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I am working on a long-term research project and I would like to maintain a somewhat large bibliography (~500 papers). I am using Lyx, but I can also deal with Latex; can anyone suggest program to efficiently maintain a bibliography. I anticipate that there will be a few papers written on this long-term topic in the coming years, and I would like to try to find an organized way to cite sources from the bibliography database I wish to construct.

Does anyone have any advice? Would bibTex be good for this? Please take into consideration that I use Lyx

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That's certainly not the answer people would like to hear, but I like EndNote a lot, because it also manages the PDF files belonging to the articles. You can export the whole database to BibTex. So far I didn't find a good BibTeX-only software that is able to manage PDFs. There is also Mendeley, which is able to keep a BibTex file in parallel at a specified directory. –  biologue Aug 2 '13 at 7:30
    
Welcome to TeX.SX! You can have a look at our starter guide to familiarize yourself further with our format. –  texenthusiast Aug 2 '13 at 7:48
    
Which front end program do you use to edit your TeX programs? Some frontends provide macros to help tidy up and maintain .bib files. –  Mico Aug 2 '13 at 8:10
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6 Answers

You could use JabRef as a frontend to maintain your BibTeX-Database, it offers extensive sorting and grouping capabilities. It also plays nice with LyX.

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I concur. I used JabRef for the majority of my PhD writeup. –  Frank_Zafka Aug 2 '13 at 9:09
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I had JabRef installed on this machine - not for long. Notepad++ with a .bib syntax highlighting addon doesn't sort or group, admittedly, but being able to collapse to just the @article{key line, and good searching including regex works for me. You can of course use it together with JabRef, but I found I never used JabRef. –  Chris H Aug 2 '13 at 9:59
    
Jabref can also link the source PDF of an article stored in the hard disk, as well as the source URL, so it is easy jump from JabRef reference to the article contents. It is also very important for me that Jabref is able to search references by keywords in several sites as Medline. –  Fran Aug 7 '13 at 20:14
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I've been using Mendeley for managing my bibliography for a while and totally satisfied. I summarize here few features of Mendeley that might worth considering:

  • After registering (free) for an account, you are offered an online storage up to 2GB (can be extended with extra cost)
  • There are free desktop versions for Windows, Linux, and Mac OS X that you can use off-line without limitation to manage the bibliography along with any kinds of attachments and synchronize with the online storage.
  • You can organize your bibliography as hierarchical structures (like folders in a file system) as well as organize the attachments with different rules.
  • You can share any parts of your bibliography with your colleagues (assuming that they also use Mendeley in order to gain access to the shared bibliographies).
  • The desktop version (at least in Mac OS X that I'm using right now) offers built-in PDF viewer and supports highlights and annotations.
  • Mendeley desktop can monitor certain folders for automatically importing files you put in those folders.
  • Mendeley desktop can also maintain simultaneously one or several underlying BibTeX databases (see the Preferences -> BibTeX) in accordant with your bibliography, which are efficient for citing in your publications (for instance, using LyX).
  • In case you import an arbitrary PDF file, Mendeley desktop might be very helpful as it can look up the online databases for additional reference information such as the conference or journal, issues, etc.
  • Mendeley desktop supports backup and restore of the bibliography databases, searching, duplication checking, and various styles of references (IEEE, Havard, Chicago, Nature, Springer, APA, etc.)

Some other features that you might be interested in, but I'm not using, and therefore, cannot comment further:

  • Integration with MS Word
  • Integration with Zotero

Disclaimer: I'm just a Mendeley user and by no means affiliated with the company.

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Mendeley is a subject of a great frustration because it is bought by Elsevier. So that won't fly for many people around the world any more. Just google Elsevier buys Mendeley for extensive discussions. –  percusse Aug 2 '13 at 8:40
    
@percusse: Yes, I'm aware of the acquisition. Perhaps you are right in future, but as far as Mendeley offers the aforementioned features, I don't worry that much. The reason is that the plan-B, which is switching back to plain BibTeX, for instance, using JabRef or BibDesk (only Mac OS X), works in the worst case too. –  Huy Aug 2 '13 at 9:59
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Well, I think we disagree, that's something very much real today. I'm actually considering Mendeley/Zotero/EndNote as no-go tools. JabRef is my number one and I'm handling something like a 1800+ references with it with all kinds of filter groups etc. Using BibLaTeX with those corporate tools is simply painful for me. –  percusse Aug 2 '13 at 10:11
    
For the extreme lazy: Google("Elsevier buys Mendeley"). –  Pål GD Aug 2 '13 at 12:48
    
@percusse why is Zotero no-go tool? isn't is open source? –  michal.h21 Aug 7 '13 at 8:36
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I would like to add few more points that were not covered in the other answers.

Version Control:

No matter what tool you use, put it under revision control. I would recommend to use git and put your file on a public repository (like github or similar service). Versioning control will give you several advantages:

  • Backup. If you indeed put it on a remote server, then you have a built in backup.
  • Safe. If your file was messed up for some reason, or went through a fundamental revision, you can always roll back to older versions.
  • Finally, if you choose git you could apply the solution proposed by Andriu Svelykislt.

Workflow:

You didn't mention what is the workflow in which you will use the file(s). If you're the only user - then I would go for one central file (which is under revision control), and link to it from the various projects. This way you could maintain only one file, and changes will be reflected in the various projects. If instead of soft links you use git submodule you could gain even more power. For example, each project will be associated with a specific version of the central file. Note the dangers of git submodule.

Everything becomes way more tricky, if you are not the only user of the bib file. This is an altogether story, and in my mind it is worthy to invest some time, and discuss a workflow with your collaborators.

Possible tools:

Answering your question more directly, I used both jabref and bibdesk and ended up with emacs. I maintain my files using emacs directly. It is not perfect but I find it efficient enough.

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I totally agree with the answer by krlmlr and I think that another useful plugin to Zotero should be mentioned here: Autozotbib

AutoZotBib is a Zotero plugin which will automatically keep a specified BibTeX file in sync with your Zotero library. Whenever you add, delete or modify a reference in Zotero the BibTeX file will be immediately updated, ready for you to use with your LaTeX file.

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If JabRef or Mendeley aren't to your taste, and you use OSX, then try BibDesk. It manages .bib files and sorts PDFs. It's also free and open source.

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I am using Zotero. I found it superior to Mendeley (I was evaluating both about half a year ago) in terms of accurary of importing references from web sites. I consider it the killer feature, and it's the main reason for me to use a reference manager. It will download the full text and associate it with your reference, all with just one click. This works both within Firefox (where you can install Zotero as add-in) and when using stand-alone Zotero (with an importer plugin in the browser).

The features are otherwise similar to that of Mendeley (see Hui's answer), except that annotations are not supported too well.

Zotero is open source and supports plugins itself. I find ZotFile very useful.

A BibTeX export exists, just remember to set the export encoding to ASCII.

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