aoptk.literature.databases.pubmed

Classes

Class to get data from PubMed based on a query.

Module Contents

class aoptk.literature.databases.pubmed.PubMed(storage: pathlib.Path, query: aoptk.literature.query.Query | None = None)[source]

Bases: aoptk.literature.get_abstract.GetAbstract, aoptk.literature.get_id.GetID, aoptk.literature.get_metadata.GetMetadata

Class to get data from PubMed based on a query.

storage[source]

search_term[source]

_ncbi[source]

build_search_term(query: aoptk.literature.query.Query) → str[source]: Convert Query to PubMed search syntax.

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

_parse_pubmed_abstract_records(records: list[dict]) → list[aoptk.literature.abstract.Abstract][source]

Parse PubMed abstract records and return a list of Abstract objects.

Parameters:: records (dict) – A dictionary containing PubMed article records.

get_publications_metadata(ids: list[aoptk.literature.id.ID]) → list[aoptk.literature.metadata.Metadata][source]: Retrieve Publication metadata.

_parse_pubmed_metadata_records(records: list[list[dict[str, Any]]]) → list[aoptk.literature.metadata.Metadata][source]

Parse PubMed metadata records and return a list of PublicationMetadata objects.

Parameters:: records (list) – A nested list containing PubMed article records.

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