Word document with Endnote references to latex

Word document with Endnote references to latex

[BerndB]

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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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Re: Word document with Endnote references to latex

[Matthew Pickering]

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 <skonietz-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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?
>
> --
> You received this message because you are subscribed to the Google Groups
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> For more options, visit https://groups.google.com/d/optout.

Re: Word document with Endnote references to latex

[BerndB]

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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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org <javascript:>> 
> 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? 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "pandoc-discuss" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <javascript:>. 
> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org 
> <javascript:>. 
> > To view this discussion on the web visit 
> > 
> https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com. 
>
> > For more options, visit https://groups.google.com/d/optout. 
>

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Re: Word document with Endnote references to latex

[Mark Szepieniec]

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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 <skonietz-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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?
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> Groups
>> > "pandoc-discuss" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> an
>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> > To view this discussion on the web visit
>> > https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-
>> 0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com.
>> > For more options, visit https://groups.google.com/d/optout.
>>
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> .
>
> For more options, visit https://groups.google.com/d/optout.
>

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Re: Word document with Endnote references to latex

[BerndB]

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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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org <javascript:>> 
> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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? 
>>> > 
>>> > -- 
>>> > You received this message because you are subscribed to the Google 
>>> Groups 
>>> > "pandoc-discuss" group. 
>>> > To unsubscribe from this group and stop receiving emails from it, send 
>>> an 
>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>>> > To view this discussion on the web visit 
>>> > https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-
>>> 0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com. 
>>> > For more options, visit https://groups.google.com/d/optout. 
>>>
>>  -- 
>> You received this message because you are subscribed to the Google Groups 
>> "pandoc-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an 
>> email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <javascript:>.
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>> <javascript:>.
>> To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/pandoc-discuss/3ee6112f-4e06-480c-ad39-008de30734d9%40googlegroups.com 
>> <https://groups.google.com/d/msgid/pandoc-discuss/3ee6112f-4e06-480c-ad39-008de30734d9%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>

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Re: Word document with Endnote references to latex

[Mark Szepieniec]

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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 <skonietz-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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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?
>>>> >
>>>> > --
>>>> > You received this message because you are subscribed to the Google
>>>> Groups
>>>> > "pandoc-discuss" group.
>>>> > To unsubscribe from this group and stop receiving emails from it,
>>>> send an
>>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>> > To view this discussion on the web visit
>>>> > https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-01
>>>> 02-4888-b1a1-9da10fe1f6b4%40googlegroups.com.
>>>> > For more options, visit https://groups.google.com/d/optout.
>>>>
>>>  --
>>> You received this message because you are subscribed to the Google
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>>> msgid/pandoc-discuss/3ee6112f-4e06-480c-ad39-008de30734d9%
>>> 40googlegroups.com
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>>> .
>>>
>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>
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Re: Word document with Endnote references to latex

[Matthew Pickering]

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 <mszepien-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 <skonietz-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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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?
>>>>> >
>>>>> > --
>>>>> > You received this message because you are subscribed to the Google
>>>>> > Groups
>>>>> > "pandoc-discuss" group.
>>>>> > To unsubscribe from this group and stop receiving emails from it,
>>>>> > send an
>>>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>>> > To view this discussion on the web visit
>>>>> >
>>>>> > https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com.
>>>>> > For more options, visit https://groups.google.com/d/optout.
>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "pandoc-discuss" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>> To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/pandoc-discuss/3ee6112f-4e06-480c-ad39-008de30734d9%40googlegroups.com.
>>>>
>>>> For more options, visit https://groups.google.com/d/optout.
>>>
>>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "pandoc-discuss" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to pandoc-discuss+unsubscribe-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> To post to this group, send email to pandoc-discuss-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/pandoc-discuss/b2730c9c-d8a2-4bee-888c-3e7a19b8bd28%40googlegroups.com.
>>
>> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "pandoc-discuss" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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>
> For more options, visit https://groups.google.com/d/optout.

Re: Word document with Endnote references to latex

[nickbart1980-Re5JQEeQqe8AvxtiuMwx3w]

[-- Attachment #1.1: Type: text/plain, Size: 9603 bytes --]

> 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 
> <javascript:>> 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 <javascript:>> 
> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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? 
> >>>>> > 
> >>>>> > -- 
> >>>>> > You received this message because you are subscribed to the Google 
> >>>>> > Groups 
> >>>>> > "pandoc-discuss" group. 
> >>>>> > To unsubscribe from this group and stop receiving emails from it, 
> >>>>> > send an 
> >>>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
> >>>>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
> >>>>> > To view this discussion on the web visit 
> >>>>> > 
> >>>>> > 
> https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com. 
>
> >>>>> > For more options, visit https://groups.google.com/d/optout. 
> >>>> 
> >>>> -- 
> >>>> You received this message because you are subscribed to the Google 
> >>>> Groups "pandoc-discuss" group. 
> >>>> To unsubscribe from this group and stop receiving emails from it, 
> send 
> >>>> an email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
> >>>> To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
> >>>> To view this discussion on the web visit 
> >>>> 
> https://groups.google.com/d/msgid/pandoc-discuss/3ee6112f-4e06-480c-ad39-008de30734d9%40googlegroups.com. 
>
> >>>> 
> >>>> For more options, visit https://groups.google.com/d/optout. 
> >>> 
> >>> 
> >> -- 
> >> You received this message because you are subscribed to the Google 
> Groups 
> >> "pandoc-discuss" group. 
> >> To unsubscribe from this group and stop receiving emails from it, send 
> an 
> >> email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <javascript:>. 
> >> To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org 
> <javascript:>. 
> >> To view this discussion on the web visit 
> >> 
> https://groups.google.com/d/msgid/pandoc-discuss/b2730c9c-d8a2-4bee-888c-3e7a19b8bd28%40googlegroups.com. 
>
> >> 
> >> For more options, visit https://groups.google.com/d/optout. 
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "pandoc-discuss" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org <javascript:>. 
> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org 
> <javascript:>. 
> > To view this discussion on the web visit 
> > 
> https://groups.google.com/d/msgid/pandoc-discuss/CAE4-1rWDn7OewemXC7r8gKVm%3DOSagH1cy0PQm7knwti7yUwQ%3Dg%40mail.gmail.com. 
>
> > 
> > For more options, visit https://groups.google.com/d/optout. 
>

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[-- Attachment #1.2: Type: text/html, Size: 15796 bytes --]

Re: Word document with Endnote references to latex

[nickbart1980-Re5JQEeQqe8AvxtiuMwx3w]

[-- Attachment #1.1: Type: text/plain, Size: 10170 bytes --]

Sorry, the last command line should of course read 

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

if you want to generate, e.g, a docx file from your Thesis.tex containing 
`\citep{}`s.

On Saturday, December 6, 2014 12:49:50 PM UTC, nickba...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org wrote:
>
> > 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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...-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> 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? 
>> >>>>> > 
>> >>>>> > -- 
>> >>>>> > You received this message because you are subscribed to the 
>> Google 
>> >>>>> > Groups 
>> >>>>> > "pandoc-discuss" group. 
>> >>>>> > To unsubscribe from this group and stop receiving emails from it, 
>> >>>>> > send an 
>> >>>>> > email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
>> >>>>> > To post to this group, send email to pandoc-...-/JYPxA39Uh5TLH3MbocFFw@public.gmane.org. 
>>
>> >>>>> > To view this discussion on the web visit 
>> >>>>> > 
>> >>>>> > 
>> https://groups.google.com/d/msgid/pandoc-discuss/e00e6fe3-0102-4888-b1a1-9da10fe1f6b4%40googlegroups.com. 
>>
>> >>>>> > For more options, visit https://groups.google.com/d/optout. 
>> >>>> 
>> >>>> -- 
>> >>>> You received this message because you are subscribed to the Google 
>> >>>> Groups "pandoc-discuss" group. 
>> >>>> To unsubscribe from this group and stop receiving emails from it, 
>> send 
>> >>>> an email to pandoc-discus...-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org 
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