I'm surprised no one mentioned Quosa (www.quosa.com). I like some of
what I've seen in Sente and some of the features in Papers look pretty
cool, but 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 and Quosa is multi-platform.
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.
I've had a colleague pull down as much of 30k citations as he could
grab in order to find the kinetic parameters for a set of proteins
(kinetic parameters are only found in the full-text of the paper and
one cannot determine if they exist based on keyword searches of the
article abstracts). After a couple of days collecting :) it took him a
few minutes to grab all of the kinetic parameters using the full-text
search. Did he get everything available? - highly doubtful as we were
limited in the number of journals licensed. Did he get everything
super-humanly possible? - oh yeah!
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 Endnote 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, ...
Disclosure - I don't have any financial interest in Quosa, but I am a happy customer.
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