Materials and the Semantic Web

CSIRO/Iowa, Melbourne, AU, 2013-02-31

Peter Murray-Rust, Unilever Centre for Molecular Sciences Informatics, University of Cambridge

Themes

• The Semantic Web is here; we should adopt it for materials
• “Computable Wikipedia for materials”
• Based on Chemical Markup Language (CML), MathML and Scalable vector Graphics
• We need tools for: authoring, conversion, display
• Create pre-competitive knowledgebases for materials
• We should have hackfests!
• “liberation software” to create robots to liberate all published public factual scientific content.
• Demos- the semantic web works (most of the time). I’ll update broken stuff

I am extremely grateful for CSIRO and Nico Adams inviting me to Australia for these months. I genuinely regard what Australia has done in eResearch and Data as outstanding and a model for the rest of the world.

Power corrupts; Powerpoint corrupts absolutely (so do Word and PDF)

blog posts

• Content mining
• AMI reports on progress
• Unilever Centre
• Panton Arms
• Tim Berners-Lee, Down Under, Hackfest
• semantic web WP
  WP
• semantic web
• radioactive
• calcitePPT
• Semantic chemical speech
• Martin Dove, Cambridge and Queen Mary
• 5-star data
• Linked Open Data
• Linked Open data
• Powerpoint problems
• SVG
• Math
• Chemistry Spectra

  Heroes of semantic chemistry
  

• IUCr molecule
• Avogadro
• Jchempaint
• JSpecview
• Data liberation. What a single 3rd year postgraduate can do
• Crystaleye
• OPSIN chemical name translator 97% recal, 99.9% accurate
• Reaction extraction
• ChemicalTagger 500,000 reactions from patents
• Blue Obelisk Open source chemical community. 20 groups; interoperable. Mantra: ODOSOS (Open Data, Open Source, Open Standards). 25USD per year (2 obelisk prizes)

  Spectral liberation. AMI2
  

• materials PDF
• Bitbucket PDF2SVG
• Bibsoup

  Open
  

• Open Knowledge Foundation
• Open Definition
• OKF open-access
• Panton Principles
• “Walled gardens” #Animalgarden https://vimeo.com/34323486
• Do walled gardens exist in #scholpub?
• Springergate
• Springergate chemistry
• Springer “copyright”
• The scholarly poor
• http://whoneedsaccess.org/
• @ccess success stories
• The scholarly poor start building… based on bibliography
• Bibsoup for malaria
• Bibliography is the map of scholarship. We are creating Open Bibliography to liberate it
• Bibsoup
• BibJSON
• We subscribe to the literature. “The right to read is the right to mine”
• Elsevier Directrix of Universal Access
• So can a few people – without funding – change the world?
• Chemical MIME 2 pints beer; viral growth in 1994 – toook 6 weeks.
• SAX-history
• Open streetmap ONE person (Steve Coates) + 500,000 volunteers. No bank account!
• Blue Obelisk Open source chemical community. 20 groups; interoperable. Mantra: ODOSOS (Open Data, Open Source, Open Standards). 25USD per year (2 obelisk prizes)
• Universal extraction of scientific content
• Extraction of content from a thesis
• Extraction of phylogenetic trees
• I am looking for collaborators who share this vision and approach
• VIVO could be the center of Truly Open academic bibliography and data – if you share this vision

addendum
Zookeys CC-NC