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Installation

pip install pub.tools

To use this tool you are advised to create an Entrez account and use the associated email and API key.

from Bio import Entrez
Entrez.email = "[email protected]"
Entrez.tool = "pub.tools"
Entrez.api_key = "mykeyhere"

Tools available:

  • entrez - a wrapper API for BioPython
  • citations - creates citations for 6 different types using IMS standards
  • date - formats dates into our desired format

Citations

Citations are based on a standard defined by PubMed https://www.ncbi.nlm.nih.gov/books/NBK7256/. For some publication types, passing the italicize parameter with a True value will return HTML with italic tagged journals or conference names.

You can easily create a citation from a retrieved PubMed record:

>>> from pub.tools import entrez
>>> from pub.tools import citations
>>> if pub := entrez.get_publication(pmid=12345678):
>>>     citations.publication_citation(publication=pub)

Alternatively, you can pass one of the following to the citation function:

  1. An instance of one of the dataclasses in schema.py
  2. Keyword arguments directly

Journals

The journals module uses the PMC source file https://www.ncbi.nlm.nih.gov/pmc/journals/?format=csv to construct a library of journals keyed by abbreviation or full title.