A user-orientated approach to provenance capture and representation for in silico experiments, explored within the atmospheric chemistry community

Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences

Volumn 367, Issue 1898, 2009, Pages 2753-2770

  Martin, Chris J ^a,b   Haji, Mohammed H ^a   Jimack, Peter K ^a   Pilling, Michael J ^a   Dew, Peter M ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b ENVIRONMENT AGENCY   (United Kingdom)

Author keywords

Atmospheric chemistry; Provenance; Semantic Web

Indexed keywords

EXPERIMENTS; SEMANTIC WEB; SEMANTICS; TERMINOLOGY;

E-SCIENCE; ELECTRONIC LABORATORY NOTEBOOK; IN-SILICO; ITERATIVE MODEL; PROVENANCE;

ATMOSPHERIC CHEMISTRY;

COMPUTER PROGRAM; COMPUTER SIMULATION;

COMPUTER SIMULATION; SOFTWARE;

EID: 67650337263     PISSN: 1364503X     EISSN: None     Source Type: Journal    
DOI: 10.1098/rsta.2009.0044     Document Type: Article

References (32)

1. Altintas, I., Barney, O. & Jaeger-Frank, E. 2006 Provenance collection support in the KEPLER scientific workflow system. In Provenance and annotation of data, pp. 118-132. Berlin, Germany: Springer. (Pubitemid 44577314)
2. Arnstein, L., Borriello, G., Consolvo, S., Hung, C.&Su, J. 2002 LABSCAPE: a smart environment for the cell biology laboratory. IEEE Pervasive Comput. 1, 13-21. (doi:10.1109/MPRV.2002.1037717) (Pubitemid 44939967)
3. Blomberg, J. 1995 Ethnography: aligning field studies of work and system design. In Perspectives on HCI: diverse approaches (eds A. F. Monk & N. Gilbert), pp. 175-197. London, UK: Academic Press.
4. Braun, U., Garfinkel, S., Holland, D. A., Muniswamy-Reddy, K.-K. & Seltzer, M. I. 2006 Issues in automatic provenance collection. In Provenance and annotation of data, pp. 171-183. Berlin, Germany: Springer. (Pubitemid 44577318)
5. Degtyarenko, K. et al. 2007 ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res. 36, D344-D350. (doi:10.1093/nar/gkm791)
6. Foster, I., 2003 The virtual data grid: a new model and architecture for data-intensive collaboration. In SSDBM 2002: Proc. 15th Int. Conf. on Scientific and Statistical Database Management (eds S. Nittel & D. Gunopulos), p. 11. Los Alamitos, CA: IEEE Computer Society.
7. Foster, I., Voeckler, J., Wilde, M. & Zhao, Y. 2002 CHIMERA: a virtual data system for representing, querying, and automating data derivation. In Proc. 14th Int. Conf. on Scientific and Statistical Database Management (ed. J. Kennedy), pp. 37-46. Los Alamitos, CA: IEEE Computer Society.
8. Heller, S. R., Stein, S. E. & Tchekhovskoi, D. V. 2005 InChI: open access/open source and the IUPAC International Chemical Identifier. Abstr. Pap. Am. Chem. Soc. 230, U1025-U1026.
9. Holliday, G. L., Murray-Rust, P. & Rzepa, H. S. 2006 Chemical markup, XML, and the World Wide Web. 6. CMLReact, an XML vocabulary for chemical reactions. J. Chem. Inf. Model. 46, 145-157. (doi:10.1021/ci0502698) (Pubitemid 43282110)
10. Horrocks, I., Patel-Schneider, P. F. & van Harmelen, F. 2003 From SHIQ and RDF to OWL: the making of a web ontology language. Web Semantics: Sci. Services Agents World Wide Web 1, 7-26. (doi:10.1016/j.websem.2003.07.001) (Pubitemid 44914724)
11. Li, D., Lina, Z., Tim, F. & Anupam, J. 2005 How the semantic web is being used: an analysis of FOAF documents. In HICSS '05. Proc. 38th Annual Hawaii Int. Conf. on System Sciences.
12. Luc, M. et al. 2008 Special issue: the first provenance challenge. Concurr. Comput. Pract. Exp. 20, 409-418. (doi:10.1002/cpe.1233)
13. Ludäscher, B., Altintas, I., Berkley, C., Higgins, D., Jaeger, E., Jones, M., Lee, E. A., Tao, J. & Zhao, Y. 2006 Scientific workflow management and the KEPLER system. Concurr. Comput. Pract. Exp. 18, 1039-1065. (doi:10.1002/cpe.994) (Pubitemid 44258497)
14. Lv, T. & Yan, P. 2007 An introduction to MathML and its applications. In Proc. 2007 Int. Symp. on Computer Science and Technology (ed. S. Zhang), pp. 603-605. American Scholars Press: Marietta, GA.
15. Martin, C., Haji, M. H., Dew, P., Pilling, M. & Jimack, P. 2008 Semantically-enhanced model-experiment-evaluation processes (SeMEEPs) within the atmospheric chemistry community. In Provenance and Annotation of Data and Processes, Second Int. Provenance and Annotation Workshop 2008, Salt Lake City, UT. Berlin, Germany: Springer.
16. Martin, C. J., Mohammed, H. H., Peter, M. D., Michael, J. P. & Peter, K. J. 2009 Semantically enhanced provenance capture for chamber model development with a master chemical mechanism. Phil. Trans. R. Soc. A 367, 987-990. (doi:10.1098/rsta.2008.0168)
17. Miller, E. 1998 An introduction to the Resource Description Framework. Bull. Am. Soc. Inf. Sci. Technol. 25, 15-19. (doi:10.1002/bult.105)
18. Oinn, T. et al. 2004 TAVERNA: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics 20, 3045-3054. (doi:10.1093/ bioinformatics/bth361) (Pubitemid 39619196)
19. Pignotti, E., Edwards, P., Preece, A. D., Gotts, N. M. & Polhill, J. G. 2008 Enhancing workflow with a semantic description of scientific intent. In Semantic Web: Research and Applications, Proc. (eds S. Bechhofer, M. Hauswirth, J. Hoffmann & M. Koubarakis), pp. 644-658. Berlin, Germany: Springer.
20. Rosson, M. B. & Carroll, J. M. 2002 Usability engineering: scenario-based development of human-computer interaction. San Francisco, CA: Morgan Kaufmann.
21. Scheidegger, C., Koop, D., Santos, E., Vo, H., Callahan, S., Freire, J. & Silva, C. 2008 Tackling the provenance challenge one layer at a time. Concurr. Comput. Pract. Exp. 20, 473-483. (doi:10. 1002/cpe.1237)
22. Schraefel, M. C., Hughes, G., Mills, H., Smith, G., Payne, T. & Frey, J. 2004 Breaking the book: translating the chemistry lab book into a pervasive computing lab environment. In CHI 2004, Human Factors in Computing Systems, Vienna, Austria. New York, NY: ACM Press.
23. Scriven, M. 1996 Types of evaluation and types of evaluator. Am. J. Eval. 17, 151-161. (doi:10. 1177/109821409601700207)
24. Simmhan, Y., Plale, B. & Gannon, D. 2005 A survey of data provenance in e-Science. SIGMOD Rec. 34, 31-36. (doi:10.1145/1084805.1084812) (Pubitemid 43152529)
25. Simmhan, Y., Plale, B. & Gannon, D. 2006 A framework for collecting provenance in data-centric scientific workflows. In Proc. IEEE Int. Conf. on Web Services. Washington, DC: IEEE Computer Society.
26. Simmhan, Y. L., Plale, B. & Gannon, D. 2008 Query capabilities of the KARMA provenance framework. Concurr. Comput. Pract. Exp. 20, 441-451. (doi:10.1002/cpe.1229)
27. Sommariva, R. et al. 2004 OH and HO2 chemistry in clean marine air during SOAPEX-2. Atmos. Chem. Phys. 4, 839-856. (Pubitemid 39000920)
28. Sportisse, B. 2001 Box models versus Eulerian models in air pollution modeling. Atmos. Environ. 35, 173-178. (doi:10.1016/S1352-2310(00))
29. Wakelin, J., Murray-Rust, P., Tyrrell, S., Zhang, Y., Rzepa, H. S. & Garcia, A. 2005 CML tools and information flow in atomic scale simulations. Mol. Simul. 31, 315-322. (doi:10.1080/ 08927020500065850) (Pubitemid 40844344)
30. Wiesen, P. 2006 The EUROCHAMP integrated infrastructure initiative. In Environmental simulation chambers: application to atmospheric chemical processes, pp. 295-299. Berlin, Germany: Springer.
31. Zhao, J., Goble, C. A., Stevens, R. & Bechhofer, S. 2004 Semantically linking and browsing provenance logs for e-Science. In Semantics of a networked world: semantics for grid databases, pp. 158-176. New York, NY: Springer. (Pubitemid 39741742)
32. Zhao, J., Goble, C. A., Stevens, R. & Turi, D. 2008 Mining TAVERNA's semantic web of provenance. Concurr. Comput. Pract. Exp. 20, 463-472. (doi:10.1002/cpe.1231)