I have a huge collection of PDFs of research papers. Many of these have valuable annotations. I also have a huge .bib file containing citations for these and many other works. Is there a reference manager software where I could import the .bib file and the collection of PDFs and somehow the entries in the .bib file could be magically linked to the corresponding PDFs? I would then like to use that tool to access my PDFs (of research papers). I think this was a feature request for mendeley long back http://feedback.mendeley.com/forums/4941-general/suggestions/80946-automatically-find-pdfs-link-them-to-imported-me . As of today, I don't think that it has been implemented. I tried Quiqqa (http://www.qiqqa.com/) , but had no luck.

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    Migrate to tex.stackexchange.com
    – Paul
    Commented Mar 6, 2014 at 23:55
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    I think that this question is more relevant to Academia that to the tex forum. I suspect the people at the tex forum would consider it off-topic (see tex.stackexchange.com/questions/121961/…). My original question did not have latex in the title. latex/bib is not the only way to manage references and it is easy to interconvert between reference formats. Commented Mar 7, 2014 at 0:00
  • have you check Papers app? it may have what you looking for.
    – seteropere
    Commented Mar 7, 2014 at 0:02
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    jabref.sourceforge.net/help/ExternalFiles.php says that you need to name PDF by the bibtex key. I want the tool to read inside the PDF file (title and authors) to do the matching. Commented Mar 7, 2014 at 1:43
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    @Fuhrmanator: PDF does have metadata. A random sampling of the PDF files I have in my reference library suggests perhaps at least 60 or 70% have the title of the article included. Commented Apr 3, 2014 at 11:15

4 Answers 4


Here is one nearly automatic way to do it using Zotero (https://www.zotero.org/):

1) import the PDFs in Zotero. One way is to select multiple PDFs and drag them into a collection (in the LHS pane) of Zotero.

2) Select the PDF items (CTRL click in Windows for multiple selections), right click and select "Retrieve metadata from PDF". Note that this step searches online databases for missing information and seems fairly robust.

3) import the .bib file in Zotero

4) Go to the duplicates collection in the LHS panel and merge all the duplicates.


1) In step 4, there may be false negatives if the automatically retrieved metadata (in step 2) is too different from the corresponding entry in the .bib file (step 3)

2) Step 2 might fail on old scanned PDFs.


One options is BibDesk (OS X), which can track links between files and associated citations.

Personally, not a fan of what it does to the .bib file, but could suit your purpose.

  • Thanks. I upvoted this answer but I would have preferred to use a tool that works on windows/linux/android. Do you think that I could use Bibdesk to do the association and then export the library to some other (cross-platform) tool in a way that the new tool would import the file associations too? Commented Mar 7, 2014 at 15:06
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    @Abhishek IIRC BibDesk stores file-system references as new fields inside citations, so yes. It's a pretty tight coupling though. I'm really not the best person to ask though; I have largely given up on automated citation tools until I can get around to building my dream tool :P
    – Matthew G.
    Commented Mar 7, 2014 at 15:18

Try Tellico

A collection manager for linux which "provides default templates for books, bibliographies, videos, music, video games, coins, stamps, trading cards, comic books, and wines."

The reference manual states the following:

"If Tellico was compiled with exempi or poppler support, metadata from PDF files can be imported. Metadata may include title, author, and date information, as well as bibliographic identifiers which are then used to update other information."

Is that useful? If so, then you can check the site for reviews of Tellico and it works on the following:

  • Debian
  • Ubuntu
  • Gentoo
  • FreeBSD
  • openSUSE
  • PC-BSD
  • Fink (Mac OS X)
  • Fedora
  • Linux Mint
  • Pardus
  • ArchLinux

EndNote x7 has this feature, known as "PDF auto import."

I tried it and it got 0/3 of my sample PDFs correct, all from IEEE conferences initially downloaded from IEEE Xplore.

One of the three articles was closer to having a correct reference (the others were useless). But that article had PDF metadata visible in Acrobat Reader (Title, Author, Subject). EndNote got page numbers right (somehow), the DOI, but failed at the conference name, and reference type (EndNote mistakenly thought it was a journal article).

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