bc_get_pride_project

Retrieve detailed metadata and experimental information for PRIDE mass spectrometry proteomics projects using project accession numbers.

Instructions

Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details.

Returns: dict: Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.

Input Schema

TableJSON Schema

Name	Required	Description
`project_accession`	Yes	PRIDE project accession (e.g., 'PRD000001')
`include_files`	No	Include file information (limited to first 20 files)
`include_similar_projects`	No	Include similar projects based on metadata (limited to 10)

Implementation Reference

src/biocontext_kb/core/pride/_get_pride_project.py:9-80 (handler)

The handler function for the 'bc_get_pride_project' tool (registered as 'get_pride_project' on core_mcp, prefixed to 'bc_' in main app). Fetches PRIDE project metadata, optional files and similar projects from EBI API.

@core_mcp.tool()
def get_pride_project(
    project_accession: Annotated[
        str,
        Field(description="PRIDE project accession (e.g., 'PRD000001')"),
    ],
    include_files: Annotated[
        bool,
        Field(description="Include file information (limited to first 20 files)"),
    ] = False,
    include_similar_projects: Annotated[
        bool,
        Field(description="Include similar projects based on metadata (limited to 10)"),
    ] = False,
) -> dict:
    """Retrieve detailed information about a specific PRIDE mass spectrometry proteomics project. Returns metadata and experimental details.

    Returns:
        dict: Project details with accession, title, description, organisms, instruments, publications, optionally files/similar_projects or error message.
    """
    base_url = "https://www.ebi.ac.uk/pride/ws/archive/v3"

    try:
        # Get basic project information
        project_url = f"{base_url}/projects/{project_accession}"
        response = requests.get(project_url)
        response.raise_for_status()

        project_data = response.json()

        if not project_data:
            return {"error": f"No data found for PRIDE project {project_accession}"}

        result = project_data

        # Optionally include file information
        if include_files:
            try:
                files_url = f"{base_url}/projects/{project_accession}/files"
                files_response = requests.get(files_url, params={"pageSize": 20})
                if files_response.status_code == 200:
                    files_data = files_response.json()
                    result["files"] = files_data[:20]  # Limit to first 20 files

                    # Get file count
                    count_url = f"{base_url}/projects/{project_accession}/files/count"
                    count_response = requests.get(count_url)
                    if count_response.status_code == 200:
                        result["total_files"] = count_response.json()

            except Exception:
                result["files"] = {"error": "Could not fetch file information"}

        # Optionally include similar projects
        if include_similar_projects:
            try:
                similar_url = f"{base_url}/projects/{project_accession}/similarProjects"
                similar_response = requests.get(similar_url, params={"pageSize": 10})
                if similar_response.status_code == 200:
                    similar_data = similar_response.json()
                    result["similar_projects"] = similar_data[:10]  # Limit to first 10
            except Exception:
                result["similar_projects"] = {"error": "Could not fetch similar projects"}

        return result

    except requests.exceptions.HTTPError as e:
        if e.response.status_code == 404:
            return {"error": f"PRIDE project {project_accession} not found"}
        return {"error": f"HTTP error: {e}"}
    except Exception as e:
        return {"error": f"Exception occurred: {e!s}"}

src/biocontext_kb/core/pride/_get_pride_project.py:10-23 (schema)

Pydantic schema definition for tool inputs using Annotated and Field, output is dict.

def get_pride_project(
    project_accession: Annotated[
        str,
        Field(description="PRIDE project accession (e.g., 'PRD000001')"),
    ],
    include_files: Annotated[
        bool,
        Field(description="Include file information (limited to first 20 files)"),
    ] = False,
    include_similar_projects: Annotated[
        bool,
        Field(description="Include similar projects based on metadata (limited to 10)"),
    ] = False,
) -> dict:

src/biocontext_kb/app.py:35-40 (registration)
Registers the core_mcp server (containing get_pride_project tool) into the main mcp_app with prefix slugify('BC') = 'bc', making tool name 'bc_get_pride_project'.
```
for mcp in [core_mcp, *(await get_openapi_mcps())]:
    await mcp_app.import_server(
        mcp,
        slugify(mcp.name),
    )
logger.info("MCP server setup complete.")
```
src/biocontext_kb/core/_server.py:3-6 (registration)
Defines the core_mcp FastMCP instance named 'BC' where tools like get_pride_project are registered via decorators.
```
core_mcp = FastMCP(  # type: ignore
    "BC",
    instructions="Provides access to biomedical knowledge bases.",
)
```

src/biocontext_kb/core/pride/__init__.py:1-9 (registration)

Imports the get_pride_project function, triggering registration via its @core_mcp.tool() decorator when the module is imported.

from ._get_pride_project import get_pride_project
from ._search_pride_projects import search_pride_projects
from ._search_pride_proteins import search_pride_proteins

__all__ = [
    "get_pride_project",
    "search_pride_projects",
    "search_pride_proteins",
]

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