Utopia documents: linking scholarly literature with research data.
BACKGROUND
In recent years, the gulf between the mass of accumulating-research data and the massive literature describing and analyzing those data has widened. The need for intelligent tools to bridge this gap, to rescue the knowledge being systematically isolated in literature and data silos, is now widely acknowledged.


RESULTS
To this end, we have developed Utopia Documents, a novel PDF reader that semantically integrates visualization and data-analysis tools with published research articles. In a successful pilot with editors of the Biochemical Journal (BJ), the system has been used to transform static document features into objects that can be linked, annotated, visualized and analyzed interactively (http://www.biochemj.org/bj/424/3/). Utopia Documents is now used routinely by BJ editors to mark up article content prior to publication. Recent additions include integration of various text-mining and biodatabase plugins, demonstrating the system's ability to seamlessly integrate on-line content with PDF articles.


BACKGROUND
http://getutopia.com.
Attwood
T K
TK
School of Computer Science, Faculty of Life Sciences, University of Manchester, Manchester, UK. teresa.k.attwood@manchester.ac.uk
Kell
D B
DB
McDermott
P
P
Marsh
J
J
Pettifer
S R
SR
Thorne
D
D
D007255:Information Services; D020407:Internet; D008091:Literature; D010506:Periodicals as Topic; D011642:Publications / Q000145:classification; D011643:Publishing; D012106:Research; D012984:Software
Comp Funct Genomics. 2004;5(1):56-60
18629035
Science. 2009 Aug 14;325(5942):828-32
19679805
Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
19880382
Nucleic Acids Res. 2003 Jan 1;31(1):365-70
12520024
Nat Biotechnol. 2009 Jun;27(6):508-10
19513049
Trends Biochem Sci. 2008 Sep;33(9):408-12
18672371
FEBS Lett. 2008 Apr 9;582(8):1210-8
18325344
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D302-5
16381872
Nature. 2006 Sep 28;443(7110):379
17006479
PLoS Comput Biol. 2009 Apr;5(4):e1000361
19381256
Nat Biotechnol. 2007 Nov;25(11):1251-5
17989687
BMC Bioinformatics. 2007 Jan 19;8:17
17239245
Nucleic Acids Res. 2007 Jan;35(Database issue):D572-4
17135203
BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S19
19534744
FEBS Lett. 2008 Apr 9;582(8):1171-7
18328820
Biochem J. 2009 Dec 10;424(3):317-33
19929850
PLoS Comput Biol. 2005 Aug;1(3):179-81
16158097
Nucleic Acids Res. 2009 Jan;37(Database issue):D169-74
18836194
Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W385-9
18515836
Microsc Res Tech. 2008 Nov;71(11):778-86
18785246
Nature. 2005 Dec 15;438(7070):900-1
16355180