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I hope this is the right place to ask this. I think it's extremely likely other TeX users have experienced the same problem I have, given its use in the academic world.

So, I have an ever-growing collection of scientific articles and books in pdf/ps format and an organizer would be extremely useful. The most important feature to me is a sensible file organization: it should allow me to have files properly named and saved to disk, so that I can get a reasonable organization even without accessing its own database. Secondly, efficiency: I'm planning to use it for self-archiving. Thirdly, ability to acquire article metadata from either the pdf file or the internet, but I know this can be pretty difficult to get right given the intrinsic sparsity of data itself

So far I have came down to two choices:

  • I,Librarian -> pro: just requires an http server and a dbms accessible from PHP, allowing for an optimal configuration for self-archiving: lighttpd+sqlite. cons: doesn't handle file renaming, is geared toward bioinformatics. I'm not sure, but it seems I can't even rename files manually once stored.
  • RefBase -> pro: handles file storing, allowing for creation of directories and the adoption of naming schemes. cons: requires MySql. Automated naming scheme may create very large file names that could get cluttered when using different filesystems.

your opinion?

EDIT: unfortunately I forgot to add "possibly free" as a requirement. This would rule out Mendeley, Papers and EndNote.

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This seems to be borderline for on-topic, and also could fall under 'subjective'. –  Joseph Wright Jun 22 '11 at 18:32
    
Take a look at the answers to tex.stackexchange.com/q/1612/86 I use refbase, and easily import metadata from the arxiv and MathSciNet (I'm a mathematician). Never heard of "I, Librarian" so can't comment on that. –  Andrew Stacey Jun 22 '11 at 19:28
    
I see the connection with LaTeX, but it is actual to general to be really on-topic. I good, comprehensive answer whould be useful for several people here, but I'm not sure if we are able to get one. –  Martin Scharrer Jun 22 '11 at 20:55
    
Not sure if that's what you are after, but did you check Mendeley? –  Vivi Jun 22 '11 at 21:55
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I don't see why "free" rules out mendeley: it has a free version, right? –  Seamus Jun 23 '11 at 11:06
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2 Answers

I am using Jabref. It is Java based and can therefor run on most platforms. Some of my Bibtex databases has at least 500 entries and the following are the advantages that I found very useful:

  • It is geared towards Latex/Bibtex and can import and export a wide ranges of formats and do web searches in JSTOR, ArXiv.org and a lot more.

  • It can export a sub-database based on your document's AUX file. Very useful for journal article submissions.

  • It is easy to add additional fields and entry types (for biblatex especially).

  • If your database is changed externally (during collaborative work) you must confirm changes before saving.

  • Every entry is linked to the PDF or PS file (if available) and can open it with the click of a button.

  • The DOI and URL fields are active and link directly to the web page of the article.

  • It has an export button to WinEDT, Lyx/Kile, EMACS, etc. that can directly insert a \cite at the cursor position in your document.

  • It has comprehensive search and grouping facilities. If you add the abstract and keywords it became a formidable tool in working with large databases during research.

  • IT IS FREE!

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I have used JabRef but to me it has the following deficiencies: no management of files, quirky interface (long labels tend to get hidden easily, making it harder to handle pathnames) and reliance of BibTeX as a storing format, caveat is that if you move your library from one disk to another, your file pathnames get useless –  Andrea Jun 23 '11 at 9:30
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@Andrea: I am not sure about the older versions, but in 2.7beta2 you can set directories per database that will override the default settings. If you use relative path names for the PDFs then you can move it easily between computers. –  Danie Els Jun 23 '11 at 11:23
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I use I, Librarian. If you want to store your PDFs with custom file names in folders, you should not use I, Librarian. (You can only rename supplementary files.) IMO, directory tree is not a good idea anyway. Once you collect thousands of PDFs, you will quickly discover that directory tree is not that useful. I don't know what field you are in. I, Librarian connects with JSTOR, NASA ADS, and arXiv, and imports RIS from bunch of other repositories, like Scopus, or just using DOI. I have never used refbase, so I don't know its features.

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