create_model
Create a new GO-CAM model for biological pathway representation. Build causal activity models to capture gene function relationships and biological processes.
Instructions
Create a new empty GO-CAM model.
Args: title: Optional title for the model
Returns: Barista API response containing the new model ID and editor URLs
Examples:
create_model("RAS-RAF signaling pathway")
Notes: - The returned model_id can be used with other tools like add_individual - Models are created in "development" state by default - To add taxon information, use add_individual after creating the model
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| title | No |
Input Schema (JSON Schema)
{
"properties": {
"title": {
"anyOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"default": null
}
},
"type": "object"
}
Implementation Reference
- src/noctua_mcp/mcp_server.py:91-152 (handler)The handler function for the 'create_model' MCP tool. Decorated with @mcp.tool(), it creates a new GO-CAM model via BaristaClient, handles errors and validation, constructs editor URLs, and returns the model ID and success status.@mcp.tool() async def create_model( title: Optional[str] = None ) -> Dict[str, Any]: """ Create a new empty GO-CAM model. Args: title: Optional title for the model Returns: Barista API response containing the new model ID and editor URLs Examples: - `create_model("RAS-RAF signaling pathway")` Notes: - The returned model_id can be used with other tools like add_individual - Models are created in "development" state by default - To add taxon information, use add_individual after creating the model """ client = get_client() resp = client.create_model(title=title) if resp.validation_failed: return { "success": False, "error": "Validation failed", "reason": resp.validation_reason, "rolled_back": True } if resp.error: return { "success": False, "error": "Operation failed", "reason": resp.error } # Build minimal response result = { "success": True, "model_id": resp.model_id, "created": True } # Add editor URLs if we have a model ID if resp.model_id: import os token = os.environ.get("BARISTA_TOKEN", "") # Graph editor with token result["graph_editor_url"] = f"http://noctua-dev.berkeleybop.org/editor/graph/{resp.model_id}?barista_token={token}" # Pathway editor without token (URL encoded model ID) from urllib.parse import quote encoded_id = quote(resp.model_id, safe="") result["pathway_editor_url"] = f"http://noctua-dev.berkeleybop.org/workbench/noctua-visual-pathway-editor/?model_id={encoded_id}" return result