Using provenance to manage knowledge of In Silico experiments

Briefings in Bioinformatics

Volumn 8, Issue 3, 2007, Pages 183-194

  Stevens, Robert ^a,b   Zhao, Jun ^b   Goble, Carole ^c  

^a BioHealth Informatics Group   (United Kingdom)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c Information Management Group

Author keywords

Data derivation; In Silico experiments; Provenance; Validation and verification of results; Workflow

Indexed keywords

ARTICLE; BIOINFORMATICS; COMPUTER LANGUAGE; COMPUTER MODEL; DATA ANALYSIS; EXPERIMENTATION; INFORMATION PROCESSING; INFORMATION STORAGE; INFORMATION SYSTEM; KNOWLEDGE MANAGEMENT; VALIDATION PROCESS;

COMPUTATIONAL BIOLOGY; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; KNOWLEDGE; RESEARCH DESIGN; SOFTWARE;

EID: 34447549205     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbm015     Document Type: Article

References (33)

1. Baker PG, Goble CA, Bechhofer S, et al. An Ontology for Bioniformatics Applications. Bioinformatics 1999;15: 510-20.
2. Stevens R, Goble CA, Bechhofer S. Ontology-based Knowledge Representation for Bioinformatics. Brief Bioinform 2000;1 398-416.
3. Goble C, Wolstencroft K, Goderis A, et al. Knowledge discovery for biology with taverna: Producing and consuming semantics in the web of science. In: Baker CJO, Cheung K-H, (eds). Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences. Springer Verlag, New York Inc., 2006, ISBN: 0387484361.
4. Wong SC, Miles S, Fang W, et al. Provenance-based validation of e-science experiments. In: Proceedings of the 4th International Semantic Web Conference, vol. 3729, Galway, Ireland, 2005; 801-15.
5. Moreau L, Groth P, Miles S, et al. The provenance of electronic data. Communications of the ACM, 2007.
6. myGrid. Bioinformatics 2004;20: I303-10.
7. Oinn T, Greenwood M, Addis M, et al. Taverna: Lessons in creating a workflow environment for the Life Sciences. Concurr Comp: Pract E 2006;18:1067-100.
8. Stevens RD, Goble CA, Baker P, Brass A. A classification of tasks in bioinformatics. Bioinformatics 2001;17:180-8.
9. Discala C, Benigni X, Barillot E, Vaysseix G. DBcat: A Catalogof500 biological databases. Nucleic Acids Res 2000; 28:8-9.
10. Davidson SB, Overton C, Buneman P. Challenges in integrating biological data sources. J Comput Biol 1995;2: 557-72.
11. Karp P. A strategy for database interoperation. J Comput Biol 1995;2:573-86.
12. Stein L. Creating a bioinformatics nation. Nature 2002;417: 119-20.
13. Alonso G, Casati F, Kuno H, Machiraju H. Web Services. Concepts, Architectures and Applications. Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2004, ISBN: 3540440089.
14. Altintas I, Barney O, Jaeger-Frank E. Provenance collection support in the Kepler scientific workflow system. In: Proceediqqs of the 3rd International Provenance and Annotation Workshops, Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 118-32.
15. Kim J, Gil Y, Ratnakar V. Semantic metadata generation for large scientific workflows. In: Proceedings of International Semantic Web Conference, Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 357-70.
16. Zhao Y, Wilde M, Foster I. Applying the virtual data provenance model. In: Proceedings of the 3rd International Provenance and Annotation Workshops; Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 148-61.
17. Ludaescher B, Goble C. Guest editors' introduction to the special section on scientific workflows. SIGMOD Record 2005;34:3-4.
18. Zhao J, Wroe C, Goble C, et al. Using semantic web technologies for representing e-science provenance. In: Proceedings of the Third International Semantic Web Conference, Lecture Notes in Computer Science, Hiroshima, Springer, Japan. 2004; 92-106.
19. Hull D, Zoan E, Bovykin A, et al. Deciding matching of stateless services. In: Proceedings, The Twenty-First National Conference on Artificial Intelligence and the Eighteenth Innovative Applications of Artificial Intelligence Conference, July 16-20, 2006, AAAI Press, Boston, Massachusetts, USA.
20. Goderis A, Li P, Goble C. Workflow discovery: The problem, a case study from e-science and a graph-based solution. In: IEEE International Conference on Web Services, IEEE Computer Society, Chicago, USA, September 18-22, 2006.
21. Groth PT. On the record: Provenancein large scale, open, distributed systems. Mini thesis, University of Southampton, July 2005.
22. Hendler J. Science and the Semantic Web. Science 2003;24: 520-521.
23. Stevens R, Wroe C, Lord P, Goble C. Ontologies in bioinformatics. In: Staab S, Studer K, (eds). Handbook on Ontologies in Information Systems. Springer-Verlag Berlin and Heidelberg GmbH & Co. K, 2003; 635-57.
24. myGrid Ontology: Bioinformatics Service Discovery. Int J Bioinformat Res Appl 2007, ISBN: 1744-5493.
25. Zhao J, Goble C, Stevens R. An identity crisis in the life sciences. In: Proceedings of the 3rd International Provenance and Annotation Workshops, Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 254-69.
26. Clark T, Martin S, Liefeld T. Globally distributed object identification for biological knowledgebases. Brief Bioinform 2004;5:59-70.
27. Frey JG, Bradley M, Essex JW, et al. Grid Computing - Making the Global Infrastructure a Reality. JohnWiley and Sons, 2005;945-62.
28. Bajcsy P, Kooper R, Marini L. et al. Ameta-workflow cyber-infrastructure system designed for environmental observatories. Technical Report ISDA01-2005, National Center for Supercomputing Applications and University of Illinois at Urbana-Champaign, 2005.
29. Miles S. Electronically querying for the provenance of entities. In: Proceedings of the 3rd International Provenance and Annotation Workshop Springer-Verlag, Berlin. and Heidelberg GmbH & Co. K, 2006; 184-92.
30. Frey J, De Roure D, Taylor K, et al. Combechem: A case study in provenance and annotation using the semantic web. In: Proceedings of the 3rd International Provenance and Annotation Workshop, Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 270-7.
31. Halaschek-Wiener C, Golbeck J, Schain A, et al. Annotation and provenance tracking in semantic web photo libraries. In: Provenance and Annotation of Data, Vol. 4145, 2006; 82-9.
32. Golbeck J. Combining provenance with trust in social networks for semantic web content filtering. In: Proceedings of the 3rd Internation Provenance and Annotation Workshop, Springer-Verlag, Berlin and Heidelberg GmbH & Co. K, 2006; 101-08.
33. Field D, Sansone S-A. A special issue on data standards. OMICS: AJ Integ Biol 2006;10:84-93.