bc_search_pride_proteins

Search for specific proteins within PRIDE mass spectrometry proteomics datasets using project accession numbers and optional keywords to identify proteins, genes, and modifications.

Instructions

Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

Returns: dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`project_accession`	Yes	PRIDE project accession to search proteins in
`keyword`	No	Search keyword for protein names or accessions
`page_size`	No	Number of results to return (max 100)
`sort_field`	No	Sort field: accession, proteinName, or gene	accession
`sort_direction`	No	Sort direction: ASC or DESC	ASC

Implementation Reference

src/biocontext_kb/core/pride/_search_pride_proteins.py:9-95 (handler)

Main handler function for the bc_search_pride_proteins tool (registered as search_pride_proteins). Queries PRIDE API for proteins in a project, supports keyword search, sorting, pagination. Includes input schema via Annotated Fields.

@core_mcp.tool()
def search_pride_proteins(
    project_accession: Annotated[
        str,
        Field(description="PRIDE project accession to search proteins in"),
    ],
    keyword: Annotated[
        Optional[str],
        Field(description="Search keyword for protein names or accessions"),
    ] = None,
    page_size: Annotated[
        int,
        Field(description="Number of results to return (max 100)"),
    ] = 20,
    sort_field: Annotated[
        str,
        Field(description="Sort field: accession, proteinName, or gene"),
    ] = "accession",
    sort_direction: Annotated[
        str,
        Field(description="Sort direction: ASC or DESC"),
    ] = "ASC",
) -> dict:
    """Search for proteins identified in a specific PRIDE mass spectrometry project. Useful for finding specific proteins in proteomics datasets.

    Returns:
        dict: Proteins list with accessions, names, genes, sequences, modifications, associated projects or error message.
    """
    base_url = "https://www.ebi.ac.uk/pride/ws/archive/v3/pride-ap/search/proteins"

    # Build query parameters
    params: dict[str, str | int] = {"projectAccession": project_accession}

    if page_size > 100:
        page_size = 100
    params["pageSize"] = page_size
    params["page"] = 0

    # Add keyword search
    if keyword:
        params["keyword"] = keyword

    # Validate and set sort parameters
    valid_sort_fields = ["accession", "proteinName", "gene"]
    if sort_field not in valid_sort_fields:
        sort_field = "accession"
    params["sortField"] = sort_field

    valid_sort_directions = ["ASC", "DESC"]
    if sort_direction.upper() not in valid_sort_directions:
        sort_direction = "ASC"
    params["sortDirection"] = sort_direction.upper()

    try:
        response = requests.get(base_url, params=params)
        response.raise_for_status()

        search_results = response.json()

        if not search_results:
            return {"results": [], "count": 0, "message": f"No proteins found in PRIDE project {project_accession}"}

        # Process results to include key information
        processed_results = []
        for protein in search_results:
            processed_protein = {
                "protein_accession": protein.get("proteinAccession"),
                "protein_name": protein.get("proteinName"),
                "gene": protein.get("gene"),
                "project_count": protein.get("projectCount", 0),
            }
            processed_results.append(processed_protein)

        return {
            "results": processed_results,
            "count": len(processed_results),
            "project_accession": project_accession,
            "search_criteria": {"keyword": keyword, "sort_field": sort_field, "sort_direction": sort_direction},
        }

    except requests.exceptions.HTTPError as e:
        if e.response.status_code == 404:
            return {"error": f"PRIDE project {project_accession} not found or has no protein data"}
        return {"error": f"HTTP error: {e}"}
    except Exception as e:
        return {"error": f"Exception occurred: {e!s}"}

src/biocontext_kb/core/__init__.py:16-16 (registration)
Registers pride tools by importing from .pride which includes search_pride_proteins decorated with @core_mcp.tool().
```
from .pride import *
```
src/biocontext_kb/core/pride/__init__.py:3-3 (registration)
Explicit import of the search_pride_proteins function in pride module for higher-level import.
```
from ._search_pride_proteins import search_pride_proteins
```
src/biocontext_kb/core/_server.py:3-6 (registration)
Defines the FastMCP instance 'core_mcp' with prefix 'BC' used to register all tools including search_pride_proteins via @core_mcp.tool() decorator. Tool names likely prefixed as 'bc_search_pride_proteins'.
```
core_mcp = FastMCP(  # type: ignore
    "BC",
    instructions="Provides access to biomedical knowledge bases.",
)
```

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