Genome MCP suffers from critical definition quality issues across nearly all dimensions. While some tools have descriptions and partial schemas, most lack proper input documentation, parameter descriptions, and output schemas. The tool portfolio shows conceptual overlap (get_data, smart_search, advanced_query all appear to perform similar operations). Descriptions are present but often vague or in Chinese only. Input schemas are visible for only 2 of 6 tools (get_data, analyze_gene_evolution, kegg_pathway_enrichment). No tools declare output schemas. Error handling guidance is absent. The codebase shows evolutionary analysis capability but the tool interface does not expose it clearly.

• Split overlapping query tools: rename get_data → query_gene_info (for ID/name lookups), smart_search → search_genes_by_annotation (for text search), advanced_query → analyze_genes (for multi-param analysis). Add 1-2 sentences to each description clarifying when to use it.
• For ALL tools, document output schema as a JSON structure. Example for analyze_gene_evolution: '{"orthologs": [{"gene_id": string, "organism": string, "identity": number}], "conservation_score": number, "phylogenetic_distribution": object}'. Include per-field descriptions.
• Add input schemas for smart_search, advanced_query, build_phylogenetic_profile. Minimum: declare parameter types (string/array/number/boolean) and describe each. Use enums for discrete options (organism codes, analysis_level values).
• Expand tool descriptions to 80-150 chars, in English. Include: (1) what it does, (2) when to use it vs related tools, (3) expected inputs, (4) sample output shape. Translate any Chinese descriptions to English.
• Add error handling guidance to each tool description. E.g., 'If gene_symbol not found, try search_genes_by_annotation() to verify the gene exists and get its canonical ID.'
• Declare valid enums: organism (e.g. 'hsa', 'mmu', 'rno', 'dre', 'sce', 'cel', 'dme', 'human', 'mouse', 'rat') and analysis_level (e.g. 'Eukaryota', 'Metazoa', 'Vertebrata', 'Mammalia', 'Primates') in parameter descriptions, or link to documentation.
• For paginated results (e.g. search tools), add limit and offset/cursor parameters if not present. Document that results cap at 20 by default. Example: 'Returns max 20 results; use limit/offset for pagination.'