Scientific Reprint Management Software for OS X

Notes from Flip Phillips "I've played with a wide variety of these sorts of databases over the years,. A few things to note -- I do vision research, I use TeX / BibTeX, many new reprints I use are available from PubMed-indexed sources, I've scanned in and OCRd a few thousand of my old reprints (with the help of several brave work study undergrads), my entire database is 3k or so papers and about 10GB. Thus, all my opinions are colored by these facts."

And William Hayes, "I have really heavy literature users where I work. I also support (I manage a biopharma library and literature informatics group) both PC's and Mac's"

Yep

Interesting, but not really geared for scientific papers (ie- no way to associate citation information w/ them easily). Not sure it would handle my entire library. Seems a bit more for the 'here's a bunch of paper I want to digitize' crowd, and for that it looks to be excellent. I found the tagging/metadata a little clumsily implemented.

Pros

aesthetically nice.

Cons

not good if you want citation information.

Papers

Pretty, honestly not even in alpha, let alone near release ready. Crashed chronically, lack of ability to locate files where I want them (ie- incomplete preference system). One nice thing - love the 'select some text and look it up in PubMed' feature to fill out the citation information. I'd love to see this in other programs (notably BibDesk). Not totally clear how the BibTeX is/will be implemented.

Pros

aesthetically nice, PubMed lookup nice.

Cons

boom! bang! They're charging for these pre-betas with a timeout on the 'trial' of 30 days. Has potential to be sure... but need to -see it work- before I'm willing to invest too many papers / $.

DEVONthink

Does a lot more than just database your PDFs. Sort of kitchen sinkish, it handles your papers, other media, web pages, tables, etc. It handles several thousand papers easily. The Office version comes with an interesting web-server to access the database from offsite (the search is wicked-fast), and a really fast OCR . Again, there's no -obviously straightforward- way to tie in the BibTeX / citation information. There are ways to do it, they just feel a little clunky. The 'find similar' and 'classify' features are really the most useful here. Have a paper on synaptic plasticity and want to find other papers in your collection that are lexically similar? You can 'see also' them using their engine (which works pretty well, but not top notch with such a large database). It uses something seemingly simple to do the matching, maybe just concordance (nothing like LSA).

Pros

cool 'similar paper' finder, web server.

Cons

showing its age aesthetically, no easy citation information linkage, have to go through acrobatics to get Spotlight to index PDFs when they're embedded in the database (ie- no good spotlight support).

WorkLife framework

Mathematica specific, it isn't really a PDF database specifically but much more in that it is an interesting diary / note system. You -can- use it as a sort of database for your PDFs if you use Mathematica . I've been using a version of MMa that WorkLife isn't quite compatible with yet, but played around this summer using 5.2 and saw some excellent potential there if you're a MMa fiend. I'm sure once the versions get synched up I'll be using it again, as I am a MMa fiend.

Pros

integration into a comprehensive tech computing environment.

Cons

same :)

BibDesk

I've used BibDesk for quite a while to keep my BibTeX in ship shape. The features keep getting better, seems to remain solid. When I migrate older papers in I wish that there was better 'grab the information from PubMed' feature like Papers, and a nifty 'find similar papers' like Think. Still, easy enough to work with, you'll be busy if you have a bunch of papers to add... The scripting feature is also useful - clean up capitalizations, massage citations. Lately I've been making the shift from the Think-world because the citation information combined with Spotlight has proven to be more useful than the 'see also' functionality, overall.

Pros

free and well supported despite this :), features continue to expand, designed for BibTeX (again, useful in my world).

Cons

not the prettiest cow at the state fair, but the pros make up for that.

Did I mention it's free?

EndNote

Well, I used it in the mid 90s, back when FrameMaker existed for the Mac <snif>. Haven't seen it since....

Quosa

Managing thousands of PDF's is easy, importing PDF's will (when able to match against Pubmed) automatically associate full bibliographic information for 30-70% of the PDF's I've loaded up. The built in text search engine (based on Lucene) has all of the fielded query capabilities and full-text search options, including regex, you could want with the ability to cluster based on provided gene/synonym or term lists. You can use multiple channels to search (Pubmed, USPTO, Ovid, Web of Knowledge, etc), basically providing federated search, followed up with a powerful local search capability after you've localized (downloaded) everything available.

Virtual folders, full-text search of the localized full-text html or PDF's, ability to pull down any journal articles that you have access to (licensed or open access), ability to import/export endnote, refmgr libraries (my writing workflow now (when I'm not allowed to use Latex) is to manage literature in Quosa and write with Endnote as ote has horrible collection mgmt capabilities), workgroup collaborative literature mgmt/sharing (in a copyright compliant manner), basic literature analysis, abiltiy to build targeted corpora for text mining. multi-platform.

Sente

Is a similar sort of program, with some built-in bibliography functionality. I've been using it for over a year now, and I like it very much. Sente's becoming more of just a reference management tool for me.

Summary

Basically I'd like to mate the innards of BibDesk and DEVONthink and put them in a prettier package like Yep or Papers. Depending on your needs each has something to offer, I'd suggest playing with each to see how it fits into your workflow.

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