PubMed MCP Server

""" Tool definitions for PubMed MCP Server. This module contains the MCP tool schema definitions for all available tools in the PubMed server. """ from typing import Any, Dict, List TOOL_DEFINITIONS: List[Dict[str, Any]] = [ { "name": "search_pubmed", "description": ("Search PubMed for articles with advanced filtering options"), "inputSchema": { "type": "object", "properties": { "query": {"type": "string", "description": "Search query using PubMed syntax"}, "max_results": { "type": "integer", "minimum": 1, "maximum": 200, "default": 20, "description": "Maximum number of results to return", }, "sort_order": { "type": "string", "enum": ["relevance", "pub_date", "author", "journal", "title"], "default": "relevance", "description": "Sort order for results", }, "date_from": { "type": "string", "description": "Start date (YYYY/MM/DD, YYYY/MM, or YYYY)", }, "date_to": { "type": "string", "description": "End date (YYYY/MM/DD, YYYY/MM, or YYYY)", }, "date_range": { "type": "string", "enum": ["1y", "5y", "10y", "all"], "description": "Predefined date range", }, "article_types": { "type": "array", "items": { "type": "string", "enum": [ "Journal Article", "Review", "Systematic Review", "Meta-Analysis", "Clinical Trial", "Randomized Controlled Trial", "Case Reports", "Letter", "Editorial", "Comment", ], }, "description": "Filter by article types", }, "authors": { "type": "array", "items": {"type": "string"}, "description": "Filter by author names", }, "journals": { "type": "array", "items": {"type": "string"}, "description": "Filter by journal names", }, "mesh_terms": { "type": "array", "items": {"type": "string"}, "description": "Filter by MeSH terms", }, "language": { "type": "string", "description": ("Language filter (e.g., 'eng', 'fre', 'ger')"), }, "has_abstract": { "type": "boolean", "description": "Only include articles with abstracts", }, "has_full_text": { "type": "boolean", "description": ("Only include articles with full text available"), }, "humans_only": {"type": "boolean", "description": "Only include human studies"}, }, "required": ["query"], }, }, { "name": "get_article_details", "description": ("Get detailed information for specific articles by PMID"), "inputSchema": { "type": "object", "properties": { "pmids": { "type": "array", "items": {"type": "string"}, "description": "List of PubMed IDs", }, "include_abstracts": { "type": "boolean", "default": True, "description": "Include abstracts in response", }, "include_citations": { "type": "boolean", "default": False, "description": "Include citation count and metrics", }, }, "required": ["pmids"], }, }, { "name": "search_by_author", "description": "Search for articles by a specific author", "inputSchema": { "type": "object", "properties": { "author_name": {"type": "string", "description": "Author name to search for"}, "max_results": { "type": "integer", "minimum": 1, "maximum": 100, "default": 20, "description": "Maximum number of results", }, "include_coauthors": { "type": "boolean", "default": True, "description": "Include co-author information", }, }, "required": ["author_name"], }, }, { "name": "find_related_articles", "description": "Find articles related to a specific PMID", "inputSchema": { "type": "object", "properties": { "pmid": {"type": "string", "description": "PMID of the reference article"}, "max_results": { "type": "integer", "minimum": 1, "maximum": 50, "default": 10, "description": "Maximum number of related articles", }, }, "required": ["pmid"], }, }, { "name": "export_citations", "description": "Export article citations in various formats", "inputSchema": { "type": "object", "properties": { "pmids": { "type": "array", "items": {"type": "string"}, "description": "List of PubMed IDs to export", }, "format": { "type": "string", "enum": ["bibtex", "endnote", "ris", "apa", "mla", "chicago", "vancouver"], "default": "bibtex", "description": "Citation format", }, "include_abstracts": { "type": "boolean", "default": False, "description": "Include abstracts in citations", }, }, "required": ["pmids"], }, }, { "name": "search_mesh_terms", "description": ("Search and explore MeSH (Medical Subject Headings) terms"), "inputSchema": { "type": "object", "properties": { "term": {"type": "string", "description": "MeSH term to search for"}, "max_results": { "type": "integer", "minimum": 1, "maximum": 100, "default": 20, "description": "Maximum number of results", }, }, "required": ["term"], }, }, { "name": "search_by_journal", "description": "Search articles from a specific journal", "inputSchema": { "type": "object", "properties": { "journal_name": {"type": "string", "description": "Journal name or abbreviation"}, "max_results": { "type": "integer", "minimum": 1, "maximum": 100, "default": 20, "description": "Maximum number of results", }, "date_from": {"type": "string", "description": "Start date (YYYY/MM/DD)"}, "date_to": {"type": "string", "description": "End date (YYYY/MM/DD)"}, }, "required": ["journal_name"], }, }, { "name": "get_trending_topics", "description": "Get trending medical topics and research areas", "inputSchema": { "type": "object", "properties": { "category": { "type": "string", "description": ( "Medical category (e.g., 'cardiology', 'oncology', " "'neurology')" ), }, "days": { "type": "integer", "minimum": 1, "maximum": 30, "default": 7, "description": "Number of days to analyze for trends", }, }, }, }, { "name": "analyze_research_trends", "description": ("Analyze publication trends for a research topic over time"), "inputSchema": { "type": "object", "properties": { "topic": {"type": "string", "description": "Research topic to analyze"}, "years_back": { "type": "integer", "minimum": 1, "maximum": 20, "default": 5, "description": "Number of years to analyze", }, "include_subtopics": { "type": "boolean", "default": False, "description": "Include analysis of related subtopics", }, }, "required": ["topic"], }, }, { "name": "compare_articles", "description": "Compare multiple articles side by side", "inputSchema": { "type": "object", "properties": { "pmids": { "type": "array", "items": {"type": "string"}, "minItems": 2, "maxItems": 5, "description": "List of PMIDs to compare (2-5 articles)", }, "comparison_fields": { "type": "array", "items": { "type": "string", "enum": [ "authors", "methods", "results", "conclusions", "mesh_terms", "citations", ], }, "default": ["authors", "methods", "conclusions"], "description": "Fields to compare", }, }, "required": ["pmids"], }, }, { "name": "get_journal_metrics", "description": "Get metrics and information about a specific journal", "inputSchema": { "type": "object", "properties": { "journal_name": {"type": "string", "description": "Journal name or abbreviation"}, "include_recent_articles": { "type": "boolean", "default": True, "description": "Include recent notable articles", }, }, "required": ["journal_name"], }, }, { "name": "advanced_search", "description": ("Perform complex PubMed searches with multiple criteria"), "inputSchema": { "type": "object", "properties": { "search_terms": { "type": "array", "items": { "type": "object", "properties": { "term": {"type": "string"}, "field": { "type": "string", "enum": ["title", "abstract", "author", "journal", "mesh", "all"], }, "operator": {"type": "string", "enum": ["AND", "OR", "NOT"]}, }, "required": ["term", "field"], }, "description": ("Complex search criteria with fields and operators"), }, "filters": { "type": "object", "properties": { "publication_types": {"type": "array", "items": {"type": "string"}}, "species": {"type": "array", "items": {"type": "string"}}, "languages": {"type": "array", "items": {"type": "string"}}, "age_groups": {"type": "array", "items": {"type": "string"}}, "sex": {"type": "string", "enum": ["male", "female", "both"]}, }, "description": "Additional filters", }, "max_results": {"type": "integer", "minimum": 1, "maximum": 200, "default": 50}, }, "required": ["search_terms"], }, }, ]