automating insertion of references and creation of bibliography

2013-12-01

azim58 - automating insertion of references and creation of bibliography

Often when I write a document I don't want to deal with any reference
software so I just put the Pubmed ID (PMID) or doi (digital object
identifier) in parenthesis in text in the document. Then later I go back
with Zotero or Endnote Web and see what document I wanted to reference
there, add this to my library, and then insert the reference. I would
like to know of a way or any software to automatically recognize PMIDs or
DOIs within a bunch of text and then put the appropriate references.

So far I haven't found a solution. However, I have found some interesting
things.

If articles with PMIDs are the only articles that someone cares about,
then NCBI efetch allows one to easily retrieve an XML file of citaiton
information if one has a list of PMIDs.
http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch
JabRef can then open the xml file from NCBI efetch, and it can save the
references as a bibtex file which can be used with LaTeX.

There are websites that will retrieve any doi.
http://dx.doi.org
http://www.crossref.org/

However, I haven't yet found a tool that will allow me to retrieve a list
of dois and save the information as an xml file.

Oh, there's also this article which may or may not have some interesting
information.
Defrosting the Digital Library: Bibliographic Tools for the Next
Generation Web
http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000204

If I could convert a LaTeX file with references and a bibliography into a
Word file with those references and a bibliography that EndNote can
recognize then I will have a complete solution.

This forum post has some solutions related to this topic.
http://www.biostars.org/p/14051/

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