aoptk.literature.databases.ncbi

Classes

NCBI	Helper class to retrieve data from NCBI databases - PubMed and PMC.

Module Contents

class aoptk.literature.databases.ncbi.NCBI(database: Literal['pmc', 'pubmed'])

Bases: aoptk.literature.get_id.GetID

Helper class to retrieve data from NCBI databases - PubMed and PMC.

max_ncbi_results = 9998

max_concurrency = 2

max_requests_per_second = 2

minimal_year_publication = 1940

datetype = 'pdat'

batch_size = 200

async_retries = 10

database

semaphore

limiter

get_ids(search_term: str) → list[aoptk.literature.id.ID]

Retrieve a list of publication IDs based on the search term.

get_abstract_records(ids: list[aoptk.literature.id.ID]) → list[dict]

Retrieve abstract records based on the list of IDs. Note: There is still the 10 000 records limit.

Parameters:

ids (list[ID]) – A list of publication IDs for which to retrieve abstracts.

get_publications_metadata_records(ids: list[aoptk.literature.id.ID]) → list[Any]

Retrieve publication metadata records based on the list of IDs.

_batch_requests(ids: list[aoptk.literature.id.ID], func: collections.abc.Callable[Ellipsis, Any]) → list[Any]

Helper function to batch requests to NCBI.

async _async_get_ids(search_term: str) → list[aoptk.literature.id.ID]

Asynchronously retrieve a list of publication IDs based on the search term.

_get_publication_count_and_ids(search_term: str, mindate: str | None = None, maxdate: str | None = None) → tuple[int, list[str]]

Helper function to retrieve the count of publications and their IDs.

Retrieves IDs and total count based on the given search term and an optional date range.

async _async_get_publication_count_and_ids(search_term: str, mindate: str | None = None, maxdate: str | None = None) → tuple[int, list[str]]

Asynchronously retrieve the count of publications and their IDs based on the search term and date range.

async _collect_ids_for_year(search_term: str, year: int) → list[str]

Collect publication IDs for a specific year, splitting by months and days if the count exceeds the limit.

async _collect_ids_split_by_months_days(search_term: str, year: int) → list[str]

Collect publication IDs for a specific year.

Split the search into months and days to avoid exceeding the result limit.