aoptk.literature.databases.pubmed

Exceptions

QueryTooLargeError

Exception raised when query returns more than maximum_results.

Classes

Class to get data from PubMed based on a query.

Module Contents

exception aoptk.literature.databases.pubmed.QueryTooLargeError(count: int, maximum: int)[source]

Bases: Exception

Exception raised when query returns more than maximum_results.

count[source]

maximum[source]

class aoptk.literature.databases.pubmed.PubMed(query: str)[source]

Bases: aoptk.literature.get_abstract.GetAbstract, aoptk.literature.get_id.GetID, aoptk.literature.get_publication_metadata.GetPublicationMetadata

Class to get data from PubMed based on a query.

maximum_results = 10000[source]

batch_size = 200[source]

max_retries = 5[source]

_query[source]

id_list[source]

publication_count[source]

get_abstracts() → list[aoptk.literature.abstract.Abstract][source]: Retrieve Abstracts based on the query.

get_publications_metadata() → list[aoptk.literature.publication_metadata.PublicationMetadata][source]: Retrieve Publication metadata based on the query.

get_publication_count() → int[source]: Return the number of publications matching the query in PubMed.

get_ids() → list[aoptk.literature.id.ID][source]: Get a list of PubMed IDs from PubMed based on the query.

_get_abstract(pmid: str) → aoptk.literature.abstract.Abstract[source]: Get the abstract for a given PubMed ID.

_get_publication_metadata(pmid: str) → aoptk.literature.publication_metadata.PublicationMetadata[source]: Get the publication metadata for a given PubMed ID.