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QualifiersMCP Agents

Overview

This document provides a code map of the QualifiersMCP server, which adds Biolink qualifier support to Tablassert.

Tool Count

This server provides 10 MCP tools organized into 3 groups.

CODE MAP

Line Tool Name Tags Purpose
27 get_biolink_qualifier_documentation biolink Fetches Biolink qualifier documentation from GitHub
61 get_table_configuration_documentation table-config Retrieves Tablassert Table Configuration documentation from GitHub
80 get_table_configuration_model_schema table-config Returns JSON schema for Tablassert Section model
97 get_biolink_qualifier_list biolink Lists all available Biolink qualifier enum values
113 read_yaml_to_sections_json table-config Converts YAML table configuration to Section JSON list
133 write_json_table_configuration_to_yaml table-config Converts JSON table configuration to YAML file
155 validate_json_table_configuration_syntax table-config Validates JSON table configuration against Section model schema
183 download_pmc_file_from_local_mirror local-services Downloads PMC file from local HTTP mirror service
222 get_curies_entity_from_dbssert_ner local-services Performs NER lookup on entity to find matching CURIEs via dbssert
248 get_canonical_curie_information_from_dbssert local-services Retrieves canonical CURIE information from dbssert

Tool Groups

biolink (2 tools)

  • get_biolink_qualifier_documentation: Fetch documentation for specific Biolink qualifiers
  • get_biolink_qualifier_list: List all available Biolink qualifier enum values

table-config (5 tools)

  • get_table_configuration_documentation: Get Tablassert configuration documentation
  • get_table_configuration_model_schema: Get JSON schema for validation
  • read_yaml_to_sections_json: Convert YAML to JSON format
  • write_json_table_configuration_to_yaml: Convert JSON to YAML format
  • validate_json_table_configuration_syntax: Validate configuration against schema

local-services (3 tools)

  • download_pmc_file_from_local_mirror: Download PMC files from local mirror (requires localhost:8051)
  • get_curies_entity_from_dbssert_ner: NER lookup for CURIEs (requires localhost:8052)
  • get_canonical_curie_information_from_dbssert: Get canonical CURIE data (requires localhost:8052)

Dependencies

  • Tablassert: Core configuration and validation models
  • Requests: HTTP client for fetching documentation and interacting with local services
  • Trafilatura: HTML content extraction from Biolink documentation
  • Local Services:
    • localhost:8051: PMC mirror service
    • localhost:8052: dbssert service for CURIE lookups