add_evidence_to_fact

Add experimental evidence and source references to facts in GO-CAM models to support biological assertions with documented proof.

Instructions

Add evidence to an existing fact in a GO-CAM model.

Args: model_id: The GO-CAM model identifier subject_id: Subject of the fact object_id: Object of the fact predicate_id: Predicate of the fact eco_id: Evidence code (e.g., "ECO:0000353") sources: List of source references (e.g., ["PMID:12345"]) with_from: Optional list of with/from references

Returns: Barista API response

Examples: # Add experimental evidence from a paper add_evidence_to_fact( "gomodel:12345", "mf1", "gp1", "RO:0002333", "ECO:0000353", # physical interaction evidence ["PMID:12345678"] )

# Add multiple sources
add_evidence_to_fact(
    "gomodel:12345", "mf1", "gp1", "RO:0002333",
    "ECO:0000314",  # direct assay evidence
    ["PMID:12345678", "PMID:87654321", "doi:10.1234/example"]
)

# Add evidence with with/from (e.g., for IPI)
add_evidence_to_fact(
    "gomodel:12345", "mf1", "gp1", "RO:0002333",
    "ECO:0000353",  # IPI
    ["PMID:12345678"],  
    ["UniProtKB:Q9Y6K9", "UniProtKB:P38398"]  # interacting partners
)

# Common evidence codes:
# ECO:0000314 - direct assay evidence
# ECO:0000353 - physical interaction evidence (IPI)
# ECO:0000315 - mutant phenotype evidence (IMP)
# ECO:0000316 - genetic interaction evidence (IGI)
# ECO:0000318 - biological aspect of ancestor evidence (IBA)
# ECO:0000269 - experimental evidence

Input Schema

TableJSON Schema

Name	Required	Description	Default
`model_id`	Yes
`subject_id`	Yes
`object_id`	Yes
`predicate_id`	Yes
`eco_id`	Yes
`sources`	Yes
`with_from`	No

Implementation Reference

src/noctua_mcp/mcp_server.py:338-437 (handler)

The primary handler implementation for the MCP tool 'add_evidence_to_fact'. This async function is decorated with @mcp.tool(), defining its schema via type hints and docstring. It delegates to BaristaClient.req_add_evidence_to_fact, executes the batch, and handles validation/errors with detailed responses.

@mcp.tool()
async def add_evidence_to_fact(
    model_id: str,
    subject_id: str,
    object_id: str,
    predicate_id: str,
    eco_id: str,
    sources: List[str],
    with_from: Optional[List[str]] = None
) -> Dict[str, Any]:
    """
    Add evidence to an existing fact in a GO-CAM model.

    Args:
        model_id: The GO-CAM model identifier
        subject_id: Subject of the fact
        object_id: Object of the fact
        predicate_id: Predicate of the fact
        eco_id: Evidence code (e.g., "ECO:0000353")
        sources: List of source references (e.g., ["PMID:12345"])
        with_from: Optional list of with/from references

    Returns:
        Barista API response

    Examples:
        # Add experimental evidence from a paper
        add_evidence_to_fact(
            "gomodel:12345", "mf1", "gp1", "RO:0002333",
            "ECO:0000353",  # physical interaction evidence
            ["PMID:12345678"]
        )

        # Add multiple sources
        add_evidence_to_fact(
            "gomodel:12345", "mf1", "gp1", "RO:0002333",
            "ECO:0000314",  # direct assay evidence
            ["PMID:12345678", "PMID:87654321", "doi:10.1234/example"]
        )

        # Add evidence with with/from (e.g., for IPI)
        add_evidence_to_fact(
            "gomodel:12345", "mf1", "gp1", "RO:0002333",
            "ECO:0000353",  # IPI
            ["PMID:12345678"],  
            ["UniProtKB:Q9Y6K9", "UniProtKB:P38398"]  # interacting partners
        )

        # Common evidence codes:
        # ECO:0000314 - direct assay evidence
        # ECO:0000353 - physical interaction evidence (IPI)
        # ECO:0000315 - mutant phenotype evidence (IMP)
        # ECO:0000316 - genetic interaction evidence (IGI)
        # ECO:0000318 - biological aspect of ancestor evidence (IBA)
        # ECO:0000269 - experimental evidence
    """
    client = get_client()
    reqs = client.req_add_evidence_to_fact(
        model_id, subject_id, object_id, predicate_id,
        eco_id, sources, with_from
    )
    resp = client.m3_batch(reqs)

    if resp.validation_failed:
        return {
            "success": False,
            "error": "Validation failed",
            "reason": resp.validation_reason,
            "rolled_back": True,
            "fact": {
                "subject": subject_id,
                "predicate": predicate_id,
                "object": object_id
            },
            "evidence": {
                "eco_id": eco_id,
                "sources": sources,
                "with_from": with_from
            }
        }

    if resp.error:
        return {
            "success": False,
            "error": resp.error,
            "model_id": model_id,
            "fact": {
                "subject": subject_id,
                "predicate": predicate_id,
                "object": object_id
            }
        }

    # Return minimal success response
    return {
        "success": True,
        "evidence_added": True,
        "eco_id": eco_id
    }

src/noctua_mcp/mcp_server.py:338-338 (registration)
The @mcp.tool() decorator registers this function as an MCP tool named 'add_evidence_to_fact' in the FastMCP instance.
```
@mcp.tool()
```
src/noctua_mcp/mcp_server.py:339-347 (schema)
Input schema defined by function parameters with type annotations: model_id (str), subject_id (str), object_id (str), predicate_id (str), eco_id (str), sources (List[str]), with_from (Optional[List[str]]). Returns Dict[str, Any]. Detailed examples in docstring.
```
async def add_evidence_to_fact(
    model_id: str,
    subject_id: str,
    object_id: str,
    predicate_id: str,
    eco_id: str,
    sources: List[str],
    with_from: Optional[List[str]] = None
) -> Dict[str, Any]:
```

Noctua MCP Server