pub.tools 5.3.0

Get publication metadata from NCBI's eUtils and generate citations.

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 = "[e-mail]"
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.