The document summarizes the oreChem project, which aims to represent scientific experiments and their provenance using semantic web technologies. It describes how oreChem models the scientific process as plans and runs, and provides a case study of applying oreChem to represent experiments in x-ray crystallography. Future work includes expanding the oreChem ontology and developing applications to support experiment planning and analysis.

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