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PubMedToolkit

class PubMedToolkit(BaseToolkit):

A toolkit for interacting with PubMed’s E-utilities API to access MEDLINE data.

This toolkit provides functionality to search and retrieve papers from the PubMed database, including abstracts, citations, and other metadata.

Parameters:

  • timeout (Optional[float]): The timeout for API requests in seconds. (default: :obj:None)

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init

def __init__(self, timeout: Optional[float] = None):

Initializes the PubMedToolkit.

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_make_request

def _make_request(
    self,
    endpoint: str,
    params: Dict[str, Union[str, int]],
    retries: int = 3
):

Makes a request to the PubMed/MEDLINE API with error handling and retries.

Parameters:

  • endpoint (str): The API endpoint to call.
  • params (Dict[str, Union[str, int]]): Query parameters.
  • retries (int, optional): Number of retry attempts. (default: :obj:3)

Returns:

Optional[Dict[str, Any]]: JSON response if successful, else None.

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search_papers

def search_papers(
    self,
    query: str,
    max_results: int = 10,
    sort: str = 'relevance',
    date_range: Optional[Dict[str, str]] = None,
    publication_type: Optional[List[str]] = None
):

Search for biomedical papers in MEDLINE via PubMed with advanced filtering options.

Parameters:

  • query (str): The search query string.
  • max_results (int, optional): Maximum number of results to return. (default: :obj:10)
  • sort (str, optional): Sort order - ‘relevance’ or ‘date’. (default: :obj:"relevance")
  • date_range (Optional[Dict[str, str]], optional): Date range filter with ‘from’ and ‘to’ dates in YYYY/MM/DD format. (default: :obj:None)
  • publication_type (Optional[List[str]], optional): Filter by publication types (e.g., [“Journal Article”, “Review”]). (default: :obj:None)

Returns:

List[Dict[str, str]]: List of papers with their metadata.

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get_paper_details

def get_paper_details(
    self,
    paper_id: Union[str, int],
    include_references: bool = False
):

Get detailed information about a specific biomedical paper from MEDLINE/PubMed.

Parameters:

  • paper_id (Union[str, int]): PubMed ID of the paper.
  • include_references (bool, optional): Whether to include referenced papers. (default: :obj:False)

Returns:

Optional[Dict[str, Any]]: Paper details including title, authors, abstract, etc., or None if retrieval fails.

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get_abstract

def get_abstract(self, paper_id: Union[str, int]):

Get the abstract of a specific biomedical paper from MEDLINE/ PubMed.

Parameters:

  • paper_id (Union[str, int]): PubMed ID of the paper.

Returns:

str: The abstract text.

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get_citation_count

def get_citation_count(self, paper_id: Union[str, int]):

Get the number of citations for a biomedical paper in MEDLINE/ PubMed.

Parameters:

  • paper_id (Union[str, int]): PubMed ID of the paper.

Returns:

int: Number of citations, or 0 if retrieval fails.

def get_related_papers(self, paper_id: Union[str, int], max_results: int = 10):

Get biomedical papers related to a specific paper in MEDLINE/ PubMed.

Parameters:

  • paper_id (Union[str, int]): PubMed ID of the paper.
  • max_results (int, optional): Maximum number of results to return. (default: :obj:10)

Returns:

List[Dict[str, Any]]: List of related papers with their metadata.

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get_tools

def get_tools(self):

Returns:

List[FunctionTool]: List of available tools.