mcot.bibtex.pubmed

Functions

biorxiv_to_doi(bioarxiv_url)	Returns doi associated with article
doi_to_bibtex(doi)	Converts a DOI into a bibtex entry using doi.org
format_author(author)	Provides formatting for the author
get_fetcher()
get_firefox()
pmid_from_doi(identifiers)	Converts a sequence of identifiers into pmids
query_mult(pmids)	Creates a list of pubmed articles from a single query
to_bibtex(article)	Converts a PubMedArticle to a bibtex entry

biorxiv_to_doi

mcot.bibtex.pubmed.biorxiv_to_doi(bioarxiv_url: str) → str

Returns doi associated with article

If available will return published url, otherwise will return None

Parameters

bioarxiv_url – Url of the website (e.g., https://www.biorxiv.org/content/early/2018/06/14/266627)

Returns

DOI

doi_to_bibtex

mcot.bibtex.pubmed.doi_to_bibtex(doi: str) → mcot.bibtex.entry.BibTexEntry

Converts a DOI into a bibtex entry using doi.org

Parameters

doi – doi

Returns

corresponding bibtex entry

format_author

mcot.bibtex.pubmed.format_author(author: metapub.pubmedauthor.PubMedAuthor)

Provides formatting for the author

Parameters

author – individual author

Returns

text for in bibtex

get_fetcher

mcot.bibtex.pubmed.get_fetcher()

get_firefox

mcot.bibtex.pubmed.get_firefox()

pmid_from_doi

mcot.bibtex.pubmed.pmid_from_doi(identifiers)

Converts a sequence of identifiers into pmids

Parameters

identifiers – list of dois or pcmids

Returns

list of pmids

query_mult

mcot.bibtex.pubmed.query_mult(pmids) → List[metapub.pubmedarticle.PubMedArticle]

Creates a list of pubmed articles from a single query

Parameters

pmids – sequence of pubmed ids

Returns

pubmed article of each pubmed id

to_bibtex

mcot.bibtex.pubmed.to_bibtex(article: metapub.pubmedarticle.PubMedArticle) → mcot.bibtex.entry.BibTexEntry

Converts a PubMedArticle to a bibtex entry

Parameters

article – article metadata from pubmed

Returns

bibtex entry