get_variation
Retrieve genetic variation details including molecular information, phenotypes, and associated strains from the WormBase database for C. elegans research.
Instructions
Get information about a genetic variation/allele including molecular details, phenotypes, and strains.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| id | Yes | Variation identifier - allele name (e.g., 'e1370') or WormBase variation ID | |
| widgets | No | Specific widgets to fetch: overview, molecular_details, phenotypes, references |
Implementation Reference
- src/index.ts:156-176 (registration)Registration of the MCP 'get_variation' tool. Includes tool name, description, input schema (Zod validation for 'id' and optional 'widgets'), and inline handler that fetches data via WormBaseClient.getEntity('variation', ...) and returns JSON or error.
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: ${error}` }], isError: true, }; } } ); - src/client.ts:111-132 (handler)Core handler logic in WormBaseClient.getEntity(), called by get_variation tool with type='variation'. Fetches data from WormBase REST API endpoints for specified widgets, cleans the data, and handles errors per widget.
async getEntity( type: EntityType, id: string, widgets?: string[] ): Promise<Record<string, unknown>> { const defaultWidgets = ["overview"]; const requestedWidgets = widgets || defaultWidgets; const result: Record<string, unknown> = { id, type }; for (const widget of requestedWidgets) { try { const url = `${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/index.ts:159-162 (schema)Zod input schema specific to get_variation tool: required 'id' string, optional 'widgets' array.
{ 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"), }, - src/types.ts:1-43 (helper)EntityType union includes 'variation', used in getEntity type parameter and schema validation.
// WormBase entity types 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;