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I am using pandoc to add BibTeX bibliographies in a chosen CSL style to documents in various output formats.

pandoc --bibliography=previews.bib --csl=american-medical-association.csl -o output.pdf input.md

The Zotero reference manager offers a vast CSL style repository with a recurring sample bibliography shown below in American Medical Association CSL style.

I am trying to reproduce what looks like an @INBOOK{Hogue entry, but I am experiencing an undesired result. I wonder if someone could help me to a BibTeX source file which correctly reproduces the Zotero sample bibliography in whatever CSL style? It would be a handy reference for testing.

  1. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual. 3rd ed. Cold Spring Harbor, NY: CSHL Press; 2001.
  2. Kötter P, Ciriacy M. Xylose fermentation by Saccharomyces cerevisiae. Appl Microbiol Biotechnol. 1993;38(6):776-783. doi:10.1007/BF00167144.
  3. Pear R. Crisis Puts Tax Moves Into Play. The New York Times. http://www.nytimes.com/2008/10/02/business/02tax.html. Published October 2, 2008. Accessed October 4, 2008.
  4. Method and system for placing a purchase order via a communications network. 1999. Available at: http://www.patentstorm.us/patents/5960411.html. Accessed October 4, 2008.
  5. Hogue CWV. Structure Databases. In: Baxevanis AD, Ouellette BFF, eds. Bioinformatics. 2nd ed. Life Sciences Series. New York, NY: Wiley-Interscience; 2001:83-109.
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  • OK, I was given the link to the original previews.json file. Zotero should be capable of converting it to BibTeX, but I am struggling. – Serge Stroobandt Jun 2 '14 at 21:19
  • I think Pandoc can use the json file as is. – dfc Jun 2 '14 at 21:44
  • 1
    @dfc There appears to be a difference between JSON citeproc and CLS JSON. This is the error message I received when trying: pandoc-citeproc: when expecting a [a], encountered Object instead pandoc: Error running filter pandoc-citeproc – Serge Stroobandt Jun 3 '14 at 0:34
2
  • Source: previews.json
  • Conversion to BibTeX: see Zotero forum discussion
  • The automatic conversion was not complete. Publication date fields had to be entered manually. The Bibtexkeys were also created manually.

Eventually, the conversion process taught an interesting lesson:

@INBOOK entries should not be used. Use @INCOLLECTION instead.

Furthermore, a CSL style bug could be corrected.

Happy CSL testing!


input.md

test file[@Sambrook.2001; @Kotter.1993; @Pear.2008; @patent; @Hogue.2001]

previews.bib

% Encoding: UTF8

@INCOLLECTION{Hogue.2001,
  author = {Hogue, Christopher W. V.},
  title = {Structure Databases},
  booktitle = {Bioinformatics},
  publisher = {Wiley-Interscience},
  year = {2001},
  editor = {Baxevanis, Andreas D. and Ouellette, B. F. Francis},
  series = {Life Sciences Series},
  pages = {83--109},
  address = {New York, {NY}},
  edition = {2},
  isbn = {0471383910}
}

@ARTICLE{Kotter.1993,
  author = {Kötter, Peter and Ciriacy, Michael},
  title = {Xylose fermentation by Saccharomyces cerevisiae},
  journal = {Applied Microbiology and Biotechnology},
  year = {1993},
  volume = {38},
  pages = {776--783},
  number = {6},
  month = {March},
  abstract = {We have performed a comparative study of xylose utilization in Saccharomyces
    cerevisiae transformants expressing two key enzymes in xylose metabolism,
    xylose reductase ({XR)} and xylitol dehydrogenase ({XDH)}, and in
    a prototypic xylose-utilizing yeast, Pichia stipitis. In the absence
    of respiration (see text), baker's yeast cells convert half of the
    xylose to xylitol and ethanol, whereas P. stipilis cells display
    rather a homofermentative conversion of xylose to ethanol. Xylitol
    production by baker's yeast is interpreted as a result of the dual
    cofactor dependence of the {XR} and the generation of {NADPH} by
    the pentose phosphate pathway. Further limitations of xylose utilization
    in S. cerevisiae cells are very likely caused by an insufficient
    capacity of the non-oxidative pentose phosphate pathway, as indicated
    by accumulation of sedoheptulose-7-phosphate and the absence of fructose-1,6-bisphosphate
    and pyruvate accumulation. By contrast, uptake at high substrate
    concentrations probably does not limit xylose conversion in S. cerevisiae
    {XYL1/XYL2} transformants.},
  doi = {10.1007/BF00167144},
  timestamp = {2008.10.04},
  url = {http://dx.doi.org/10.1007/BF00167144}
}

@ARTICLE{Pear.2008,
  author = {Pear, Robert},
  title = {Crisis Puts Tax Moves Into Play},
  journal = {The New York Times},
  year = {2008},
  month = {October},
  chapter = {Business},
  timestamp = {2008.10.04},
  url = {http://www.nytimes.com/2008/10/02/business/02tax.html}
}

@BOOK{Sambrook.2001,
  title = {Molecular Cloning: A Laboratory Manual},
  publisher = {{CSHL} Press},
  year = {2001},
  author = {Sambrook, Joe and Russell, David William},
  address = {Cold Spring Harbor, {NY}},
  edition = {3},
  month = {January},
  isbn = {0879695773},
  shorttitle = {Molecular Cloning}
}

@PATENT{patent,
  nationality = {US},
  number = {5960411},
  year = {1999},
  yearfiled = {1997},
  title = {Method and system for placing a purchase order via a communications
    network},
  day = {28},
  month = {September},
  url = {http://www.google.com/patents/US5960411},
  abstract = {A method and system for placing an order to purchase an item via the
    Internet. The order is placed by a purchaser at a client system and
    received by a server system. The server system receives purchaser
    information including identification of the purchaser, payment information,
    and shipment information from the client system. The server system
    then assigns a client identifier to the client system and associates
    the assigned client identifier with the received purchaser information.
    The server system sends to the client system the assigned client
    identifier and an {HTML} document identifying the item and including
    an order button. The client system receives and stores the assigned
    client identifier and receives and displays the {HTML} document.
    In response to the selection of the order button, the client system
    sends to the server system a request to purchase the identified item.
    The server system receives the request and combines the purchaser
    information associated with the client identifier of the client system
    to generate an order to purchase the item in accordance with the
    billing and shipment information whereby the purchaser effects the
    ordering of the product by selection of the order button.},
  timestamp = {2008.10.04},
}

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