metapub 0.1.0

Pubmed / NCBI / eutils interaction library, handling the metadata of pubmed papers.

Metapub is a Python library that provides python objects fetched via eutils that represent papers and concepts found within the NLM.

PubMedArticle / PubMedFetcher

Basic usage:

fetch = PubMedFetcher()
article = fetch.article_by_pmid('123456')
print article.title
print article.journal, article.year, article.volume, article.issue
print article.authors

MedGenConcept / MedGenFetcher

Basic usage:

fetch = MedGenFetcher()
concept = fetch.concept_by_uid('336867')
print concept.name
print concept.description
print concept.associated_genes
print concept.modes_of_inheritance

These objects abstract some interactions with pubmed, and intends to encompass as many types of database lookups and summaries as can be provided via Eutils / Entrez.

Metapub relies on the very neat eutils package created by Reece Hart, which you can check out here:

http://bitbucket.org/uta/eutils

This library is in its very early stages and there’s a lot that may change, and quite a bit planned for implementation in 2014-2015.

Feel free to use the library with confidence that each released version is well tested – and in a couple of cases, some of its code is already in production – but until (say) version 0.5, don’t expect consistency between versions.

YMMV, At your own risk, etc.

–Naomi Most (@nthmost)