Adam Marsall of Portland Press provides an exclusive look at how they built and launched Utopia

1. A new
dimension in
scientific
publishing
has arrived
www.BiochemJ.org
Bringing life sciences to life

2. 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.

3. 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

4. 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‟

6. 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

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

8. Horizon…
Next release:
• Commenting (private and public)
Future releases:
• Utopia Library
• Integration of ChemSpider
• Utopia Conferences
Get other publishers involved

9. 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

10. And the Semantic Biochemical
Journal

11. Utopia Documents
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