acore.publications_analysis package

acore.publications_analysis package#

getMedlineAbstracts(idList)[source]#
get_publications_abstracts(data, publication_col='publication', join_by=['publication', 'Proteins', 'Diseases'], index='PMID')[source]#

Accesses NCBI PubMed over the WWW and retrieves the abstracts corresponding to a list of one or more PubMed IDs.

Parameters:

  • data – pandas dataframe of diseases and publications linked to a list of proteins (columns: ‘Diseases’, ‘Proteins’, ‘linkout’ and ‘publication’).

  • publication_col (str) – column label containing PubMed ids.

  • join_by (list) – column labels to be kept from the input dataframe.

  • index (str) – column label containing PubMed ids from the NCBI retrieved data.

Returns:

Pandas dataframe with publication information and columns ‘PMID’, ‘abstract’, ‘authors’, ‘date’, ‘journal’, ‘keywords’, ‘title’, ‘url’, ‘Proteins’ and ‘Diseases’.

Example:

result = get_publications_abstracts(data,
            publication_col='publication',
            join_by=['publication','Proteins','Diseases'],
            index='PMID')