ITIS MCP Server

import { Server } from '@modelcontextprotocol/sdk/server/index.js'; import { ListPromptsRequestSchema, GetPromptRequestSchema, Prompt, } from '@modelcontextprotocol/sdk/types.js'; // Define the prompts export const prompts: Prompt[] = [ { name: 'complete_taxonomy_profile', description: 'Build a complete taxonomic profile for any organism including hierarchy, related species, and classification details', arguments: [ { name: 'organism_name', description: 'Scientific name of the organism to profile', required: true } ] }, { name: 'compare_species_relationships', description: 'Compare the taxonomic relationships between multiple species to understand their connections', arguments: [ { name: 'species_list', description: 'Comma-separated list of scientific names to compare', required: true } ] }, { name: 'biodiversity_survey', description: 'Conduct a biodiversity survey of a specific taxonomic group to understand species diversity and distribution', arguments: [ { name: 'taxonomic_group', description: 'The taxonomic group to survey (kingdom, phylum, class, order, family, or genus)', required: true }, { name: 'group_name', description: 'Name of the specific taxonomic group', required: true }, { name: 'sample_size', description: 'Number of species to include in detailed analysis (default: 20)', required: false } ] }, { name: 'taxonomic_verification_audit', description: 'Verify and audit a list of scientific names for taxonomic accuracy and current classification status', arguments: [ { name: 'names_to_verify', description: 'Comma-separated list of scientific names to verify', required: true } ] }, { name: 'taxonomy_teaching_module', description: 'Create educational content demonstrating taxonomic principles using real organism examples', arguments: [ { name: 'education_level', description: 'Target education level: elementary, middle_school, high_school, undergraduate, graduate', required: true }, { name: 'concept_focus', description: 'Specific concept to teach: hierarchy, classification, binomial_nomenclature, evolution, biodiversity', required: true } ] }, { name: 'random_creature_discovery', description: 'Intelligently discover random creatures based on free-form descriptions or terms', arguments: [ { name: 'creature_type', description: 'Free-form description of creatures to discover (e.g., "big cats", "birds of prey", "sea turtles", "poisonous plants", "deep sea fish")', required: true }, { name: 'count', description: 'Number of creatures to discover (default: 3)', required: false }, { name: 'focus_area', description: 'Optional additional focus or constraint (e.g., "tropical", "endangered", "large species")', required: false } ] }, ]; export function setupPromptHandlers(server: Server) { // List available prompts server.setRequestHandler(ListPromptsRequestSchema, async () => { return { prompts, }; }); // Handle prompt requests server.setRequestHandler(GetPromptRequestSchema, async (request) => { const { name, arguments: args } = request.params; switch (name) { case 'complete_taxonomy_profile': { const organismName = args?.organism_name || 'Homo sapiens'; return { messages: [ { role: 'user', content: { type: 'text', text: `I need to build a complete taxonomic profile for ${organismName}. Please: 1. First, try search_by_scientific_name to find the organism. If not found, try search_by_vernacular_name in case it's a common name 2. Use get_hierarchy to retrieve the complete taxonomic hierarchy from Kingdom to Species 3. Use explore_taxonomy with level 'siblings' to find other species in the same genus (results will include vernacular names where available) 4. Use explore_taxonomy with level 'family' to find other species in the same family (results will include vernacular names where available) 5. Present the information in a structured format showing: - Basic organism details (TSN, scientific name, rank, common names) - Complete taxonomic hierarchy - Related species at genus level (with common names where available) - Related species at family level (with common names where available) - Summary of taxonomic relationships Format the response as a comprehensive taxonomic report.` } } ] }; } case 'compare_species_relationships': { const speciesList = args?.species_list || 'Homo sapiens, Pan troglodytes'; return { messages: [ { role: 'user', content: { type: 'text', text: `I need to compare the taxonomic relationships between these species: ${speciesList}. Please: 1. For each species in the list, use search_by_scientific_name to get basic taxonomic information 2. For each species, use get_hierarchy to get the complete taxonomic classification 3. Analyze the hierarchies to identify: - Shared taxonomic levels (where they diverge in classification) - Common ancestors at different taxonomic ranks - Degree of relatedness 4. Present a comparative analysis showing: - Side-by-side taxonomic classifications - Evolutionary relationships and divergence points - Shared taxonomic groups - Summary of how closely related these species are Format as a comparative taxonomic analysis with clear relationship mappings.` } } ] }; } case 'biodiversity_survey': { const taxonomicGroup = args?.taxonomic_group || 'kingdom'; const groupName = args?.group_name || 'Animalia'; const sampleSize = args?.sample_size || '20'; return { messages: [ { role: 'user', content: { type: 'text', text: `I need to conduct a biodiversity survey of ${taxonomicGroup} ${groupName}. Please: 1. Use the appropriate search tool (search_by_kingdom, search_by_rank, or search_itis with filters) to get an overview of species in this group 2. Get statistics on total number of species using get_statistics or targeted searches 3. Sample ${sampleSize} representative species and for each: - Get detailed taxonomic information - Retrieve hierarchical classification 4. Analyze patterns in the data: - Diversity at different taxonomic levels - Representative families/genera - Distribution across higher taxonomic groups 5. Present findings as: - Executive summary of biodiversity - Statistical overview - Representative species profiles - Taxonomic diversity analysis - Conservation implications if relevant Format as a scientific biodiversity assessment report.` } } ] }; } case 'taxonomic_verification_audit': { const namesToVerify = args?.names_to_verify || 'Homo sapiens, Tyrannosaurus rex'; return { messages: [ { role: 'user', content: { type: 'text', text: `I need to verify the taxonomic accuracy of these names: ${namesToVerify}. Please: 1. For each name, first try search_by_scientific_name. If not found, try search_by_vernacular_name in case it's a common name 2. For valid names, use get_hierarchy to confirm current taxonomic classification 3. Use autocomplete_search with partial names to find potential alternatives for invalid names 4. For each name, determine: - Validity status (valid/invalid/uncertain) - Current accepted classification - TSN (Taxonomic Serial Number) - Common names (vernacular names) where available - Potential synonyms or alternatives 5. Present results as: - Summary table of verification results - Detailed findings for each name (including common names) - Recommendations for invalid names - Standard reference format for valid names Format as a taxonomic verification report with clear recommendations.` } } ] }; } case 'taxonomy_teaching_module': { const educationLevel = args?.education_level || 'high_school'; const conceptFocus = args?.concept_focus || 'hierarchy'; return { messages: [ { role: 'user', content: { type: 'text', text: `I need to create educational content about ${conceptFocus} for ${educationLevel} students. Please: 1. Select appropriate example organisms based on education level (familiar species for lower levels, diverse examples for higher levels) 2. Use search_by_scientific_name and get_hierarchy to get complete taxonomic information for examples 3. Use explore_taxonomy to find related species that illustrate key concepts 4. For ${conceptFocus}, develop: - Clear explanations with real examples - Progressive complexity appropriate to level - Interactive elements using the data - Assessment questions 5. Present as: - Structured lesson plan - Example organism profiles - Activities and exercises - Assessment materials - Extension activities Format as a complete educational module with engaging, level-appropriate content.` } } ] }; } case 'random_creature_discovery': { const creatureType = args?.creature_type || 'any'; const count = args?.count || '3'; const focusArea = args?.focus_area || ''; return { messages: [ { role: 'user', content: { type: 'text', text: `I want to discover ${count} random creatures related to "${creatureType}"${focusArea ? ` with focus on "${focusArea}"` : ''}. Please help me find these creatures intelligently: **Step 1: Understand the Request** First, interpret what "${creatureType}" means: - If it's a general term like "big cat", "bird of prey", "sea turtle", etc., use search_by_vernacular_name or search_itis to find relevant species and identify their taxonomic characteristics - If it's already a taxonomic term like "Mammalia" or "Carnivora", use that directly - If it's a specific species name, find related species in the same taxonomic group **Step 2: Determine Search Strategy** Based on your understanding, decide the best approach: - Use search_by_vernacular_name if the term is likely a common name - Use search_itis with appropriate queries to find taxonomic patterns - Use autocomplete_search if you need to explore partial matches **Step 3: Extract Taxonomic Context** From your search results, identify: - What kingdom, phylum, class, order, family, or genus these creatures belong to - What taxonomic filters would capture similar creatures **Step 4: Get Random Species** Use get_random_species with the taxonomic filters you discovered: - Set appropriate kingdom, class, order, family, or genus filters based on Step 3 - Set count to ${count} - Set requireVernacular to true for better results **Step 5: Present Results** For each creature discovered, provide: - Scientific name and common names - Brief description of what makes this species interesting - How it relates to the original "${creatureType}" request - Habitat and distribution information if available - Fun facts or unique characteristics - Taxonomic classification context **Example Process:** If user asks for "big cats": 1. Search for "big cat" to understand it refers to large felids 2. Discover these are typically in family Felidae, subfamily Pantherinae 3. Use get_random_species with family="Felidae" and appropriate size/genus filters 4. Present results explaining how each species fits the "big cat" concept Make this an intelligent, educational discovery process that adapts to any creature type request!` } } ] }; } default: throw new Error(`Unknown prompt: ${name}`); } }); }