Adaptive Graph of Thoughts MCP Server

runtime: "container" build: dockerfile: "Dockerfile" dockerBuildPath: "." startCommand: type: "http" containerPort: 8000 healthCheckPath: "/health" mcpEndpoint: "/mcp" command: - "/entrypoint.sh" - "http" # Main configuration schema for the server configSchema: type: "object" properties: NEO4J_URI: type: "string" description: "Neo4j connection URI (bolt://host:port)" default: "bolt://neo4j:7687" NEO4J_USER: type: "string" description: "Neo4j username" default: "neo4j" NEO4J_PASSWORD: type: "string" description: "Neo4j password" default: "password" NEO4J_DATABASE: type: "string" description: "Neo4j database name" default: "neo4j" ENABLE_EVIDENCE_SOURCES: type: "boolean" description: "Enable external evidence sources (PubMed, Google Scholar, Exa Search)" default: true MAX_REASONING_DEPTH: type: "integer" description: "Maximum reasoning depth for graph analysis (1-10)" default: 5 minimum: 1 maximum: 10 CONFIDENCE_THRESHOLD: type: "number" description: "Minimum confidence threshold for results (0.0-1.0)" default: 0.7 minimum: 0.0 maximum: 1.0 LOG_LEVEL: type: "string" description: "Logging level" enum: ["DEBUG", "INFO", "WARNING", "ERROR"] default: "INFO" BASIC_AUTH_USER: type: "string" description: "Admin dashboard username (optional)" default: "admin" BASIC_AUTH_PASS: type: "string" description: "Admin dashboard password (optional)" default: "changeme" PORT: type: "integer" description: "HTTP server port" default: 8000 required: - NEO4J_URI - NEO4J_USER - NEO4J_PASSWORD exampleConfig: NEO4J_URI: "bolt://neo4j:7687" NEO4J_USER: "neo4j" NEO4J_PASSWORD: "password" NEO4J_DATABASE: "neo4j" ENABLE_EVIDENCE_SOURCES: true MAX_REASONING_DEPTH: 5 CONFIDENCE_THRESHOLD: 0.7 LOG_LEVEL: "INFO" PORT: 8000 # MCP Tools Definition - This is what Smithery uses to display available tools tools: - name: "scientific_reasoning_query" description: "Perform advanced scientific reasoning using the Adaptive Graph of Thoughts framework. Analyzes complex scientific questions through graph-based reasoning with multi-dimensional confidence scoring." inputSchema: type: "object" properties: query: type: "string" description: "The scientific question or research query to analyze" maxLength: 2000 include_reasoning_trace: type: "boolean" description: "Include detailed step-by-step reasoning trace in the response" default: true include_graph_state: type: "boolean" description: "Include the full graph state representation in the response" default: true max_nodes_in_response_graph: type: "integer" description: "Maximum number of nodes to include in response graph visualization" default: 50 minimum: 0 maximum: 1000 output_detail_level: type: "string" description: "Level of detail in the output response" enum: ["summary", "detailed"] default: "summary" session_id: type: "string" description: "Optional session ID for tracking related queries" required: ["query"] - name: "analyze_research_hypothesis" description: "Analyze and evaluate research hypotheses using graph-based reasoning with confidence scoring and evidence integration from scientific databases (PubMed, Google Scholar)." inputSchema: type: "object" properties: hypothesis: type: "string" description: "The research hypothesis to analyze and evaluate" research_domain: type: "string" description: "The scientific domain or field of research (e.g., 'cancer biology', 'microbiome research', 'neuroscience')" evidence_sources: type: "array" items: type: "string" enum: ["pubmed", "google_scholar", "exa_search"] description: "External evidence sources to query for supporting/contradicting evidence" default: ["pubmed", "google_scholar"] confidence_threshold: type: "number" description: "Minimum confidence threshold for evidence evaluation (0.0-1.0)" default: 0.7 minimum: 0.0 maximum: 1.0 required: ["hypothesis"] - name: "explore_scientific_relationships" description: "Explore and map relationships between scientific concepts, entities, or phenomena using advanced graph-based analysis. Ideal for understanding complex interdisciplinary connections." inputSchema: type: "object" properties: primary_concept: type: "string" description: "The primary scientific concept to explore" related_concepts: type: "array" items: type: "string" description: "List of related concepts to analyze relationships with" relationship_types: type: "array" items: type: "string" enum: ["causal", "correlational", "mechanistic", "temporal", "hierarchical"] description: "Types of relationships to explore and analyze" default: ["causal", "correlational"] depth_level: type: "integer" description: "Depth of relationship exploration (1=direct relationships, 5=deep network analysis)" minimum: 1 maximum: 5 default: 3 required: ["primary_concept"] - name: "validate_scientific_claims" description: "Validate scientific claims against existing evidence using multi-dimensional confidence scoring and comprehensive evidence integration from multiple scientific databases." inputSchema: type: "object" properties: claim: type: "string" description: "The scientific claim to validate against existing evidence" evidence_threshold: type: "number" description: "Minimum confidence threshold for evidence validation (0.0-1.0)" minimum: 0.0 maximum: 1.0 default: 0.7 validation_criteria: type: "array" items: type: "string" enum: ["reproducibility", "peer_review", "sample_size", "methodology", "statistical_significance"] description: "Criteria to use for claim validation" default: ["peer_review", "methodology", "statistical_significance"] include_counterevidence: type: "boolean" description: "Include analysis of contradictory or conflicting evidence" default: true required: ["claim"] - name: "generate_research_insights" description: "Generate novel research insights and potential research directions based on existing knowledge graphs, evidence synthesis, and gap analysis." inputSchema: type: "object" properties: research_area: type: "string" description: "The research area or scientific field to generate insights for" current_knowledge: type: "string" description: "Summary of current knowledge or recent findings in the research area" research_gaps: type: "array" items: type: "string" description: "Known research gaps or limitations to address" innovation_focus: type: "string" enum: ["methodology", "theory", "application", "interdisciplinary"] description: "Focus area for generating novel insights" default: "theory" required: ["research_area"] # Resources that the MCP server provides access to resources: - uri: "graph://current-session" name: "Current Session Graph State" description: "Access to the current reasoning session's graph state and intermediate results" - uri: "evidence://pubmed" name: "PubMed Evidence Database" description: "Access to PubMed scientific literature for evidence gathering and validation" - uri: "evidence://scholar" name: "Google Scholar Database" description: "Access to Google Scholar for broader academic literature search" - uri: "evidence://exa" name: "Exa Search Database" description: "Access to Exa Search for web-based scientific content and research" # Predefined prompts for common scientific reasoning tasks prompts: - name: "analyze_complex_research_question" description: "Analyze a complex, multi-faceted research question using comprehensive graph-based reasoning" arguments: - name: "research_question" description: "The complex research question to analyze" required: true - name: "discipline" description: "Primary scientific discipline or field" required: false - name: "synthesize_literature_findings" description: "Synthesize findings from multiple research papers into coherent insights and conclusions" arguments: - name: "papers_summary" description: "Summary of key papers or findings to synthesize" required: true - name: "synthesis_focus" description: "Focus area for synthesis (e.g., 'mechanisms', 'outcomes', 'methodologies')" required: false - name: "identify_research_gaps" description: "Identify potential research gaps and opportunities in a scientific field" arguments: - name: "field_overview" description: "Overview of the scientific field or research area" required: true - name: "recent_advances" description: "Recent advances or breakthroughs in the field" required: false