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The semantic smart laboratory: a system for supporting the chemical eScientist

Hughes, G., Mills, H., de Roure, D., Frey, J., Moreau, L., schraefel, m. c., Smith, G. and Zaluska, E. (2004) The semantic smart laboratory: a system for supporting the chemical eScientist. Organic and Biomolecular Chemistry, 2 . pp. 1-10.

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Abstract

One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project
we have developed an innovative human-centred system which captures the process of a chemistry experiment from
plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled
in a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users,
we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we
concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to
describe the record of an experiment, and a storage system for the data from our lab book software. Just as the
interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need
to be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web
technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it
can store, compared to the use of rigid relational databases.

Item Type:Article
Creator/Authors:
Gareth Hughes
Hugo Mills
David de Roure
Jeremy Frey
Luc Moreau
m.c. schraefel
Graham Smith
Ed Zaluska
Keywords:smart labratory, semantic web, smart tea
Research Group:Current ECS Groups > Web and Internet Science
Old ECS Groups > Intelligence, Agents, Multimedia
Current ECS Groups > Agents, Interaction and Complexity
Date:2004
Information about this record:
Performance Indicator:EZ~08~07~11
Citations:ISI: 13, Google Scholar: 39
Downloads (2010):1
ID Code:10099
Last Modified:23 Sep 2011 10:31
Deposited On:11 Nov 2004 by schraefel, monica

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References in Article

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1 J. Frey, D. De Roure, m. c. schraefel, H. Mills, H. Fu, S. Peppe, G. Hughes, G. Smith, and T. R. Payne, Context Slicing the Chemical Aether, Proceedings of First International Workshop on Hypermedia and the Semantic Web, ed. M. David, University of Southampton EPrints Service Southampton, UK, 2003.

2 J. G. Frey, D. De Roure and L. Carr, Publication at Source: Scientific Communication from a Publication Web to a Data Grid, Proceedings of Euroweb 2002, British Computer Society, Swindon, 2002, pp. 88–90.

3 m. c. schraefel, G. Hughes, H. Mills, G. Smith and J. Frey, Making Tea: Iterative Design through Analogy, Proceedings of Designing Interactive Systems, ACM Press, New York NY, 2002, pp. 49–58.

4 m. c. schraefel, G. Hughes, H. Mills, G. Smith, T. Payne and J. Frey, Breaking the Book: Translating the Chemistry Lab Book into a Pervasive Computing Lab Environment, Proceedings of CHI 2004, ACM Press, New York NY, pp. 25–32. 5 COSHH Essentials. UK Health and Safety Executive. http:// www.coshh-essentials.org.uk/.

6 Jena, A Semantic Web Framework for Java. http:// jena.sourceforge.net/. 7 Resource Description Framework (RDF): Concepts and Abstract Syntax, ed. G. Klyne and J. J. Carroll, W3C, Geneva, 2004. http://www.w3.org/TR/2004/REC-rdf-concepts-20040210/.

8 RDF Vocabulary Description Language 1.0: RDF Schema, ed. D. Brickley and R.V Guha, W3C, Geneva, 2004. http://www.w3.org/ TR/2004/REC-rdf-schema-20040210/.

9 OWL Web Ontology Language Semantics and Abstract Syntax, W3C Recommendation, ed. P. F. Patel-Schneider, P. Hayes and I Horrocks, 10 February 2004. http://www.w3.org/TR/2004/REC-owl-semantics- 20040210/.

10 AKT project reference ontology. http://www.aktors.org/publications/ ontology/.

11 R. Heery, M. Duke, M. Day, L. Lyon, S. Coles, J. Frey, M. Hursthouse, L. Carr, and C. Gutteridge, Integrating research data into the publication workflow: eBank experience, PV-2004: Ensuring the Long-Term Preservation and Adding Value to the Scientific and Technical Data, held 5–7 October 2004, Frascati, Italy.

12 Protégé Project. http://protege.stanford.edu/.

13 BEA, IBM, Microsoft, SAP AG and Siebel Systems, Business Process Execution Language for Web Services Version 1.1, May 2003. http://www-106.ibm.com/developerworks/webservices/library/ ws-bpel/.

14 DAML Services Coalition, OWL-S specification. http:// www.daml.org/services/owl-s/1.0/.

15 SCRIP-SAFE, PatentPad. http://www.scrip-safe.com/laboratory_ notebooks.htm/. 16 L. Arnstein, G. Borriello, S. Consolvo, C. Hung and J. Su, Labscape: A Smart Environment for the Cell Biology Laboratory, IEEE Pervas. Comput. Mag., 2002, 1(3), 13–21.

17 K. Bøegh, C. Letondal, W. E. Mackay, G. Pothier and H. E. Sørensen, The Missing Link: Augmenting Biology Laboratory Notebooks, Proc. UIST, ACM Press, New York NY, 2002, pp. 41–50.

18 J. D. Myers, Collaborative Electronic Notebooks as Electronic Records: Design Issues for the Secure Electronic Laboratory Notebook (ELN), Proc. CTS’03, Society for Modelling and Simulation (SCS), http://www.scs.org. Proceedings: http:// www.scs.org/scsarchive/search.cfm?presearch=db&dbrec=29. Paper: http://www.scs.org/scsarchive/getDoc.cfm?id=2051. Metadata: http: //www.scs.org/scsarchive/docInfo.cfm?get=2051.

19 Amphora Research Ltd., http://www.amphora-research.com/.

20 ChemOffice, CambridgeSoft Corporation. http://www.camsoft.com/.

21 NoteBookMaker, NoteBookMaker ltd. http://www.notebookmaker. com/.

22 Open Biological Ontologies. http://obo.sourceforge.net/.

23 C. J. Stoeckert Jr, H. C. Causton and H. A. Ball, Microarray databases: standards and ontologies, Nat. Genet., 2002, 32, 469–473. 24 C. D. Hafner, N. Fridman Noy, Ontological Foundations for Biology Knowledge Models, 4th International Conference on Intelligent Systems for Molecular Biology, AAAI Press, St. Louis MO, 1996, 78–87.

25 L. Pouchard, L. Cinquini, B. Drach, et al., Exploring Ontologies in ESG, Symposium on Cluster Computing and the Grid (CCGrid 2003), IEEE Comp. Soc., Los Alamitos, pp. 626–632.

26 Chemical Markup Language project. http://cml.sourceforge.net/.

27 P. Murray-Rust and H. S. Rzepa, Chemical markup, XML and the Worldwide Web, Part 4: CML Schema, J. Chem. Inf. Comput. Sci., 2003, 43(4), 757–772.

28 C. M. Pancerella, J. D. Myers, et al., Metadata in the Collaboratory for Multi-Scale Chemical Science, Proceedings of the 2003 Dublin Core Conference: Supporting Communities of Discourse and Practice- Metadata Research and Applications (DC 2003). Conference proceedings: http://www.siderean.com/dc2003/search.jsp. Paper: http://www.siderean.com/dc2003/401_Paper67.pdf.

29 J. D. Myers, A. Chappell, M. Elder, A. Geist and J. Schwidder, Re-integrating the research record, IEEE Comput. Sci. Eng., 2003, 5(3), 44–50.

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