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oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
oreChem: Planning and Enacting Chemistry on the Semantic Web
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oreChem: Planning and Enacting Chemistry on the Semantic Web

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  • 1. oreChem: Planning and Enacting Chemistry on the Semantic Web Microsoft Research eScience Workshop 2010 Berkeley, CA USA Mark Borkum, Simon Coles and Jeremy Frey 12 October 2010
  • 2. Overview • Introduction • Ontology • Case Study: X-ray Crystallography • Future Work • Summary 2
  • 3. The Scientific Method • A systematic process for knowledge acquisition • Becoming increasingly data-intensive Planning Enactment Analysis Publication 3
  • 4. The Data Deluge 4 • In Haiku: – Lots of producers; Generating more data than ever before. • 40 years ago, a PhD student would determine 3 structures over the entire course of their study! The Great Wave off Kanagawa by Katsushika Hokusai
  • 5. The Scientific Method (on the Web) 5
  • 6. Provenance (The Elephant in the Room) • The 7 W’s [Goble 2002] – Who, What, Where, Why, When, Which, & (W)How • The Why aspect is often ignored  6 Why Planning Who Authorship What & (W)How Enactment Where & When Annotations
  • 7. The oreChem Project • Funded by Microsoft Research • Investigating the design and deployment of a semantic- based eScience infrastructure for Chemistry • Project website: – http://research.microsoft.com/ en-us/projects/orechem/ 7 Why Planning Who Authorship What & (W)How Enactment Where & When Annotations oreChem Dublin Core, FOAF, SIOC, OWL Time, GeoNames, etc…
  • 8. oreChem Core Ontology 8
  • 9. Planning • Prospective provenance • Describes a scientific experiment that will be enacted (in the future) • Three entity types: – Plan – Plan Stage – Plan Object 9
  • 10. Enactment • Retrospective provenance • Describes a scientific experiment that was enacted • Three entity types: – Run – Stage – Object 10
  • 11. “In theory, there is no difference between theory and practice. But, in practice, there is.” Unknown (possibly Yogi Berra)
  • 12. Realisation (is not Instantiation) • Each ‘run thing’ is linked to zero or one ‘plan thing’ – Deviation from the plan is allowed 12
  • 13. X-RAY CRYSTALLOGRAPHY Case Study 13
  • 14. Current Practice in Crystallography • Crystallography data is highly structured – The de facto standard adopted by the community is the CIF (Crystallographic Information File) • Relatively few crystal structures are openly available online 14 http://www.rin.ac.uk/our-work/data-management-and- curation/share-or-not-share-research-data-outputs
  • 15. Crystallography and Fraud 15
  • 16. The eCrystals Federation • JISC project • Network of crystallography resources • All published records are available as Open Data • Based on EPrints repository 16 http://ecrystals.chem.soton.ac.uk/
  • 17. eCrystal #20 • Each eCrystals record contains: – Bibliographic metadata – Fundamental and derived data (excluding raw images) – Final structure solution 17
  • 18. Single Crystal Structure Determination 18 1. Take powder specimen of chemical substance 2. Measure diffraction of X-rays 3. Compute electron densities 4. Solve for crystal structure
  • 19. oreChem Plan for eCrystals • Machine-readable representation of methodology • Describes requirements for software and data products • Available online at: – http://ecrystals.chem.soton. ac.uk/plan.rdf 19
  • 20. oreChem Run for eCrystal #20 • Exported by “oreChem” plug-in for EPrints 3.1 – RDF/XML serialisation – Uses SWRL rules to infer causal relationships • Describes: – Software – Data products 20 http://ecrystals.chem.soton.ac.uk/cgi/export/20/ORE_Chem/ecry stals-eprint-20.xml?include_xsl=1
  • 21. Retrospective Provenance Graphs for eCrystal #20 Stages and Objects Objects 21 used (dashed) emitted (solid) derivedFrom (solid) used(?s, ?o1) & emitted(?s, ?o2)  derivedFrom(?o2, ?o1)
  • 22. Crystallography and Fraud – SPARQL PREFIX orechem: <http://www.openarchives.org/2010/05/24-orechem-ns#> PREFIX ecrystals: <http://ecrystals.chem.soton.ac.uk/plan.rdf#> SELECT ?run ?raw ?derived ?reported WHERE { ?run a orechem:Run ; orechem:hasPlan ecrystals:Ecrystals ; orechem:containsObject ?raw ; orechem:containsObject ?derived ; orechem:containsObject ?reported . ?raw a orechem:File ; orechem:hasPlanObject ecrystals:HKL . ?derived a orechem:File ; orechem:derivedFrom ?raw . ?reported a orechem:File ; orechem:hasPlanObject ecrystals:CIF ; orechem:derivedFrom ?derived . } 22
  • 23. Crystallography and Fraud – SPARQL (2) 23
  • 24. Crystallography and Fraud – SPARQL (3) 24 ?run ?raw ?reported ?derived http://ecrystals.chem.soton.ac.uk/cgi/export/20/ORE_Chem/ecry stals-eprint-20.xml?include_xsl=1
  • 25. Crystallography and Fraud – SPARQL (4) ?run ?raw ?derived ?reported _:eCrystal_20_Run 02sot126.hkl 02sot126.prp 02sot126.cif _:eCrystal_20_Run 02sot126.hkl 02sot126.lst 02sot126.cif _:eCrystal_20_Run 02sot126.hkl 02sot126.res 02sot126.cif 25
  • 26. Future Work • oreChem Core Ontology – Support for conditionals and continuations • oreChem Lower Ontology – Specialised for Physical and Computational Chemistry • Applications and Services – oreChem Plan Designer and Enactor – oreChem Run Inspector 26
  • 27. Summary • <summary/> 27
  • 28. Acknowledgements • Microsoft Research – Tony Hey – Lee Dirks – Savas Parastatidis – Alex Wade • oreChem Project – Carl Lagoze, Theresa Velden – Jeremy Frey, Simon Coles – Peter Murray-Rust, Nick Day, Jim Downing – C. Lee Giles, Prasenjit Mitra, William Brouwer, Na Li – Marlon Pierce, Sashi Kiran Challa 28
  • 29. Thank You • Questions? 29

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