aoptk.literature.databases.pubmed
=================================

.. py:module:: aoptk.literature.databases.pubmed


Classes
-------

.. autoapisummary::

   aoptk.literature.databases.pubmed.PubMed


Module Contents
---------------

.. py:class:: PubMed(storage: pathlib.Path, query: aoptk.literature.query.Query | None = None)

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


   Class to get data from PubMed based on a query.


   .. py:attribute:: storage


   .. py:attribute:: search_term


   .. py:attribute:: _ncbi


   .. py:method:: build_search_term(query: aoptk.literature.query.Query) -> str

      Convert Query to PubMed search syntax.



   .. py:method:: get_abstracts(ids: list[aoptk.literature.id.ID]) -> list[aoptk.literature.abstract.Abstract]

      Retrieve Abstracts based on the query.



   .. py:method:: _parse_pubmed_abstract_records(records: list[dict]) -> list[aoptk.literature.abstract.Abstract]

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

      :param records: A dictionary containing PubMed article records.
      :type records: dict



   .. py:method:: get_publications_metadata(ids: list[aoptk.literature.id.ID]) -> list[aoptk.literature.metadata.Metadata]

      Retrieve Publication metadata.



   .. py:method:: _parse_pubmed_metadata_records(records: list[list[dict[str, Any]]]) -> list[aoptk.literature.metadata.Metadata]

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

      :param records: A nested list containing PubMed article records.
      :type records: list



   .. py:method:: get_ids() -> list[aoptk.literature.id.ID]

      Get a list of PubMed IDs from PubMed based on the query.