BioContextAI Knowledgebase MCP

Instructions

Implementation Reference

• src/biocontext_kb/core/europepmc/_get_europepmc_articles.py:10-72 (handler)

  The main handler function that implements the logic to search and retrieve articles from Europe PMC using their REST API. Decorated with @core_mcp.tool() to register it as an MCP tool named 'get_europepmc_articles'.

  @core_mcp.tool()
  def get_europepmc_articles(
      query: Annotated[Optional[str], Field(description="General search query")] = None,
      title: Annotated[Optional[str], Field(description="Search in article titles")] = None,
      abstract: Annotated[Optional[str], Field(description="Search in abstracts")] = None,
      author: Annotated[Optional[str], Field(description="Author name (e.g., 'lastname,firstname')")] = None,
      search_type: Annotated[str, Field(description="'and' or 'or' (default: 'or')")] = "or",
      sort_by: Annotated[
          Optional[str],
          Field(description="'recent' or 'cited' (default: none)"),
      ] = None,
      page_size: Annotated[int, Field(description="Results per page (1-1000)", ge=1, le=1000)] = 25,
  ) -> dict:
      """Search Europe PMC articles by query, title, abstract, or author. Combine search terms with 'and'/'or' logic.
  
      Returns:
          dict: Search results with resultList containing articles (title, authors, abstract, journal, PMC/DOI IDs) or error message.
      """
      # Ensure at least one search parameter was provided
      if not any([query, title, abstract, author]):
          return {"error": "At least one of query, title, abstract, or author must be provided"}
  
      # Build query components
      query_parts = []
  
      if query:
          query_parts.append(query)
  
      if title:
          query_parts.append(f"title:{title}")
  
      if abstract:
          query_parts.append(f"abstract:{abstract}")
  
      if author:
          query_parts.append(f"auth:{author}")
  
      # Join query parts based on search type
      query = " AND ".join(query_parts) if search_type.lower() == "and" else " OR ".join(query_parts)
  
      # If multiple parts and not explicitly AND, wrap in parentheses for OR
      if len(query_parts) > 1 and search_type.lower() == "or":
          query = f"({query})"
  
      # Add sort parameter
      if sort_by is not None:
          if sort_by.lower() == "cited":
              query += " sort_cited:y"
          else:  # default to recent
              query += " sort_date:y"
  
      # URL encode the query
      encoded_query = quote(query)
  
      url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/search?query={encoded_query}&format=json&resultType=core&pageSize={page_size}"
  
      try:
          response = requests.get(url)
          response.raise_for_status()
          return response.json()
      except requests.exceptions.RequestException as e:
          return {"error": f"Failed to fetch Europe PMC articles: {e!s}"}

• src/biocontext_kb/app.py:35-40 (registration)

  Registers the core_mcp server (containing the get_europepmc_articles tool) into the main MCP app with a prefix 'bc' (slugify('BC')), making the tool available as 'bc_get_europepmc_articles'.

  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/__init__.py:9-9 (registration)

  Imports all tools from the europepmc module, which triggers the execution of decorators and registers get_europepmc_articles on core_mcp.

  from .europepmc import *

• src/biocontext_kb/core/europepmc/_get_europepmc_articles.py:11-22 (schema)

  Pydantic schema defined via Annotated type hints and Field descriptions for input parameters and return type.

  def get_europepmc_articles(
      query: Annotated[Optional[str], Field(description="General search query")] = None,
      title: Annotated[Optional[str], Field(description="Search in article titles")] = None,
      abstract: Annotated[Optional[str], Field(description="Search in abstracts")] = None,
      author: Annotated[Optional[str], Field(description="Author name (e.g., 'lastname,firstname')")] = None,
      search_type: Annotated[str, Field(description="'and' or 'or' (default: 'or')")] = "or",
      sort_by: Annotated[
          Optional[str],
          Field(description="'recent' or 'cited' (default: none)"),
      ] = None,
      page_size: Annotated[int, Field(description="Results per page (1-1000)", ge=1, le=1000)] = 25,
  ) -> dict:

• src/biocontext_kb/core/europepmc/__init__.py:3-3 (registration)

  Imports the get_europepmc_articles function into the europepmc package namespace.

  from ._get_europepmc_articles import get_europepmc_articles