bc_get_string_network_image

Generate protein-protein interaction network visualizations from the STRING database for specific proteins and species, returning PNG images of biological networks.

Instructions

Generate protein-protein interaction network image from STRING database. Always provide species parameter.

Returns: Image or dict: Network visualization as PNG image object or error message.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`protein_symbol`	Yes	Protein name to search for (e.g., 'TP53')
`species`	Yes	Species taxonomy ID (e.g., '10090' for mouse)
`flavor`	No	Network flavor (e.g., 'confidence', 'evidence', 'actions')	confidence
`min_score`	No	Minimum combined score threshold (0-1000)

Implementation Reference

src/biocontext_kb/core/stringdb/_get_string_network_image.py:13-48 (handler)

The primary handler function for the 'bc_get_string_network_image' tool. It uses inline Pydantic schema for input validation, fetches the STRING protein ID using a helper, constructs the API URL for the network image, retrieves and processes the PNG image, and returns it as an Image object or an error dictionary.

@core_mcp.tool()
def get_string_network_image(
    protein_symbol: Annotated[str, Field(description="Protein name to search for (e.g., 'TP53')")],
    species: Annotated[str, Field(description="Species taxonomy ID (e.g., '10090' for mouse)")],
    flavor: Annotated[
        str, Field(description="Network flavor (e.g., 'confidence', 'evidence', 'actions')")
    ] = "confidence",
    min_score: Annotated[int, Field(description="Minimum combined score threshold (0-1000)", ge=0, le=1000)] = 700,
) -> Image | dict:
    """Generate protein-protein interaction network image from STRING database. Always provide species parameter.

    Returns:
        Image or dict: Network visualization as PNG image object or error message.
    """
    # First resolve the protein name to a STRING ID
    try:
        string_id = get_string_id.fn(protein_symbol=protein_symbol, species=species)

        if not string_id or not isinstance(string_id, str):
            return {"error": f"No STRING ID found for protein: {protein_symbol}"}

        url = f"https://string-db.org/api/image/network?identifiers={string_id}&species={species}&required_score={min_score}&network_flavor={flavor}&format=png"
        response = requests.get(url)
        response.raise_for_status()
        img = PILImage.open(BytesIO(response.content))

        buffer = BytesIO()
        img.save(buffer, format="PNG")
        img_bytes = buffer.getvalue()

        return Image(data=img_bytes, format="png")
    except requests.exceptions.RequestException as e:
        return {"error": f"Failed to fetch image: {e!s}"}
    except Exception as e:
        return {"error": f"An error occurred: {e!s}"}

src/biocontext_kb/core/stringdb/_get_string_id.py:9-41 (helper)

Helper tool 'get_string_id' (likely 'bc_get_string_id') called by the main handler to resolve the protein_symbol and species to a STRING database ID.

@core_mcp.tool()
def get_string_id(
    protein_symbol: Annotated[str, Field(description="Protein name or identifier (e.g., 'TP53')")],
    species: Annotated[str, Field(description="Species taxonomy ID (e.g., '9606' for human)")] = "",
    return_field: Annotated[str, Field(description="Field to return: 'stringId' or 'preferredName'")] = "stringId",
    limit: Annotated[int, Field(description="Maximum number of matches to return")] = 1,
) -> Union[dict, str]:
    """Map protein identifiers (gene names, synonyms, UniProt IDs) to STRING database IDs. Using STRING IDs improves reliability.

    Returns:
        str or dict: STRING ID string (e.g., '9606.ENSP00000269305') or dict with error message.
    """
    url = f"https://string-db.org/api/json/get_string_ids?identifiers={protein_symbol}&echo_query=1&limit={limit}"

    if species:
        url += f"&species={species}"

    try:
        response = requests.get(url)
        response.raise_for_status()

        data = response.json()

        if isinstance(data, dict) and "error" in data:
            return data

        if not data:
            return {"error": f"No STRING ID found for protein: {protein_symbol}"}

        return data[0].get(return_field)
    except requests.exceptions.RequestException as e:
        return {"error": f"Failed to fetch STRING ID: {e!s}"}

src/biocontext_kb/core/_server.py:1-7 (registration)
Defines core_mcp FastMCP instance with name 'BC' (providing the 'bc_' prefix for tools) where all core tools including get_string_network_image are registered via @core_mcp.tool() decorators.
```
from fastmcp import FastMCP

core_mcp = FastMCP(  # type: ignore
    "BC",
    instructions="Provides access to biomedical knowledge bases.",
)
```
src/biocontext_kb/app.py:35-40 (registration)
Imports the core_mcp server (with 'BC' tools) into the main 'BioContextAI' FastMCP app using slugify('BC')='bc' as the prefix, making tools available as 'bc_*'.
```
for mcp in [core_mcp, *(await get_openapi_mcps())]:
    await mcp_app.import_server(
        mcp,
        slugify(mcp.name),
    )
logger.info("MCP server setup complete.")
```

BioContextAI Knowledgebase MCP