bc_search_pride_projects
Search and filter mass spectrometry proteomics projects in the PRIDE Archive by keywords, organism, instrument, or experiment type to identify datasets for analysis or validation.
Instructions
Search PRIDE Archive projects by various criteria.
This function searches the PRIDE database for mass spectrometry proteomics projects using keywords and filters. Useful for finding relevant datasets for comparative analysis or method validation.
Args: keyword (str, optional): Search keywords for project titles/descriptions. organism_filter (str, optional): Filter by organism name. instrument_filter (str, optional): Filter by mass spectrometer instrument. experiment_type_filter (str, optional): Filter by experimental approach. page_size (int, optional): Number of results (max 100). Defaults to 20. sort_field (str, optional): Sort field. Defaults to "submissionDate". sort_direction (str, optional): Sort direction. Defaults to "DESC".
Returns: dict: Search results with matching PRIDE projects and metadata
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| experiment_type_filter | No | Filter by experiment type (e.g., 'TMT', 'Label-free') | |
| instrument_filter | No | Filter by instrument type (e.g., 'Orbitrap', 'LTQ') | |
| keyword | No | Search keywords (e.g., 'proteome', 'cancer', 'human') | |
| organism_filter | No | Filter by organism (e.g., 'Homo sapiens', 'human') | |
| page_size | No | Number of results to return (max 100) | |
| sort_direction | No | Sort direction: ASC or DESC | DESC |
| sort_field | No | Field to sort by: submissionDate, publicationDate | submissionDate |
Implementation Reference
- The core handler function for the 'search_pride_projects' tool (prefixed to 'bc_search_pride_projects' when registered), decorated with @core_mcp.tool(). It builds a query to the PRIDE WS API, fetches projects based on keyword and filters, processes the results, and returns a structured dict with project details.@core_mcp.tool() def search_pride_projects( keyword: Annotated[ Optional[str], Field(description="Search keywords (e.g., 'proteome', 'cancer', 'human')"), ] = None, organism_filter: Annotated[ Optional[str], Field(description="Organism filter (e.g., 'Homo sapiens', 'human')"), ] = None, instrument_filter: Annotated[ Optional[str], Field(description="Instrument type filter (e.g., 'Orbitrap', 'LTQ')"), ] = None, experiment_type_filter: Annotated[ Optional[str], Field(description="Experiment type filter (e.g., 'TMT', 'Label-free')"), ] = None, page_size: Annotated[ int, Field(description="Number of results to return (max 100)"), ] = 20, sort_field: Annotated[ str, Field(description="Sort field: submissionDate or publicationDate"), ] = "submissionDate", sort_direction: Annotated[ str, Field(description="Sort direction: ASC or DESC"), ] = "DESC", ) -> dict: """Search PRIDE database for mass spectrometry proteomics projects using keywords and filters. Returns: dict: Results array with project accessions, titles, descriptions, organisms, instruments, experiment types, count, search_criteria or error message. """ base_url = "https://www.ebi.ac.uk/pride/ws/archive/v3/search/projects" # Build query parameters params: dict[str, str | int] = {} if page_size > 100: page_size = 100 params["pageSize"] = page_size params["page"] = 0 # Add keyword search if keyword: params["keyword"] = keyword # Build filter string for specific criteria filters = [] if organism_filter: filters.append(f"organisms=={organism_filter}") if instrument_filter: filters.append(f"instruments=={instrument_filter}") if experiment_type_filter: filters.append(f"experimentTypes=={experiment_type_filter}") if filters: params["filter"] = ",".join(filters) # Validate and set sort parameters - use only known working fields valid_sort_fields = ["submissionDate", "publicationDate"] if sort_field not in valid_sort_fields: sort_field = "submissionDate" params["sortFields"] = sort_field valid_sort_directions = ["ASC", "DESC"] if sort_direction.upper() not in valid_sort_directions: sort_direction = "DESC" 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": "No PRIDE projects found matching the search criteria", "search_criteria": { "keyword": keyword, "organism_filter": organism_filter, "instrument_filter": instrument_filter, "experiment_type_filter": experiment_type_filter, "sort_field": sort_field, "sort_direction": sort_direction, }, } # Process results to include key information processed_results = [] for project in search_results: processed_project = { "accession": project.get("accession"), "title": project.get("title"), "description": project.get("projectDescription", "")[:500] + "..." if len(project.get("projectDescription", "")) > 500 else project.get("projectDescription", ""), "submission_date": project.get("submissionDate"), "publication_date": project.get("publicationDate"), "organisms": project.get("organisms", []), "instruments": project.get("instruments", []), "experiment_types": project.get("experimentTypes", []), "keywords": project.get("keywords", []), "submitters": project.get("submitters", []), "download_count": project.get("downloadCount", 0), } processed_results.append(processed_project) return { "results": processed_results, "count": len(processed_results), "search_criteria": { "keyword": keyword, "organism_filter": organism_filter, "instrument_filter": instrument_filter, "experiment_type_filter": experiment_type_filter, "sort_field": sort_field, "sort_direction": sort_direction, }, } except requests.exceptions.HTTPError as e: return {"error": f"HTTP error: {e}"} except Exception as e: return {"error": f"Exception occurred: {e!s}"}
- src/biocontext_kb/app.py:35-39 (registration)Registers the core_mcp server (named 'BC', slugged to 'bc') into the main FastMCP app, automatically prefixing all its tools (including search_pride_projects) with 'bc_' to create 'bc_search_pride_projects'.for mcp in [core_mcp, *(await get_openapi_mcps())]: await mcp_app.import_server( mcp, slugify(mcp.name), )
- src/biocontext_kb/core/_server.py:3-6 (registration)Defines the core_mcp FastMCP server instance named 'BC'. Tools decorated with @core_mcp.tool() are registered here, later imported with 'bc_' prefix.core_mcp = FastMCP( # type: ignore "BC", instructions="Provides access to biomedical knowledge bases.", )
- src/biocontext_kb/core/pride/__init__.py:2-2 (registration)Imports the search_pride_projects handler function into the pride package __init__, making it available to the core_mcp server.from ._search_pride_projects import search_pride_projects
- Pydantic-based input schema for the tool parameters using Annotated and Field for descriptions and optionality.def search_pride_projects( keyword: Annotated[ Optional[str], Field(description="Search keywords (e.g., 'proteome', 'cancer', 'human')"), ] = None, organism_filter: Annotated[ Optional[str], Field(description="Organism filter (e.g., 'Homo sapiens', 'human')"), ] = None, instrument_filter: Annotated[ Optional[str], Field(description="Instrument type filter (e.g., 'Orbitrap', 'LTQ')"), ] = None, experiment_type_filter: Annotated[ Optional[str], Field(description="Experiment type filter (e.g., 'TMT', 'Label-free')"), ] = None, page_size: Annotated[ int, Field(description="Number of results to return (max 100)"), ] = 20, sort_field: Annotated[ str, Field(description="Sort field: submissionDate or publicationDate"), ] = "submissionDate", sort_direction: Annotated[ str, Field(description="Sort direction: ASC or DESC"), ] = "DESC", ) -> dict: