search_annotations
Search for Gene Ontology annotations with filtering by bioentity, GO term, evidence type, organism, aspect, and source to find biological evidence relationships.
Instructions
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"
)
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| bioentity | No | ||
| go_term | No | ||
| evidence_types | No | ||
| taxon | No | ||
| aspect | No | ||
| assigned_by | No | ||
| limit | No |
Input Schema (JSON Schema)
{
"properties": {
"aspect": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"assigned_by": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"bioentity": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"evidence_types": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"go_term": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
},
"limit": {
"default": 10,
"type": "integer"
},
"taxon": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
}
},
"type": "object"
}
Implementation Reference
- src/noctua_mcp/mcp_server.py:1562-1665 (handler)The handler function for the 'search_annotations' MCP tool. It normalizes inputs, calls AmigoClient.search_annotations with filters, formats 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) }