oreChem: Planning and Enacting Chemistry on the Semantic Web

oreChem: Planning and Enacting Chemistry on the Semantic Web
Microsoft Research eScience Workshop 2010Berkeley, CA USA
Mark Borkum, Simon Coles and Jeremy Frey12 October 2010

Overview
Introduction
Ontology
Case Study: X-ray Crystallography
Future Work
Summary
2

The Scientific Method
A systematic process for knowledge acquisition
Becoming increasingly data-intensive
3

The Data Deluge
4
In Haiku:
Lots of producers;Generating more datathan 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

The Scientific Method (on the Web)
5

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

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
oreChem
Dublin Core, FOAF, SIOC, OWL Time, GeoNames, etc…

oreChem Core Ontology
8

Planning
Prospective provenance
Describes a scientific experiment that will be enacted (in the future)
Three entity types:
Plan
Plan Stage
Plan Object
9

Enactment
Retrospective provenance
Describes a scientific experiment that was enacted
Three entity types:
Run
Stage
Object
10

“In theory, there is no difference between theory and practice.But, in practice, there is.” Unknown (possibly Yogi Berra)

Realisation (is not Instantiation)
Each ‘run thing’ is linked to zero or one ‘plan thing’
Deviation from the plan is allowed
12

X-ray Crystallography
Case Study
13

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

Crystallography and Fraud
15

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/

eCrystal #20
Each eCrystals record contains:
Bibliographic metadata
Fundamental and derived data (excluding raw images)
Final structure solution
17

Single Crystal Structure Determination
18
Take powder specimen of chemical substance
Measure diffraction of X-rays
Compute electron densities
Solve for crystal structure

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

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/ecrystals-eprint-20.xml?include_xsl=1

Retrospective Provenance Graphs for eCrystal #20
Stages and Objects
Objects
21
used(?s, ?o1) & emitted(?s, ?o2)  derivedFrom(?o2, ?o1)
derivedFrom (solid)
used (dashed)
emitted (solid)

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:hasPlanecrystals:Ecrystals ;
orechem:containsObject ?raw ;
orechem:containsObject ?derived ;
orechem:containsObject ?reported .
?raw a orechem:File ;
orechem:hasPlanObjectecrystals:HKL .
?derived a orechem:File ;
orechem:derivedFrom ?raw .
?reported a orechem:File ;
orechem:hasPlanObjectecrystals:CIF ;
orechem:derivedFrom ?derived .
}
22

Crystallography and Fraud – SPARQL (2)
23

24
?run
?raw
?derived
?reported
http://ecrystals.chem.soton.ac.uk/cgi/export/20/ORE_Chem/ecrystals-eprint-20.xml?include_xsl=1

25

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

Summary
<summary/>
27

Acknowledgements
Microsoft Research
Tony Hey
Lee Dirks
SavasParastatidis
Alex Wade
oreChem Project
Carl Lagoze, Theresa Velden
Jeremy Frey, Simon Coles
Peter Murray-Rust, Nick Day, Jim Downing
C. Lee Giles, PrasenjitMitra, William Brouwer, Na Li
Marlon Pierce, SashiKiranChalla
28

Thank You
Questions?
29

oreChem: Planning and Enacting Chemistry on the Semantic Web

by Mark Borkum on Nov 04, 2010

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oreChem: Planning and Enacting Chemistry on the Semantic Web — Presentation Transcript