> I think there might be specific endnote -> bibtex conversion tools …

bibutils is one such program, and pandoc-citeproc uses this under the hood to convert RIS, EndNote, EndNote XML, ISI, MEDLINE, and Copac to MODS which pandoc-citeproc can parse.

For an Endnote file, try:

`end2xml yourendnotefile.enl | xml2bib > yourbibfile.bib`

or for an EndNote XML file:

`endx2xml yourendnotefile.xml | xml2bib > yourbibfile.bib`

You could also try using your EndNote file directly:

pandoc Thesis.docx -s -o Thesis.tex --bibliography=yourendnotefile.enl --csl=vancouver.csl

In any case you will have to replace all references of the type `\hyperref[ux5fENREFux5f1]` by an appropriate `\citep{bibTexKey}` in your latex source file. (Use `\citep{}` instead of `\cite{}` if you want numbers such as "(1)" as in-text citations.)


On Friday, 5 December 2014 22:08:13 UTC, Matthew Pickering wrote:

I think there might be specific endnote -> bibtex conversion tools as
well which would probably work better.

On Fri, Dec 5, 2014 at 9:51 PM, Mark Szepieniec <msze...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
> Pandoc is just seeing your citations as internal hyperlinks (to the
> respective references), it just read your reference list as text, and
> doesn't realize they are actually references. You will need to convert your
> references to bibtex form, either manually, or with the tool Matthew
> mentioned.
>
> The transformation of \hyperrefs into \cites could be done with a pandoc
> filter (if you can code python or haskell), or you could do a search and
> replace in your text editor.
>
>
>
> On Fri, Dec 5, 2014 at 10:41 PM, BerndB <skon...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
>>
>> Okay... I used pandoc and could create a file looking like a LaTex file
>> which also compiles.
>>
>> pandoc Thesis.docx -s -o Thesis.tex
>>
>> ==== The compiled PDF file
>> ============================================================================================
>>
>> On the first look, it is impressive. Looks like I would need it. However,
>> I do not understand how the literature references are transformed. In fact,
>> I would need something like an additional bibliography output.
>>
>> === Inside the .tex file
>> =======================================================================================================
>>
>> Looking into the .tex file, [1] has been replaced by
>> "{[}\hyperref[ux5fENREFux5f1]{1}{]}" which obviously corresponds to the
>> following entry at the end of the document:
>>
>> "References
>>
>> \hyperdef{}{ux5fENREFux5f1}{}{}1. Ogawa J, Shimizu S: Microbial enzymes:
>> new industrial applications from traditional screening methods. Trends
>> in biotechnology 1999, 17:13-21."
>>
>>
>> ===========================================================================================================================
>>
>> So, I am pretty close. But I would need \cite{bibTexKey} instead of
>> \hyperref[ux5fENREFux5f1], and I would need to access an extra bibliography
>> file, such that I can change the references in the .tex file afterwards.
>> .
>>
>> On Friday, December 5, 2014 10:20:08 PM UTC+1, Mark Szepieniec wrote:
>>>
>>> I think Matthew means that the tool he linked to does a good job of
>>> transforming text such as
>>>
>>> Watscon JD, Crick F, "Molecular Structure of Nucleic Acids: A Structure
>>> for Deoxyribose Nucleic Acid", Nature (1953)
>>>
>>> into a structured reference that latex can work with. However, one would
>>> then still need to manually change each instance of "[1]" in the original
>>> document to "\cite{watsoncrick}", or something similar.
>>>
>>> In your case, if I understand correctly, your references would also have
>>> to be transformed from EndNote's format to bibtex (Latex's format). This is
>>> not something that pandoc can do.
>>>
>>> On Fri, Dec 5, 2014 at 9:11 PM, BerndB <skon...@gmail.com> wrote:
>>>>
>>>> Hi, thanks for trying to help! ;)
>>>>
>>>> But I do not understand what you mean with "manually".
>>>>
>>>> I maintained and included references with Endnote. It is a reference
>>>> manager for Word.
>>>>
>>>> On Friday, December 5, 2014 9:07:10 PM UTC+1, Matthew Pickering wrote:
>>>>>
>>>>> If you have manually typed out the references then I don't think there
>>>>> is. I had success using this tool to convert[1] references to a more
>>>>> suitable format but I had to manually update all the citation points
>>>>> obviously.
>>>>>
>>>>> [1]: http://text2bib.economics.utoronto.ca/
>>>>>
>>>>> On Fri, Dec 5, 2014 at 7:51 PM, BerndB <skon...@gmail.com> wrote:
>>>>> > Hello,
>>>>> >
>>>>> > I have a huge Word document with about 100 references that I included
>>>>> > with
>>>>> > Endnote. (I started with Word to maintain comment bubbles for the
>>>>> > references
>>>>> > and to use track changes. However, I would now prefer to have the
>>>>> > final
>>>>> > version as a latex document to apply to the common standards.)
>>>>> >
>>>>> > ==================================
>>>>> > Example
>>>>> > ==================================
>>>>> > Somewhere in the text: Genes are coded in the DNA of an organism [1].
>>>>> >
>>>>> > (...)
>>>>> >
>>>>> > References (at the end of the document): 1. Watscon JD, Crick F,
>>>>> > "Molecular
>>>>> > Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic
>>>>> > Acid",
>>>>> > Nature (1953)
>>>>> > ==================================
>>>>> >
>>>>> > Is there any possibility to convert the Word file into a LaTex file
>>>>> > (while
>>>>> > also transforming the references into proper LaTex references)?
>>>>> >
>>>>> > How would I do it with pandoc?
>>>>> >
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>>>
>>>
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