Noctua MCP Server

Instructions

# Get only experimental evidence
get_annotations_for_bioentity(
    "UniProtKB:P53762",
    evidence_types="IDA,IPI,IMP"
)

# Get annotations for specific GO terms
get_annotations_for_bioentity(
    "UniProtKB:P53762",
    go_terms="GO:0005634,GO:0005737"
)

# Get only molecular function annotations
get_annotations_for_bioentity(
    "UniProtKB:P53762",
    aspect="F"
)

Implementation Reference

• src/noctua_mcp/mcp_server.py:1668-1769 (handler)

  The primary handler function for the MCP tool 'get_annotations_for_bioentity'. It parses input parameters, queries the AmigoClient for GO annotations associated with a specific bioentity (with optional filters), computes summary statistics, and formats the response.

  async def get_annotations_for_bioentity(
      bioentity_id: str,
      go_terms: Optional[str] = None,
      evidence_types: Optional[str] = None,
      aspect: Optional[str] = None,
      limit: int = 100
  ) -> Dict[str, Any]:
      """
      Get all GO annotations (evidence) for a specific bioentity.
  
      Args:
          bioentity_id: The bioentity ID (e.g., "UniProtKB:P12345")
          go_terms: Comma-separated GO terms to filter (includes child terms)
          evidence_types: Comma-separated evidence codes to filter (e.g., "IDA,IPI")
          aspect: GO aspect filter - "C", "F", or "P"
          limit: Maximum number of results (default: 100)
  
      Returns:
          Dictionary containing:
          - bioentity_id: The queried bioentity
          - annotations: List of annotation results
          - summary: Count by aspect and evidence type
  
      Examples:
          # Get all annotations for a protein
          get_annotations_for_bioentity("UniProtKB:P53762")
  
          # Get only experimental evidence
          get_annotations_for_bioentity(
              "UniProtKB:P53762",
              evidence_types="IDA,IPI,IMP"
          )
  
          # Get annotations for specific GO terms
          get_annotations_for_bioentity(
              "UniProtKB:P53762",
              go_terms="GO:0005634,GO:0005737"
          )
  
          # Get only molecular function annotations
          get_annotations_for_bioentity(
              "UniProtKB:P53762",
              aspect="F"
          )
      """
      # Parse comma-separated lists
      go_terms_list = None
      if go_terms:
          go_terms_list = [t.strip() for t in go_terms.split(",")]
  
      evidence_list = None
      if evidence_types:
          evidence_list = [e.strip() for e in evidence_types.split(",")]
  
      try:
          with AmigoClient() as client:
              results = client.get_annotations_for_bioentity(
                  bioentity_id=bioentity_id,
                  go_terms_closure=go_terms_list,
                  evidence_types=evidence_list,
                  aspect=aspect,
                  limit=limit
              )
  
              # Calculate summary statistics
              aspect_counts: Dict[str, int] = {}
              evidence_counts: Dict[str, int] = {}
              for r in results:
                  aspect_counts[r.aspect] = aspect_counts.get(r.aspect, 0) + 1
                  evidence_counts[r.evidence_type] = evidence_counts.get(r.evidence_type, 0) + 1
  
              return {
                  "bioentity_id": bioentity_id,
                  "annotations": [
                      {
                          "go_term": r.annotation_class,
                          "go_term_label": r.annotation_class_label,
                          "aspect": r.aspect,
                          "evidence_type": r.evidence_type,
                          "evidence": r.evidence,
                          "evidence_label": r.evidence_label,
                          "reference": r.reference,
                          "assigned_by": r.assigned_by,
                          "date": r.date,
                          "qualifier": r.qualifier,
                          "annotation_extension": r.annotation_extension
                      }
                      for r in results
                  ],
                  "summary": {
                      "total": len(results),
                      "by_aspect": aspect_counts,
                      "by_evidence_type": evidence_counts
                  }
              }
  
      except Exception as e:
          return {
              "error": "Failed to get annotations",
              "message": str(e)
          }