Conversion to BiBTeX format

Here are some tools that allow the conversion to BiBTeX format from various sources.

DOI to .bib

We can use the command line to convert this DOI (10.1101/gr.6339607) to the .bib format:

curl -LH "Accept: text/bibliography; style=bibtex" http://dx.doi.org/10.1101/gr.6339607
 @article{Gerstein_2007, title={What is a gene, post-ENCODE? History and updated definition}, volume={17}, ISSN={1088-9051}, url={http://dx.doi.org/10.1101/gr.6339607}, DOI={10.1101/gr.6339607}, number={6}, journal={Genome Research}, publisher={Cold Spring Harbor Laboratory Press}, author={Gerstein, M. B. and Bruce, C. and Rozowsky, J. S. and Zheng, D. and Du, J. and Korbel, J. O. and Emanuelsson, O. and Zhang, Z. D. and Weissman, S. and Snyder, M.}, year={2007}, month={Jun}, pages={669-681}}

We can also use the doi2bib webtool; copying and pasting the DOI returns:

@article{Gerstein2007,
  doi = {10.1101/gr.6339607},
  url = {http://dx.doi.org/10.1101/gr.6339607},
  year = {2007},
  month = {Jun},
  publisher = {Cold Spring Harbor Laboratory Press},
  volume = {17},
  number = {6},
  pages = {669-681},
  author = {M. B. Gerstein and C. Bruce and J. S. Rozowsky and D. Zheng and J. Du and J. O. Korbel and O. Emanuelsson and Z. D. Zhang and S. Weissman and M. Snyder},
  title = {What is a gene, post-ENCODE? History and updated definition},
  journal = {Genome Research}
}

PubMed ID to .bib

The TeXMed tool converts PubMed IDs to .bib. Copying and pasting 17567988 returns:

@Article{pmid17567988,
   Author="Gerstein, M. B.  and Bruce, C.  and Rozowsky, J. S.  and Zheng, D.  and Du, J.  and Korbel, J. O.  and Emanuelsson, O.  and Zhang, Z. D.  and Weissman, S.  and Snyder, M. ",
   Title="{{W}hat is a gene, post-{E}{N}{C}{O}{D}{E}? {H}istory and updated definition}",
   Journal="Genome Res.",
   Year="2007",
   Volume="17",
   Number="6",
   Pages="669--681",
   Month="Jun"
}

RIS to .bib

The Nature Publishing Group provides a citation button for their articles, however they only return in RIS format (for some reason). Here's the RIS format for an article published recently in Nature:

TY  - JOUR
AU  - Major, J. D.
AU  - Treharne, R. E.
AU  - Phillips, L. J.
AU  - Durose, K.
TI  - A low-cost non-toxic post-growth activation step for CdTe solar cells
JA  - Nature
PY  - 2014/06/25/online
VL  - advance online publication
SP  - 
EP  - 
PB  - Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.
SN  - 1476-4687
UR  - http://dx.doi.org/10.1038/nature13435
L3  - 10.1038/nature13435
M3  - Letter
ER  - 

I found this blog that shows how to use bibutils to convert between the two formats.

#download and compile bibutils
wget http://sourceforge.net/projects/bibutils/files/bibutils_5.4_src.tgz
tar -xzf bibutils_5.4_src.tgz
cd bibutils_5.4
./configure --install-dir bin2 --install-lib bin2
make && make install

#I saved the RIS format in a file called cit.ris
#convert from ris to xml to bib
bin/bin2/ris2xml cit.ris | bin/bin2/xml2bib > cit.bib

cat cit.bib
{
@Article{Major2014,
author="Major, J. D.
and Treharne, R. E.
and Phillips, L. J.
and Durose, K.",
title="A low-cost non-toxic post-growth activation step for CdTe solar cells",
journal="Nature",
year="2014",
month="Jun",
day="25",
publisher="Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.",
volume="advance online publication",
note="Letter",
issn="1476-4687",
url="http://dx.doi.org/10.1038/nature13435"
}

#there are also other utilities from bibutils
ls -1 bin/bin2
bib2xml
biblatex2xml
copac2xml
ebi2xml
end2xml
endx2xml
isi2xml
med2xml
modsclean
ris2xml
wordbib2xml
xml2ads
xml2bib
xml2end
xml2isi
xml2ris
xml2wordbib

ISBN to .bib

The webtool OttoBib converts ISBN to .bib. Inputting 978-0451524935 (select the BibTeX radio button) returns:

@Book{orwell19611984,
 author = {Orwell, George},
 title = {1984 : a novel},
 publisher = {Signet Classic},
 year = {1961},
 address = {New York, N.Y},
 isbn = {978-0451524935}
 }

Google Scholar

Google Scholar can export articles to .bib; just click the "cite" link and then "Import into BibTeX". For example, when viewing this search, clicking cite and Import into BibTeX from the top result returns:

@article{gerstein2007gene,
  title={What is a gene, post-ENCODE? History and updated definition},
  author={Gerstein, Mark B and Bruce, Can and Rozowsky, Joel S and Zheng, Deyou and Du, Jiang and Korbel, Jan O and Emanuelsson, Olof and Zhang, Zhengdong D and Weissman, Sherman and Snyder, Michael},
  journal={Genome research},
  volume={17},
  number={6},
  pages={669--681},
  year={2007},
  publisher={Cold Spring Harbor Lab}
}
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One comment Add yours
  1. There are also several online tools for RIS to bibtex. Since many people may be reluctant to command line tools, they may be worth mentioning!

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