The myGrid ontology: Bioinformatics service discovery

International Journal of Bioinformatics Research and Applications

Volumn 3, Issue 3, 2007, Pages 303-325

  Wolstencroft, Katy ^a   Alper, Pinar ^a   Hull, Duncan ^a   Wroe, Christopher ^b   Lord, Phillip W ^c   Stevens, Robert D ^a   Goble, Carole A ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b BRITISH TELECOM   (United Kingdom)

^c NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

myGrid ontology; Annotation; Bioinformatics; Description logic; in silico life cycle; OWL; RDFS; Service discovery

Indexed keywords

BIOINFORMATICS; COMPUTER MODEL; REVIEW; SCIENTIST; SEMANTIC DIFFERENTIAL METHOD; TECHNOLOGY;

EID: 34447558591     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2007.015005     Document Type: Review

References (24)

1. Baader, F., Calvanese, D., McGuinness, D., Nardi, D. and Patel-Schneider, P. (Eds.) (2003) The Description Logic Handbook, Cambridge University Press, ISBN 0-521-78176-0.
2. Cochrane, G., Aldebert, P., Althorpe, N., Andersson, M., Baker, W., Baldwin, A., Bates, K., Bhattacharyya, S., Browne, P., van den Broek, A., Castro, M., Duggan, K., Eberhardt, R., Faruque, N., Gamble, J., Kanz, C., Kulikova, T., Lee, C., Leinonen, R., Lin, Q., Lombard, V., Lopez, R., McHale, M., McWilliam, H., Mukherjee, G., Nardone, F., Pastor, M.P., Sobhany, S., Stoehr, P., Tzouvara, K., Vaughan, R., Wu, D., Zhu, W. and Apweiler, R. (2006) 'EMBL nucleotide sequence database: developments in 2005', Nucleic Acids Res., Vol. 34, pp.D10-15.
3. Curcin, V., Ghanem, M. and Guo, Y. (2005) 'Web services in the life sciences', Drug Discov. Today, Vol. 10, No. 12, pp.865-871.
4. Davidson, S.B., Overton, C. and Buneman, P. (1995) 'Challenges in integrating biological data sources', J. Comput. Biol., Vol. 2, No. 4, pp.557-572.
5. Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., de Moor, B., Brazma, A. and Huber, W. (2005) 'BioMart and bioconductor: a powerful link between biological databases and microarray data analysis', Bioinformatics, Vol. 21, No. 16, 15 August, pp.3439, 3440.
6. Galperin, M.Y. (2006) 'The molecular biology database collection: 2006 update', Nucleic Acids Res., Vol. 34, Database Issue, pp.D3-5.
7. Harris, M.A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., Richter, J., Rubin, G.M., Blake, J.A., Bult, C., Dolan, M., Drabkin, H., Eppig, J.T., Hill, D.P., Ni, L., Ringwald, M., Balakrishnan, R., Cherry, J.M., Christie, K.R., Costanzo, M.C., Dwight, S.S., Engel, S., Fisk, D.G., Hirschman, J.E., Hong, E.L., Nash, R.S., Sethuraman, A., Theesfeld, C.L., Botstein, D., Dolinski, K., Feierbach, B., Berardini, T., Mundodi, S., Rhee, S.Y., Apweiler, R., Barrell, D., Camon, E., Dimmer, E., Lee, V., Chisholm, R., Gaudet, P., Kibbe, W., Kishore, R., Schwarz, E.M., Sternberg, P., Gwinn, M., Hannick, L., Wortman, J., Berriman, M., Wood, V., de la Cruz, N., Tonellato, P., Jaiswal, P., Seigfried, T. and White, R. (2004) 'The gene ontology (GO) database and informatics resource', Nucleic Acids Res., Vol. 32, Database Issue, pp.D258-261.
8. Hayes, P. (Ed.) (2004) RDF Semantics, W3C Recommendation, 10 February, http://www.w3.org/TR/2004/REC-rdf-mt-20040210/.
9. Hull, D., Zolin, E., Bovykin, A., Horrocks, I., Sattler, U. and Stevens, R. (2006) 'Deciding matching of stateless services', Twenty-First National Conference on Artificial Intelligence (AAAI'06), Boston, MA, USA.
10. myGrid Methodologies, 3rd UK e-Science All Hands Meeting, Nottingham UK.
11. Lord, P., Alper, P., Wroe, C. and Goble, C. (2005) 'Feta: a light-weight architecture for user oriented semantic service discovery', 2nd European Semantic Web Conference, Heraklion, Springer-Verlag, Greece.
12. Martin, D., Paolucci, M., McIlraith, S., Burstein, M., McDermott, D., McGuinness, D., Parsia, B., Payne, T., Sabou, M., Solanki, M., Srinivasan, N. and Sycara, K. (2004) 'Bringing semantics to web services: the OWL-S approach', First International Workshop on Semantic Web Services and Web Process Composition (SWSWPC 2004), San Diego, California, USA.
13. Oinn, T., Addis, M., Ferris, J., Marvin, D., Senger, M., Greenwood, M., Carver, T., Glover, K., Pocock, M.R., Wipat, A. and Li, P. (2004) 'Taverna: A tool for the composition and enactment of bioinformatics workflows', Bioinformatics Journal, Vol. 20, No. 17, pp.3045-3054.
14. Oinn, T., Greenwood, M., Addis, M., Alpdemir, M.N., Ferris, J., Glover, K., Goble, C., Goderis, A., Hull, D., Marvin, D., Li, P., Lord, P., Pocock, M.R., Senger, M., Stevens, R., Wipat, A. and Wroe, C. (2006) 'Taverna: lessons in creating a workflow environment for the life sciences', Concurrency and Computation: Practice and Experience.
15. Radetzki, U., Leser, U., Schulze-Rauschenbach, S.C., Zimmermann, J., Lussem, J., Bode, T. and Cremers, A.B. (2006) 'Adapters, shims, and glue - service interoperability for in silico experiments', Bioinformatics, Vol. 22, No. 9, pp.1137-1143.
16. Roman, D., Keller, U. et al. (2005) 'Web service modeling ontology', Applied Ontology, Vol. 1, No. 1, pp.77-106.
17. Senger, M., Rice, P. and Oinn, T. (2003) 'Soaplab - a unified Sesame door to analysis tools', Proc. UK e-Science All Hands Meeting, Nottingham, UK, pp.509-513.
18. Smith, M.K., Welty, C. and McGuinness, D.L. (Eds.) (2004) OWL Web Ontology Language Guide, W3C Recommendation, 10 February, http://www.w3.org/TR/2004/REC-owl-guide-20040210/.
19. Stevens, R., Wroe, C., Bechhofer, S., Lord, P., Rector, A. and Goble, C. (2003) 'Building ontologies in DAML+OIL', Comparitive and Functional Genomics, Vol. 4, No. 1, pp.133-141.
20. myGrid, 12th International Conference on Intelligent Systems in Molecular Biology, Glasgow, UK, Bioinformatics.
21. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., DiCuccio, M., Edgar, R., Federhen, S., Geer, L.Y., Helmberg, W., Kapustin, Y., Kenton, D.L., Khovayko, O., Lipman, D.J., Madden, T.L., Maglott, D.R., Ostell, J., Pruitt, K.D., Schuler, G.D., Schriml, L.M., Sequeira, E., Sherry, S.T., Sirotkin, K., Souvorov, A., Starchenko, G., Suzek, T.O., Tatusov, R., Tatusova, T.A., Wagner, L. and Yaschenko, E. (2006) 'Database resources of the national center for biotechnology information', Nucleic Acids Res., Vol. 34, Database Issue, pp.D173-180.
22. Wilkinson, M.D. (2004) 'BioMOBY: The MOBY-S platform for interoperable data-service provision', in Grant, R.P. (Ed.): Computational Genomics, Horizon Scientific Press, Norfolk, UK, pp.273-295.
23. Wroe, C., Stevens, R., Goble, C., Roberts, A. and Greenwood, M. (2003) 'A suite of DAML+OIL ontologies to describe bioinformatics web services and data', The International Journal of Cooperative Information Systems, Vol. 12, No. 2, pp.597-624.
24. Wu, C.H., Apweiler, R. et al. (2006) 'The universal protein resource (UniProt): an expanding universe of protein information', Nucleic Acids Res., Vol. 34, Database issue, pp.D187-191.