Noctua MCP Server

Instructions

Implementation Reference

• src/noctua_mcp/mcp_server.py:1562-1665 (handler)

  The main handler function for the 'search_annotations' MCP tool. It normalizes inputs, calls AmigoClient.search_annotations, formats the results into a structured dictionary, and handles errors.
  @mcp.tool() async def search_annotations( bioentity: Optional[str] = None, go_term: Optional[str] = None, evidence_types: Optional[str] = None, taxon: Optional[str] = None, aspect: Optional[str] = None, assigned_by: Optional[str] = None, limit: int = 10 ) -> Dict[str, Any]: """ Search for GO annotations (evidence) with filtering. Args: bioentity: Specific bioentity ID to filter by (e.g., "UniProtKB:P12345") go_term: Specific GO term ID to filter by (e.g., "GO:0008150") evidence_types: Comma-separated evidence codes (e.g., "IDA,IPI,IMP") taxon: Organism filter - accepts numeric (9606) or full ID (NCBITaxon:9606) aspect: GO aspect filter - "C" (cellular component), "F" (molecular function), or "P" (biological process) assigned_by: Annotation source filter (e.g., "GOC", "UniProtKB", "MGI") limit: Maximum number of results (default: 10, max: 1000) Returns: Dictionary containing: - annotations: List of annotation results with evidence details - total: Number of results returned Examples: # Find all evidence for a specific protein search_annotations(bioentity="UniProtKB:P53762") # Find proteins with experimental evidence for a GO term search_annotations(go_term="GO:0005634", evidence_types="IDA,IPI") # Find human proteins in nucleus with experimental evidence search_annotations( go_term="GO:0005634", taxon="9606", evidence_types="IDA,IPI,IMP", aspect="C" ) # Find all UniProt annotations for apoptosis search_annotations( go_term="GO:0006915", assigned_by="UniProtKB" ) """ # Normalize taxon ID if taxon and not taxon.startswith("NCBITaxon:"): if taxon.isdigit(): taxon = f"NCBITaxon:{taxon}" # Parse evidence types evidence_list = None if evidence_types: evidence_list = [e.strip() for e in evidence_types.split(",")] # Limit bounds limit = min(max(1, limit), 1000) try: with AmigoClient() as client: results = client.search_annotations( bioentity=bioentity, go_term=go_term, evidence_types=evidence_list, taxon=taxon, aspect=aspect, assigned_by=assigned_by, limit=limit ) return { "annotations": [ { "bioentity": r.bioentity, "bioentity_label": r.bioentity_label, "bioentity_name": r.bioentity_name, "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, "taxon": r.taxon, "taxon_label": r.taxon_label, "qualifier": r.qualifier, "annotation_extension": r.annotation_extension } for r in results ], "total": len(results) } except Exception as e: return { "error": "Failed to search annotations", "message": str(e) }