WormBase MCP Server

Instructions

Implementation Reference

• src/index.ts:110-130 (registration)

  Registers the 'get_disease' MCP tool with input schema (id, optional widgets) and handler that fetches data using WormBaseClient.getEntity for disease entities.
  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, }; } } );
• src/client.ts:111-132 (handler)

  Core handler logic for fetching WormBase entity data (used by get_disease with type='disease') via REST API widget endpoints, aggregating multiple widgets.
  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; }
• src/client.ts:237-305 (helper)

  Helper function cleanWidgetData used by getEntity to process and simplify raw API responses from WormBase.
  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; }
• src/types.ts:2-43 (schema)

  Type definitions including ENTITY_TYPES const array which includes 'disease', used in getEntity type parameter.
  export const ENTITY_TYPES = [ "gene", "protein", "transcript", "cds", "pseudogene", "phenotype", "disease", "strain", "variation", "transgene", "rnai", "anatomy_term", "life_stage", "go_term", "interaction", "expression_cluster", "expr_pattern", "paper", "person", "laboratory", "clone", "sequence", "feature", "operon", "gene_class", "molecule", "antibody", "construct", "motif", "homology_group", "rearrangement", "transposon", "transposon_family", "pcr_oligo", "position_matrix", "microarray_results", "structure_data", "analysis", "gene_cluster", "expr_profile", ] as const;