bc_search_interpro_entries
Search InterPro protein family and domain entries by name, type, database, GO term, or species to retrieve matching entries with metadata from biomedical knowledge bases.
Instructions
Search InterPro entries by name, type, database, GO term, or species. Returns matching entries with metadata.
Returns: dict: Search results with results array (InterPro entries), count, total_available, search_criteria or error message.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | Search term for entry names/descriptions | |
| entry_type | No | family, domain, homologous_superfamily, repeat, conserved_site, binding_site, active_site, or ptm | |
| source_database | No | pfam, prosite, panther, smart, cdd, hamap, pirsf, prints, etc. | |
| go_term | No | GO term filter (e.g., 'GO:0006122') | |
| species_filter | No | Taxonomy ID filter (e.g., '9606') | |
| page_size | No | Results per page (max 200) |
Implementation Reference
- The core handler function for the 'bc_search_interpro_entries' tool. It uses the @core_mcp.tool() decorator and implements the search logic against the InterPro API, including input validation and parameter building.@core_mcp.tool() def search_interpro_entries( query: Annotated[ Optional[str], Field(description="Search term for entry names/descriptions"), ] = None, entry_type: Annotated[ Optional[str], Field( description="family, domain, homologous_superfamily, repeat, conserved_site, binding_site, active_site, or ptm" ), ] = None, source_database: Annotated[ Optional[str], Field(description="pfam, prosite, panther, smart, cdd, hamap, pirsf, prints, etc."), ] = None, go_term: Annotated[ Optional[str], Field(description="GO term filter (e.g., 'GO:0006122')"), ] = None, species_filter: Annotated[ Optional[str], Field(description="Taxonomy ID filter (e.g., '9606')"), ] = None, page_size: Annotated[ int, Field(description="Results per page (max 200)"), ] = 20, ) -> dict: """Search InterPro entries by name, type, database, GO term, or species. Returns matching entries with metadata. Returns: dict: Search results with results array (InterPro entries), count, total_available, search_criteria or error message. """ base_url = "https://www.ebi.ac.uk/interpro/api/entry/interpro" # Build query parameters params: dict[str, str | int] = {} if page_size > 200: page_size = 200 params["page_size"] = page_size # Add the search query if provided (this is the key fix!) if query: params["search"] = query # Add filters if entry_type: valid_types = [ "family", "domain", "homologous_superfamily", "repeat", "conserved_site", "binding_site", "active_site", "ptm", ] if entry_type not in valid_types: return {"error": f"Invalid entry_type. Valid options: {', '.join(valid_types)}"} params["type"] = entry_type if source_database: valid_dbs = [ "pfam", "prosite", "panther", "smart", "cdd", "hamap", "pirsf", "prints", "prodom", "ssf", "tigrfams", "cathgene3d", "sfld", ] if source_database not in valid_dbs: return {"error": f"Invalid source_database. Valid options: {', '.join(valid_dbs)}"} params["signature_in"] = source_database if go_term: # Validate GO term format if not go_term.upper().startswith("GO:") or len(go_term) != 10: return {"error": "Invalid GO term format. Expected format: GO:0006122"} params["go_term"] = go_term.upper() if species_filter: params["tax_id"] = species_filter # Add extra fields for more informative results params["extra_fields"] = "short_name,description,entry_date" try: response = requests.get(base_url, params=params) response.raise_for_status() search_results = response.json() if not search_results.get("results"): return {"results": [], "count": 0, "message": "No InterPro entries found matching the search criteria"} # Results are already filtered by the API's search parameter results = search_results["results"] return { "results": results, "count": len(results), "total_available": search_results.get("count", len(results)), "search_criteria": { "query": query, "entry_type": entry_type, "source_database": source_database, "go_term": go_term, "species_filter": species_filter, }, } except requests.exceptions.HTTPError as e: return {"error": f"HTTP error: {e}"} except Exception as e: return {"error": f"Exception occurred: {e!s}"}
- src/biocontext_kb/core/_server.py:3-6 (registration)Definition of the FastMCP server instance 'BC' which automatically prefixes registered tool names with 'bc_' (resulting in 'bc_search_interpro_entries').core_mcp = FastMCP( # type: ignore "BC", instructions="Provides access to biomedical knowledge bases.", )
- src/biocontext_kb/core/__init__.py:11-12 (registration)Imports all tools from the interpro module, including search_interpro_entries, making it available for registration via the core_mcp FastMCP instance.from .interpro import * from .ols import *
- src/biocontext_kb/core/interpro/__init__.py:3-3 (registration)Re-exports the search_interpro_entries handler function for inclusion in the core module imports.from ._search_interpro_entries import search_interpro_entries