WormBase MCP Server

import { EntityType, SearchResponse, EntityData, InteractionData } from "./types.js"; const BASE_URL = "http://rest.wormbase.org"; const WORMMINE_URL = "https://wormmine.alliancegenome.org/wormmine/service"; export class WormBaseClient { private baseUrl: string; private wormmineUrl: string; constructor(baseUrl?: string) { this.baseUrl = baseUrl || BASE_URL; this.wormmineUrl = WORMMINE_URL; } private async fetch<T>(url: string): Promise<T> { const response = await fetch(url, { headers: { "Accept": "application/json", "Accept-Language": "en-US,en;q=0.9", "User-Agent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36", "Sec-Fetch-Dest": "empty", "Sec-Fetch-Mode": "cors", "Sec-Fetch-Site": "cross-site", }, }); if (!response.ok) { throw new Error(`HTTP ${response.status}: ${response.statusText}`); } return response.json() as Promise<T>; } /** * Search WormBase using WormMine */ async search( query: string, type?: EntityType, limit: number = 10 ): Promise<SearchResponse> { const url = `${this.wormmineUrl}/search?q=${encodeURIComponent(query)}&size=${limit}`; try { const response = await this.fetch<any>(url); const results = this.parseWormMineResults(response, type, limit); return { query, results, total: response.totalHits || results.length, }; } catch (error) { return { query, results: [], total: 0 }; } } /** * Resolve gene name to WBGene ID using WormMine */ async resolveGeneId(name: string): Promise<string | null> { const url = `${this.wormmineUrl}/search?q=${encodeURIComponent(name)}&facet_Category=Gene&size=1`; try { const response = await this.fetch<any>(url); if (response.results?.[0]?.fields?.primaryIdentifier) { return response.results[0].fields.primaryIdentifier; } } catch { // Fall through } return null; } /** * Get detailed gene information */ async getGene( id: string, widgets?: string[] ): Promise<Record<string, unknown>> { // Resolve gene name to WBGene ID if needed let geneId = id; if (!id.startsWith("WBGene")) { const resolved = await this.resolveGeneId(id); if (resolved) { geneId = resolved; } } const defaultWidgets = ["overview", "phenotype", "expression", "ontology"]; const requestedWidgets = widgets || defaultWidgets; const result: Record<string, unknown> = { id: geneId, query: id }; for (const widget of requestedWidgets) { try { const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(geneId)}/${widget}`; const data = await this.fetch<any>(url); result[widget] = this.cleanWidgetData(data); } catch (error) { result[widget] = { error: `Failed to fetch ${widget}` }; } } return result; } /** * Get any entity by type and ID */ async getEntity( type: EntityType, id: string, widgets?: string[] ): Promise<Record<string, unknown>> { const defaultWidgets = ["overview"]; const requestedWidgets = widgets || defaultWidgets; const result: Record<string, unknown> = { id, type }; for (const widget of requestedWidgets) { try { const url = `${this.baseUrl}/rest/widget/${type}/${encodeURIComponent(id)}/${widget}`; const data = await this.fetch<any>(url); result[widget] = this.cleanWidgetData(data); } catch (error) { result[widget] = { error: `Failed to fetch ${widget}` }; } } return result; } /** * Get interactions for a gene */ async getInteractions( id: string, interactionType: string = "all" ): Promise<InteractionData> { const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(id)}/interactions`; const data = await this.fetch<any>(url); const interactions = this.cleanWidgetData(data); if (interactionType === "all") { return interactions as InteractionData; } // Filter by interaction type const filtered: Record<string, unknown> = {}; const interactionsObj = interactions as Record<string, unknown>; if (interactionType === "physical" && interactionsObj.physical) { filtered.physical = interactionsObj.physical; } if (interactionType === "genetic" && interactionsObj.genetic) { filtered.genetic = interactionsObj.genetic; } if (interactionType === "regulatory" && interactionsObj.regulatory) { filtered.regulatory = interactionsObj.regulatory; } return filtered as InteractionData; } /** * Get expression data for a gene */ async getExpression(id: string): Promise<Record<string, unknown>> { const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(id)}/expression`; const data = await this.fetch<any>(url); return this.cleanWidgetData(data); } /** * Get ontology annotations for a gene */ async getOntology(id: string): Promise<Record<string, unknown>> { const url = `${this.baseUrl}/rest/widget/gene/${encodeURIComponent(id)}/ontology`; const data = await this.fetch<any>(url); return this.cleanWidgetData(data); } /** * Get field data for an entity */ async getField( type: EntityType, id: string, field: string ): Promise<unknown> { const url = `${this.baseUrl}/rest/field/${type}/${encodeURIComponent(id)}/${field}`; const data = await this.fetch<any>(url); return data[field] || data; } // Helper methods private parseWormMineResults( response: any, type: EntityType | undefined, limit: number ): Array<{ id: string; label: string; class: string; taxonomy?: string; description?: string; }> { if (!response?.results) return []; let results = response.results; // Filter by type if specified if (type) { const typeMap: Record<string, string> = { gene: "Gene", protein: "Protein", strain: "Strain", variation: "Allele", rnai: "RNAi", phenotype: "Phenotype", }; const mappedType = typeMap[type] || type; results = results.filter((r: any) => r.type === mappedType); } return results.slice(0, limit).map((hit: any) => ({ id: hit.fields?.primaryIdentifier || hit.fields?.secondaryIdentifier || String(hit.id), label: hit.fields?.symbol || hit.fields?.name || hit.fields?.primaryIdentifier || "", class: hit.type?.toLowerCase() || "", taxonomy: hit.fields?.["organism.name"] || "", description: hit.fields?.briefDescription || "", })); } private cleanWidgetData(data: any): Record<string, unknown> { if (!data) return {}; // The API typically wraps data in a "fields" object const fields = data.fields || data; // Clean and simplify the data structure const cleaned: Record<string, unknown> = {}; for (const [key, value] of Object.entries(fields)) { if (value === null || value === undefined) continue; // Handle nested data structures if (typeof value === "object" && value !== null) { const obj = value as Record<string, unknown>; if ("data" in obj) { cleaned[key] = obj.data; } else if ("id" in obj && "label" in obj) { // Entity reference cleaned[key] = { id: obj.id, label: obj.label, class: obj.class || obj.taxonomy, }; } else { cleaned[key] = this.simplifyValue(value); } } else { cleaned[key] = value; } } return cleaned; } private simplifyValue(value: unknown): unknown { if (Array.isArray(value)) { return value.map(v => this.simplifyValue(v)); } if (typeof value === "object" && value !== null) { const obj = value as Record<string, unknown>; // Handle entity references if ("id" in obj && "label" in obj) { return { id: obj.id, label: obj.label, class: obj.class, }; } // Handle data wrapper if ("data" in obj && Object.keys(obj).length <= 2) { return this.simplifyValue(obj.data); } // Recursively simplify nested objects const simplified: Record<string, unknown> = {}; for (const [k, v] of Object.entries(obj)) { if (v !== null && v !== undefined) { simplified[k] = this.simplifyValue(v); } } return simplified; } return value; } private extractLabel(overview: any): string | null { if (typeof overview === "object" && overview !== null) { const obj = overview as Record<string, any>; return obj.name?.label || obj.name?.data?.label || obj.label || null; } return null; } private extractDescription(overview: any): string | undefined { if (typeof overview === "object" && overview !== null) { const obj = overview as Record<string, any>; return obj.description?.data || obj.concise_description?.data || obj.description || obj.concise_description; } return undefined; } }