Abstract
Phenomics, the systematic study of phenotypes, is an emerging field of research in biology. It complements genomics, the study of genotypes, and is becoming an increasingly critical tool to understand phenomena such as plant morphology and human diseases. Phenomics studies make use of both high- and low-throughput imaging and measurement devices to capture data, which are subsequently used for analysis. As a result, high volumes of data are generated on a regular basis, making storage, management, annotation and distribution a challenging task. Sufficient contextual information, the metadata, must also be maintained to facilitate the dissemination of these data. The challenge is further complicated by the need to support emerging technologies and processes in phenomics research. This paper describes our effort in designing and developing an ontology-driven, open, extensible data repository to support collaborative phenomics research in Australia.
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References
Ashburner, M., Ball, C.A., Blake, J.A., et al.: Gene Ontology: Tool for the Unification of Biology. Nat. Genet. 25(1), 25–29 (2000)
Horrocks, I., Patel-Schneider, P.F., van Harmelen, F.: From \(\mathcal{SHIQ}\) and RDF to OWL: The Making of a Web Ontology Language. Journal of Web Semantics 1(1), 7–26 (2003)
Houle, D.: Numbering the Hairs on Our Heads: The Shared Challenge and Promise of Phenomics. Proceedings of the National Academy of Sciences (October 2009)
Jones, A.R., Miller, M., Aebersold, R., et al.: The Functional Genomics Experiment model (FuGE): an Extensible Framework for Standards in Functional Genomics. Nature Biotechnology 25(10), 1127–1133 (2007)
Manola, F., Miller, E. (eds.): RDF Primer (February 2004), http://www.w3.org/TR/rdf-primer/
McGuinness, D.L.: Configuration. In: Baader, F., Calvanese, D., McGuinness, D., Nardi, D., Patel-Schneider, P.F. (eds.) Description Logic Handbook, pp. 388–405. Cambridge University Press, Cambridge (2003)
Nevo, E.: Evolution of genome-phenome diversity under environmental stress. Proceedings of the National Academy of Sciences 98(11), 6233–6240 (2001)
Prud’hommeaux, E., Seaborne, A.: SPARQL Query Language for RDF (April 2006), http://www.w3.org/TR/2006/CR-rdf-sparql-query-20060406/
Rajasekar, A., Moore, R., Vernon, F.: iRODS: A Distributed Data Management Cyberinfrastructure for Observatories. In: American Geophysical Union, Fall Meeting 2007 (December 2007)
Ruttenberg, A., Rees, J., Samwald, M., Marshall, M.S.: Life Sciences on the Semantic Web: the Neurocommons and Beyond. Briefings in Bioinformatics 10(2), 193–204 (2009)
Sauer, U.: High-throughput Phenomics: Experimental Methods for Mapping Fluxomes. Current Opinion in Biotechnology 15(1), 58–63 (2004)
Smith, B., Ashburner, M., Rosse, C., et al.: The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nature Biotechnology 25(11), 1251–1255 (2007)
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Li, YF., Kennedy, G., Davies, F., Hunter, J. (2010). PODD: An Ontology-Driven Data Repository for Collaborative Phenomics Research. In: Chowdhury, G., Koo, C., Hunter, J. (eds) The Role of Digital Libraries in a Time of Global Change. ICADL 2010. Lecture Notes in Computer Science, vol 6102. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13654-2_22
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DOI: https://doi.org/10.1007/978-3-642-13654-2_22
Publisher Name: Springer, Berlin, Heidelberg
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