maximum results"),
},
async ({ query, limit }) => {
try {
const results = await client.searchDiseases(query, limit);
return {
content: [{ type: "text", text: JSON.stringify(results, null, 2) }],
};
} catch (error) {
return {
content: [
{ type: "text", text: `Error searching diseases: ${error}` },
],
isError: true,
};
}
}
);
// Tool: Get Gene Expression
server.tool(
"get_gene_expression",
"Get expression data for a gene including tissue/cell type expression and developmental stages.",
{
gene_id: z.string().describe("Gene identifier"),
limit: z.number().optional().default(100).describe("Maximum results"),
},
async ({ gene_id, limit }) => {
try {
const data = await client.getGeneExpression(gene_id, limit);
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [
{ type: "text", text: `Error fetching expression: ${error}` },
],
isError: true,
};
}
}
);
// Tool: Find Orthologs
server.tool(
"find_orthologs",
"Find orthologous genes across species. Returns homologs from all Alliance model organisms.",
{
gene_id: z.string().describe("Gene identifier"),
},
async ({ gene_id }) => {
try {
const data = await client.getOrthologs(gene_id);
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [
{ type: "text", text: `Error fetching orthologs: ${error}` },
],
isError: true,
};
}
}
);
// Tool: Get Gene Phenotypes
server.tool(
"get_gene_phenotypes",
"Get phenotype annotations for a gene.",
{
gene_id: z.string().describe("Gene identifier"),
limit: z.number().optional().default(100).describe("Maximum results"),
},
async ({ gene_id, limit }) => {
try {
const data = await client.getGenePhenotypes(gene_id, limit);
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [
{ type: "text", text: `Error fetching phenotypes: ${error}` },
],
isError: true,
};
}
}
);
// Tool: Get Gene Interactions
server.tool(
"get_gene_interactions",
"Get molecular and genetic interactions for a gene.",
{
gene_id: z.string().describe("Gene identifier"),
limit: z.number().optional().default(100).describe("Maximum results"),
},
async ({ gene_id, limit }) => {
try {
const data = await client.getGeneInteractions(gene_id, limit);
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 Gene Alleles
server.tool(
"get_gene_alleles",
"Get alleles/variants associated with a gene.",
{
gene_id: z.string().describe("Gene identifier"),
limit: z.number().optional().default(100).describe("Maximum results"),
},
async ({ gene_id, limit }) => {
try {
const data = await client.getGeneAlleles(gene_id, limit);
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [{ type: "text", text: `Error fetching alleles: ${error}` }],
isError: true,
};
}
}
);
// Tool: Search Alleles
server.tool(
"search_alleles",
"Search for alleles/variants in the Alliance database.",
{
query: z.string().describe("Allele name or keyword"),
limit: z.number().optional().default(20).describe("Maximum results"),
},
async ({ query, limit }) => {
try {
const results = await client.searchAlleles(query, limit);
return {
content: [{ type: "text", text: JSON.stringify(results, null, 2) }],
};
} catch (error) {
return {
content: [{ type: "text", text: `Error searching alleles: ${error}` }],
isError: true,
};
}
}
);
// Tool: Get Species List
server.tool(
"get_species_list",
"Get list of model organisms supported by Alliance of Genome Resources.",
{},
async () => {
try {
const data = await client.getSpeciesList();
return {
content: [{ type: "text", text: JSON.stringify(data, null, 2) }],
};
} catch (error) {
return {
content: [
{ type: "text", text: `Error fetching species list: ${error}` },
],
isError: true,
};
}
}
);
// Resource: Entity types
server.resource("entity-types", "agr://entity-types", async () => ({
contents: [
{
uri: "agr://entity-types",
mimeType: "application/json",
text: JSON.stringify(
{
description: "Entity types available in Alliance of Genome Resources",
types: ENTITY_TYPES.map((t) => ({
name: t,
description: getEntityDescription(t),
})),
},
null,
2
),
},
],
}));
// Resource: Species
server.resource("species", "agr://species", async () => {
const data = await client.getSpeciesList();
return {
contents: [
{
uri: "agr://species",
mimeType: "application/json",
text: JSON.stringify(data, null, 2),
},
],
};
});
function getEntityDescription(type: EntityType): string {
const descriptions: Record<EntityType, string> = {
gene: "Genes across all model organisms",
allele: "Genetic variants and alleles",
disease: "Human diseases and disease models",
phenotype: "Observable characteristics and traits",
expression: "Gene expression data",
orthology: "Cross-species ortholog relationships",
interaction: "Molecular and genetic interactions",
variant: "Sequence variants",
transgenic_allele: "Transgenic constructs",
construct: "Molecular constructs",
affected_genomic_model: "Animal models with genetic modifications",
go_term: "Gene Ontology terms",
do_term: "Disease Ontology terms",
publication: "Scientific publications",
};
return descriptions[type] || `${type} entities`;
}
// Start server
async function main() {
const transport = new StdioServerTransport();
await server.connect(transport);
console.error("AGR Genomics MCP server running on stdio");
}
main().catch(console.error);
