Reference Manager and Citation in Linux

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Work Flow

Mendeley => Helm-bibtex => Org-ref

Pdf-tools and org-noter are used for note-taking.

Reference Manager Mendeley is used to:

  1. to rename files


  2. generate bibtex file


PDF-tools to render and annotate pdf, and generate notes in individual org files. see here for more info.

Org-ref to take care of the citation duty.

Notes: org-ref needs lots of other emacs extensions, including helmet-bibtex, which requires helm, to name a few.

Some Tweaks

open pdf file defined in file field generated by Mendeley,

open the notes file -not working yet??

Temp alternative solution for above: open PDF first, then use C-c n to open the note file if exist. -tan

Special additional tweaks for helm-bibtex to work with Mendeley generated database

thread here. add following in bibtex-completion-find-pdf-in-field in file bibtex-completion.el

Another tweak is to open the note file from helm-bibtex:

Reference Management with Helm-Bibtex

Access reference

M-x helm-bibtex to start off, search for reference, Tab for options mendeley-03.png

M-o in ivy-bibitex


Email reference as email attachments

Helm-bibtex: Start an email session ( C-x m) and execute helm-bibtex ( M-x helm-bibtex). Search for your new publications and mark them with C-<space>, then press <f7> to execute the action “Attach PDF to email”. Then M-x helm-resume (the publications are still marked) and press <f6> to execute the action “Insert BibTeX entry”. Optionally insert more human readable references using M-x helm-resume and <f4> to execute the action “Insert reference”. Send email ( C-c C-c). Done. This takes less than 10 seconds.

Conversion of reference database


There are cases that you will need to communicate with the Microsoft Word world during manuscript editing phase. What I do is to use Scimax package to convert the org-ref enhanced org file to Word format. And the following procedure was applied to render the references to an Endnote format.

Export bibtex from org-ref

You would need to export the entries from org-ref to bibtex format.

You will then need export the bibtex format with JabRef in RIS format and then import into EndNote. Please find the steps below.

Convert BibTex to Endnotes or RIS

Export to RIS format with JabRef:

  1. Open the database you want to export with JabRef.
  2. To export only selected entries (press the “Control” button on keyboard and select the entries to export).
  3. Click on the File menu and select “Export selected entries” Note: To export whole database, click on the File menu and select “Export all entries”


  4. Choose a location to save the RIS file.


  5. In Files of type, select RIS(*.ris).
  6. In the File name box, enter a name and click on Save.

Now you should have a .ris file created.

Convert from bibtex to endnotes format with bibutils

Import into EndNote.


  1. Open the EndNote database into which you want to import the references.
  2. From the File menu, choose Import -> File.
  3. From Import Options, select RefMan(RIS).
  4. Click on Choose and browse to the file location which was exported from JabRef.
  5. In Files of type, select “All Files (.)”.
  6. Now locate the RIS file exported from JabRef and select it.
  7. Click Import to begin importing references.

Now you should have your JabRef references imported into EndNote.


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