Add Detailed Instructions to MCP Tools ✅

• Review current MCP tool descriptions in the codebase
• Enhance McpSearchService tool descriptions with detailed instructions
  • Improve 'search' tool description - added comprehensive details about parameters, return values, and usage
  • Improve 'fetch' tool description - updated with exact field types and structure from code analysis
• Enhance McpClassService tool descriptions with detailed instructions
  • Improve 'searchClasses' tool description - added examples, parameter details, and pagination info
  • Improve 'getAncestors' tool description - explained hierarchical relationships and use cases
  • Improve 'getDescendants' tool description - explained subtypes and practical applications
• Enhance McpOntologyService tool descriptions with detailed instructions
  • Improve 'listOntologies' tool description - added comprehensive information about ontologies and examples
• Build and validate changes - Maven build successful
• Run security checks - No vulnerabilities detected
• Address feedback - Updated fetch description with exact field types from code

Summary

Enhanced the MCP (Model Context Protocol) tool descriptions in the OLS4 backend with detailed, comprehensive instructions. All 6 MCP tools now include:

Enhanced Tools:

1. search - Full-text search across all ontologies with clear parameter and return format documentation
2. fetch - Retrieve detailed term information with exact field types (String vs List), structure of metadata object including McpEntityReference fields
3. searchClasses - Search ontology classes with filtering options and pagination
4. getAncestors - Get parent classes in hierarchy with practical use cases
5. getDescendants - Get child classes with subtypes examples
6. listOntologies - List all available ontologies with common examples

Improvements Made:

• Added detailed parameter descriptions with examples
• Documented return value structures accurately based on actual implementation code
• Specified exact field types (String, List, List) from McpFetchResult, McpClass, and McpEntityReference classes
• Included practical use cases and workflow guidance
• Added examples of common ontologies (GO, EFO, HP, MONDO, etc.)
• Explained relationships between tools (e.g., use 'search' then 'fetch')
• Clarified data formats and expected inputs

Files Modified:

• backend/src/main/java/uk/ac/ebi/spot/ols/controller/mcp/McpSearchService.java
• backend/src/main/java/uk/ac/ebi/spot/ols/controller/mcp/McpClassService.java
• backend/src/main/java/uk/ac/ebi/spot/ols/controller/mcp/McpOntologyService.java

Validation:
✅ Maven build successful (1:38 min)
✅ CodeQL security check passed (0 vulnerabilities)
✅ No breaking changes to API contracts

Security Summary

No security vulnerabilities were introduced or discovered during the implementation. The changes are purely documentation enhancements to existing @Tool annotations.

Original prompt

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This section details on the original issue you should resolve

<issue_title>Add detailed instructions to the MCP tools</issue_title>
<issue_description></issue_description>

Comments on the Issue (you are @copilot in this section)

Fixes #1016

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.