Module poldracklab.pubmed

Functions to work with pubmed data

This module provides functions to work with pubmed data, including querying pubmed for articles and parsing the results.

The module contains the following functions:

• get_processed_query_results(): Query pubmed for articles and return a dictionary of processed results.
• run_pubmed_query(): Query pubmed for articles and return the raw pubmed records.
• parse_pubmed_query_result(): Parse the pubmed records into a dictionary.
• get_pubmed_journal_name(): Get the journal name from a pubmed record.
• get_pubmed_title(): Get the title from a pubmed record.
• get_pubmed_pmid(): Get the PMID from a pubmed record.
• get_pubmed_doi(): Get the DOI from a pubmed record.
• get_pubmed_pmcid(): Get the PMCID from a pubmed record.
• get_pubmed_year(): Get the year from a pubmed record.
• get_pubmed_volume(): Get the volume from a pubmed record.
• get_pubmed_pages(): Get the pages from a pubmed record.
• get_pubmed_authors(): Get the authors from a pubmed record.
• get_pubmed_abstract(): Get the abstract from a pubmed record.
• parse_pubmed_record(): Parse a pubmed record into a dictionary.

Functions

def get_email_from_dotenv() ‑> str

Expand source code

def get_email_from_dotenv() -> str:
    email = os.getenv("ENTREZ_EMAIL")
    if email is None:
        dotenv.load_dotenv()
        email = os.getenv("ENTREZ_EMAIL")
    if email is None:
        raise ValueError(
            "ENTREZ_EMAIL is not set in env - set in .env file or set as environment variable"
        )
    return email

def get_processed_query_results(query: str, email: str | None = None, retmax: int = 1000, verbose: bool = False) ‑> dict

Expand source code

def get_processed_query_results(
    query: str, email: Optional[str] = None, retmax: int = 1000, verbose: bool = False
) -> dict:
    """
    Get processed query results for a pubmed query

    Args:
        query (str): the query to search for
        email (str): the email to use for the Entrez service
        retmax (int): the maximum number of results to return
        verbose (bool): whether to print verbose output

    Returns:
        dict: a dictionary of processed query results
    """
    if email is None:
        email = get_email_from_dotenv()

    pubmed_records = run_pubmed_query(query, email, retmax, verbose)
    return parse_pubmed_query_result(pubmed_records)

Get processed query results for a pubmed query

Args

query : str

the query to search for

email : str

the email to use for the Entrez service

retmax : int

the maximum number of results to return

verbose : bool

whether to print verbose output

Returns

dict

a dictionary of processed query results

def get_pubmed_abstract(record: dict) ‑> str

Expand source code

def get_pubmed_abstract(record: dict) -> str:
    """
    Get the abstract from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the abstract
    """
    abstract = None
    if "Abstract" in record["MedlineCitation"]["Article"]:
        if "AbstractText" in record["MedlineCitation"]["Article"]["Abstract"]:
            abstract = " ".join(
                record["MedlineCitation"]["Article"]["Abstract"]["AbstractText"]
            )
    return abstract

Get the abstract from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the abstract

def get_pubmed_authors(record: dict) ‑> str

Expand source code

def get_pubmed_authors(record: dict) -> str:
    """
    Get the authors from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the authors
    """
    authors = None
    if "AuthorList" in record["MedlineCitation"]["Article"]:
        authorlist = [
            " ".join([author["LastName"], author["Initials"]])
            for author in record["MedlineCitation"]["Article"]["AuthorList"]
            if "LastName" in author and "Initials" in author
        ]

        authors = ", ".join(authorlist)
    return authors

Get the authors from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the authors

def get_pubmed_doi(record: dict) ‑> str

Expand source code

def get_pubmed_doi(record: dict) -> str:
    """
    Get the DOI from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the DOI
    """
    doi = None
    for j in record["PubmedData"]["ArticleIdList"]:
        if j.attributes["IdType"] == "doi":
            doi = str(j).lower().replace("http://dx.doi.org/", "")
    return doi

Get the DOI from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the DOI

def get_pubmed_journal_name(record: dict) ‑> str

Expand source code

def get_pubmed_journal_name(record: dict) -> str:
    """
    Get the journal name from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the journal name
    """
    return record["MedlineCitation"]["Article"]["Journal"]["ISOAbbreviation"]

Get the journal name from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the journal name

def get_pubmed_pages(record: dict) ‑> str

Expand source code

def get_pubmed_pages(record: dict) -> str:
    """
    Get the pages from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the pages
    """
    pages = None
    if "Pagination" in record["MedlineCitation"]["Article"]:
        pages = record["MedlineCitation"]["Article"]["Pagination"]["MedlinePgn"]
    return pages

Get the pages from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the pages

def get_pubmed_pmcid(record: dict) ‑> str

Expand source code

def get_pubmed_pmcid(record: dict) -> str:
    """
    Get the PMCID from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the PMCID
    """
    pmc = None
    for j in record["PubmedData"]["ArticleIdList"]:
        if j.attributes["IdType"] == "pmc":
            pmc = str(j)
    return pmc

Get the PMCID from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the PMCID

def get_pubmed_pmid(record: dict) ‑> int

Expand source code

def get_pubmed_pmid(record: dict) -> int:
    """
    Get the PMID from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        int: the PMID
    """
    return int(record["MedlineCitation"]["PMID"])

Get the PMID from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

int

the PMID

def get_pubmed_title(record: dict) ‑> str

Expand source code

def get_pubmed_title(record: dict) -> str:
    """
    Get the title from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the title
    """
    return record["MedlineCitation"]["Article"]["ArticleTitle"]

Get the title from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the title

def get_pubmed_volume(record: dict) ‑> str

Expand source code

def get_pubmed_volume(record: dict) -> str:
    """
    Get the volume from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        str: the volume
    """
    volume = None
    if "Volume" in record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]:
        volume = record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"][
            "Volume"
        ]
    return volume

Get the volume from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

str

the volume

def get_pubmed_year(record: dict) ‑> int

Expand source code

def get_pubmed_year(record: dict) -> int:
    """
    Get the year from a pubmed record

    Args:
        record (dict): the pubmed record to parse

    Returns:
        int: the year
    """
    year = None
    if (
        "Year"
        in record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"]
    ):
        year = int(
            record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"][
                "Year"
            ]
        )
    elif (
        "MedlineDate"
        in record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"]
    ):
        year = int(
            record["MedlineCitation"]["Article"]["Journal"]["JournalIssue"]["PubDate"][
                "MedlineDate"
            ].split(" ")[0]
        )
    return year

Get the year from a pubmed record

Args

record : dict

the pubmed record to parse

Returns

int

the year

def parse_pubmed_query_result(pubmed_records: dict) ‑> dict

Expand source code

def parse_pubmed_query_result(pubmed_records: dict) -> dict:
    """
    Parse the pubmed records into a dictionary

    Args:
        pubmed_records (dict): the pubmed records to parse

    Returns:
        dict: a dictionary of parsed pubmed records
    """
    pubs = {}
    for i in pubmed_records["PubmedArticle"]:
        parsed_record = parse_pubmed_record(i)
        pubs[parsed_record["DOI"]] = parsed_record
    return pubs

Parse the pubmed records into a dictionary

Args

pubmed_records : dict

the pubmed records to parse

Returns

dict

a dictionary of parsed pubmed records

def parse_pubmed_record(record: dict) ‑> dict

Expand source code

def parse_pubmed_record(record: dict) -> dict:
    """
    Parse a pubmed record into a dictionary

    Args:
        record (dict): the pubmed record to parse

    Returns:
        dict: a dictionary of parsed pubmed record
    """
    return {
        "DOI": get_pubmed_doi(record),
        "Abstract": get_pubmed_abstract(record),
        "PMC": get_pubmed_pmcid(record),
        "PMID": get_pubmed_pmid(record),
        "type": "journal-article",
        "journal": get_pubmed_journal_name(record),
        "year": get_pubmed_year(record),
        "volume": get_pubmed_volume(record),
        "title": get_pubmed_title(record),
        "page": get_pubmed_pages(record),
        "authors": get_pubmed_authors(record),
    }

Parse a pubmed record into a dictionary

Args

record : dict

the pubmed record to parse

Returns

dict

a dictionary of parsed pubmed record

def run_pubmed_query(query: str, email: str, retmax: int = 1000, verbose: bool = False) ‑> dict

Expand source code

def run_pubmed_query(
    query: str, email: str, retmax: int = 1000, verbose: bool = False
) -> dict:
    """
    Run a pubmed query and return the raw pubmed records

    Args:
        query (str): the query to search for
        email (str): the email to use for the Entrez service
        retmax (int): the maximum number of results to return
        verbose (bool): whether to print verbose output

    Returns:
        dict: a dictionary of pubmed records
    """
    Entrez.email = email
    if verbose:
        print(f"using {email} for Entrez service")
        print("searching for", query)
    handle = Entrez.esearch(db="pubmed", retmax=retmax, term=query)
    record = Entrez.read(handle)
    handle.close()
    pmids = [int(i) for i in record["IdList"]]
    if verbose:
        print("found %d matches" % len(pmids))

    # load full records
    handle = Entrez.efetch(
        db="pubmed",
        id=",".join(["%d" % i for i in pmids]),
        retmax=retmax,
        retmode="xml",
    )
    return Entrez.read(handle)

Run a pubmed query and return the raw pubmed records

Args

query : str

the query to search for

email : str

the email to use for the Entrez service

retmax : int

the maximum number of results to return

verbose : bool

whether to print verbose output

Returns

dict

a dictionary of pubmed records