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 = "myemailhere@imsweb.com"
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 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:
- An instance of one of the dataclasses in schema.py
- Keyword arguments directly
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.
