Noctua MCP Server

Instructions

# Find models containing "Wnt signaling" in title
results = search_models(title="Wnt signaling")

# Find models for a specific gene product
results = search_models(gene_product="UniProtKB:P38398")

# Find models from a specific paper
results = search_models(pmid="PMID:30194302")

# Find models by a specific contributor
results = search_models(
    contributor="https://orcid.org/0000-0002-6601-2165"
)

# Combine filters
results = search_models(
    state="production",
    title="kinase",
    limit=10
)

# Pagination example
page1 = search_models(limit=50, offset=0)
page2 = search_models(limit=50, offset=50)

# Find models from specific research group
results = search_models(group="http://www.wormbase.org")

# Search for development models with specific gene
results = search_models(
    state="development",
    gene_product="MGI:MGI:97490"
)

Implementation Reference

• src/noctua_mcp/mcp_server.py:1347-1440 (handler)

  The core handler implementation for the 'search_models' tool. This async function is decorated with @mcp.tool(), which both defines the input schema via type hints/docstring and registers/executes the tool logic. It uses BaristaClient.list_models to perform the search with optional filters and handles exceptions.

  @mcp.tool()
  async def search_models(
      title: Optional[str] = None,
      state: Optional[str] = None,
      contributor: Optional[str] = None,
      group: Optional[str] = None,
      pmid: Optional[str] = None,
      gene_product: Optional[str] = None,
      limit: int = 50,
      offset: int = 0
  ) -> Dict[str, Any]:
      """
      Search for GO-CAM models based on various criteria.
  
      Allows searching models by title, state, contributor, group, publication, or gene product.
      Returns a list of matching models with their metadata.
  
      Args:
          title: Search for models containing this text in their title
          state: Filter by model state (production, development, internal_test)
          contributor: Filter by contributor ORCID (e.g., 'https://orcid.org/0000-0002-6601-2165')
          group: Filter by group/provider (e.g., 'http://www.wormbase.org')
          pmid: Filter by PubMed ID (e.g., 'PMID:12345678')
          gene_product: Filter by gene product (e.g., 'UniProtKB:Q9BRQ8', 'MGI:MGI:97490')
          limit: Maximum number of results to return (default: 50)
          offset: Offset for pagination (default: 0)
  
      Returns:
          Dictionary containing search results with model metadata
  
      Examples:
          # Search for all production models
          results = search_models(state="production")
  
          # Find models containing "Wnt signaling" in title
          results = search_models(title="Wnt signaling")
  
          # Find models for a specific gene product
          results = search_models(gene_product="UniProtKB:P38398")
  
          # Find models from a specific paper
          results = search_models(pmid="PMID:30194302")
  
          # Find models by a specific contributor
          results = search_models(
              contributor="https://orcid.org/0000-0002-6601-2165"
          )
  
          # Combine filters
          results = search_models(
              state="production",
              title="kinase",
              limit=10
          )
  
          # Pagination example
          page1 = search_models(limit=50, offset=0)
          page2 = search_models(limit=50, offset=50)
  
          # Find models from specific research group
          results = search_models(group="http://www.wormbase.org")
  
          # Search for development models with specific gene
          results = search_models(
              state="development",
              gene_product="MGI:MGI:97490"
          )
  
      Notes:
          - Results include model ID, title, state, contributors, and dates
          - Use pagination (offset/limit) for large result sets
          - Filters can be combined for more specific searches
          - Gene products can be from various databases (UniProt, MGI, RGD, etc.)
      """
      client = get_client()
  
      try:
          results = client.list_models(
              title=title,
              state=state,
              contributor=contributor,
              group=group,
              pmid=pmid,
              gp=gene_product,
              limit=limit,
              offset=offset
          )
          return results
      except Exception as e:
          return {
              "error": "Failed to search models",
              "message": str(e)
          }