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)
1 maintainer
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