JABREF and Atlas.ti

Help
1

Hi there,

Is there a possibility to export my JABREF biblio to the Endnote XML format?
Endnote XML format ids the the format Atlas.ti uses to be able to import from reference managers.

If it’s not possible at the moment, is this something that could come as a feature in the future?

Thank you.

2

Hi,

JabRef can export to EndNote. The Endnote Exporter is built using custom formatters.
As far as I see, this only a textual export:

It should be possible to create also an export for the XML variant.
For the docbook.xml we have also a custom layout.

3

Hi, thank you for your reply.

Is creating the XML variant something I can do?
Or is that something the programmers of JABREF would have to add?

Thank you.

4

Hi,
I don’t know how the EndNote xml format is looking like, but you could orientate yourself at how docbook format is created:

See also the help:
https://docs.jabref.org/import-export/export/customexports

5

HI, thank you.
I exported a bibtex xml from JABREF and add some wrappers I found in endnotexml type, these worked (Iwas able to import into Atlas.ti) you can see here below:

Screenshot 2020-05-01 at 11.26.10
Screenshot 2020-05-01 at 11.26.10603×558 36 KB

I tried this same modification on an exported DocBook51XML and it doesn’t work. I get this error: Invalid reference manager data file format: missing title. Here is the file:

Screenshot 2020-05-01 at 11.28.44
Screenshot 2020-05-01 at 11.28.44652×745 38.6 KB

I have come to the conclusion that what is need for the xml function properly in atlas.ti is the records and record wrapper and urls wrapper with url being path to "internal-pdf:.

How can I create an export filter to include these parameters.
Thank you.

6

Hi,

I was just mentioning the docbook as an example. You need to create your own custom layout files.
You need to create at least 3 files:
The begin and end file are applied only once. The other .layout file are applied for each entry.

  1. the endnotexml.begin.layout this contains the XML header stuff and the opening tags
    Here you would write the XML header stuff and the opening tags:
<?xml.....?>
<file xmlns=...>
<records>
  1. the endnotexml.layout file, one file for each entry type + one for default
    Here you do the main layout stuff. It represents the formatting of a single entry
    You probably need to apply some Formatters

Your “main” layout file endnotexml.layout should be structured as follows:

<record>
<entry id="\bibtexkey"`>
<article>
  \begin{author}<author>      \author} </author>  \end{author}
  \begin{title} <title> \title         </title>    \end{title}

...
<urls>
  <pdf-urls> 
      <url>\file</url>
</pdf-urls> 
</urls>
</article>
</entry>
</record>
  1. the file endnotexml.end.layout, here you simply write the closing tags
 </records>
</file>
7

Hi Thank you for this. It’s very helpful.
I have a little problem, maybe you have some ideas on how it can be solved.
The \file only writes the the subfolder and the pdf file—how can i get it to write the write the full path/ Thank you

8

Ok. I added a filed formatter and that worked. Thanks again

1 Like
9

Cool! It would be also really nice if you could contribute your layout files, so we could integrate them into JabRef

10

How do I do that? Where? Via GitHub?

11

Yes, create a fork and then put the files into the folder: You can directly do “Upload files”

Afterwards you can create a PR

12

Ok. I sent it on GITHUB.

Thank again.

1 Like