list_species
Retrieve available species and genome assemblies from Ensembl's genomic database to identify organisms for biological research and data analysis.
Instructions
Get list of available species and assemblies
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| division | No | Ensembl division (e.g., vertebrates, plants, fungi) |
Implementation Reference
- src/index.ts:1501-1522 (handler)The handler function that implements the list_species tool. It makes a GET request to the Ensembl REST API '/info/species' endpoint, optionally filtering by division, and returns the JSON response containing available species and assemblies.
private async handleListSpecies(args: any) { try { const params: any = {}; if (args.division) { params.division = args.division; } const response = await this.apiClient.get('/info/species', { params }); return { content: [ { type: 'text', text: JSON.stringify(response.data, null, 2), }, ], }; } catch (error) { return this.handleError(error, 'listing species'); } } - src/index.ts:869-870 (registration)Registration of the list_species tool handler in the CallToolRequestSchema switch statement.
case 'list_species': return this.handleListSpecies(args); - src/index.ts:765-775 (schema)Tool schema definition including name, description, and input schema (optional division parameter) registered in ListToolsRequestSchema response.
// Species & Assembly Information { name: 'list_species', description: 'Get list of available species and assemblies', inputSchema: { type: 'object', properties: { division: { type: 'string', description: 'Ensembl division (e.g., vertebrates, plants, fungi)' }, }, required: [], }, - src/index.ts:108-117 (schema)TypeScript interface defining the structure of Ensembl species data returned by the list_species tool.
interface EnsemblSpecies { name: string; display_name: string; taxonomy_id: number; assembly: string; release: number; division: string; strain?: string; strain_collection?: string; }