A new dimension in

scientific publishing has arrived

www.BiochemJ.orgBringing life sciences to life

Amos Bairoch’s lament

“It is quite depressive to think that we are spending

millions in grants for people to perform

experiments, produce new knowledge, hide this

knowledge in a often badly written text and then

spend some more millions trying to second guess

what the authors really did and found”

Bairoch A (2009) The future of annotation/biocuration.

Nature Precedings doi:10.1038/npre.2009.3092.1.

Utopia Documents...

Blends the best of The Semantic Web…

…with the ease of use, stability & elegance of PDF files

Articles remain as stable Versions of Record while being dynamic, interactive and evolving repositories of knowledge

Enriching document metadata

• Utopia documents ‘reads’ a PDF much like a human would

• It recognizes the content of a document– Title, authors, keywords– Citations and references are automatically linked to

online repositories– Identifies important features such as ‘materials and

methods’

Interacting with document content

• Utopia Documents brings static PDF files to life

• Interactive visualizations – Molecules realised as 3D rotating images– Protein sequences become live and interactive– Tables of data become live ‘spreadsheets’– Graphs generated on the fly, linked to source data

• Dynamically include data/text-mining results

“After downloading Utopia Documents, very quickly you become the

master of the information in an article. To have all the definitions

of terms used, readily displayed as you read, takes away much of

the hassle of reading a paper. Having the opportunity to

graphically plot data provides a tractable insight of behaviour,

which a results table just cannot do. And, most importantly as a

biophysicist interested in protein structure and function, being

able to visualize a protein in three dimensions whilst you read

about its detail and mechanism, makes a complex molecule more

tangible. This is truly a revolution in the interface between the

scientist and their primary source of information”.

Professor John Ladbury, Deputy Chair, Biochemical Journal

M D Anderson Cancer Center

@Villavelius Instead of "de-PDFy science", as I used to argue, I'm now enlightened: embrace PDF, it *works* for the semantic web http://getutopia.comJan Velterop

Still really impressed with how Utopia Documents breathes life into research papers by connecting them to #LinkedData http://getutopia.comLeigh Dodds (Talis)

Horizon…Next release:• Commenting (private and public)

Future releases:• Utopia Library• Integration of ChemSpider• Utopia Conferences

Get other publishers involved

Our vision

• PDF reader of choice for academics• Wide uptake by other organisations• Build into XML workflows• Enable researchers to unlock the vast

array of knowledge currently in data tombs

And the Semantic Biochemical Journal

Watch video at:

http://www.biochemj.org/demo

Download Utopia Documents at:

Getutopia.com

Read: Attwood, T.K. et al (2009)

‘Calling International Rescue: knowledge lost in literature and data landslide!’

Reference Biochem J. (2009) 424, 317-333

Utopia Documents