Abstract
The core part of the Web Ontology Language (OWL) is based on Description Logic (DL) theory, which has been investigated for more than 25 years. OWL reasoning systems offer various DL-based inference services such as (i) checking class descriptions for consistency and automatically organizing them into classification hierarchies, (ii) checking descriptions about individuals for consistency and recognizing individuals as instances of class descriptions. These services can therefore be utilized in a variety of application domains concerned with representation of and reasoning about knowledge, for example, in biological sciences. Classification is an integral part of all biological sciences, including the new discipline of genomics. Biologists not only wish to build complex descriptions of the categories of biological molecules, but also to classify instances of new molecules against these class level descriptions. In this chapter we introduce to the non-expert reader the basics of OWL DL and its related reasoning patterns such as classification. We use a case study of building an ontology of a protein family and then classifying all members of that family from a genome using DL technology. We show how a technically straight-forward use of these technologies can have far-reaching effects in genomic science.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ouzounis C.A., and Valencia A.. Early bioinformatics: the birth of a discipline—a personal view. Bioinformatics 19:2176–2190, 2003.
Borsani G., Ballabio A., and Banfi S. A practical guide to orient yourself in the labyrinth of genome databases. Hum Mol Genet 7:1641–1648, 1998.
Wheeler D.L., Barrett L.T., Benson D.A., Bryant, S.H. Canese K., Church D.M., DiCuccio M., Edgar R., Federhen S., Helmberg W., Kenton D.L., Khovayko O., Lipman D.J., Madden T.L., Maglott D.R., Ostell J., Pontius J.U., Pruitt K.D., Schuler G.D., Schriml L.M., Sequeira E., Sherry S., Sirotkin K., Starchenko G., Suzek T.O., Tatusov R., Tatusova T.A., Wagner L., and Yaschenko E.. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 33:D39–45, 2005.
Ouzounis C. A., Karp P. D. The past, present and future of genome-wide re-annotation. Genome Biol 3:COMMENT2001, 2002.
Ge H., Walhout A.J., and Vidal M. Integrating ‘omic’ information: a bridge between genomics and systems biology. Trends Genet 19:551–560, 2003.
Altschul S. F., Madden T. L., Schaffer A. A., Zhang J., Zhang Z, Miller W., and Lipman D. J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402, 1997.
Mulder N. J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., Bradley P., Bork P., Bucher P., Cerutti L., Copley R., Courcelle E., Das U., Durbin R., Fleischmann W., Gough J., Haft D., Harte N., Hulo N., Kahn D., Kanapin A., Krestyaninova M., Lonsdale D., Lopez R., Letunic I., Madera M., Maslen J., McDowall J., Mitchell A., Nikolskaya A.N., Orchard S., Pagni M., C.P. Ponting C.P., Quevillon E., Selengut J., Sigrist C.J., Silventoinen V., Studholme D. J., Vaughan R., and Wu C. H. InterPro, progress and status in 2005. Nucleic Acids Res 33:D201–205, 2005.
Gilks W.R., Audit B., De Angelis D., Tsoka S., and Ouzounis C.A. Modeling the percolation of annotation errors in a database of protein sequences. Bioinformatics 18:1641–1649, 2002.
Hulo N., Sigrist C.J., Le Saux V., Langendijk-Genevaux P.S., Bordoli L., Gattiker A., De Castro E., Bucher P, and Bairoch A. Recent improvements to the PROSITE database. Nucleic Acids Res 32:D134–137, 2004.
Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., Studholme D.J., Yeats C, and Eddy S.R. The Pfam protein families database. Nucleic Acids Res 32:D138–141, 2004.
Stevens R., Goble C, Horrocks I., and Bechhofer S. OILing the way to machine understandable bioinformatics resources. IEEE Trans Inf Technol Biomed 6:129–134, 2002a.
The Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res 11:1425–1433, 2001.
Horrocks I. Patel-Schneider P.F, and van Harlem F. From SHIQ and RDF to OWL: The making of a web ontology language. J. of Web Semantics, 1(1):7–26, 2003.
Bollen M., and Stalmans W. The structure, role, and regulation of type 1 protein phosphatases. Crit Rev Biochem Mol Biol 27:227–281, 1992.
Kile B.T., Nicola N.A., and Alexander W.S. Negative regulators of cytokine signaling. Int J Hematol 73:292–298, 2001.
Cohen P. The origins of protein phosphorylation. Nat Cell Biol. 4:E127–130, 2002a.
Cohen P. Signal integration at the level of protein kinases, protein phosphatases and their substrates. Trends Biochem Sci 17:408–413, 1992.
Alonso A., Sasin J., Bottini N., Friedberg I., Friedberg I., Osterman A., Godzik A., Hunter T., Dixon J., and Mustelin T. Protein tyrosine phosphatases in the human genome. Cell 117:699–711, 2004.
Cohen P.T. Novel protein serine/threonine phosphatases: variety is the spice of life. Trends Biochem Sci 22:245–251, 1997.
Andersen J.N., Mortensen O.H., Peters G.H., Drake P.G., Iversen L.F., Olsen O.H., Jansen P.G., Andersen H.S., Tonks N.K., and Moller N.P.. Structural and evolutionary relationships among protein tyrosine phosphatase domains. Mol Cell Biol 21:7117–7136, 2001.
Goldstein B.J. Protein-tyrosine phosphatase IB (PTP1B): a novel therapeutic target for type 2 diabetes mellitus, obesity and related states of insulin resistance. Curr Drug Targets Immune Endocr Metabol Disord 1:265–275, 2001.
Schonthal A.H. Role of serine/threonine protein phosphatase 2A in cancer. Cancer Lett 170:1–13, 2001.
Zhang Z.Y. Protein tyrosine phosphatases: prospects for therapeutics. Curr Opin Chem Biol 5:416–423, 2001
Tian Q. and Wang J. Role of serine/threonine protein phosphatase in Alzheimer’s disease. Neurosignals 11:262–269, 2002.
Baader F., Calvanese D., McGuinness D., Nardi D., and Patel-Schneider P.F., editors. The Description Logic Handbook: Theory, Implementation and Applications. Cambridge University Press, 2003.
Wessel M. and Möller, R. A High Performance Semantic Web Query Answering Engine. In I. Horrocks, U. Sattler, and F. Wolter, editors, Proc. International Workshop on Description Logics, 2005.
Haarslev V. and Möller R. RACER system description. In Proceedings of the International Joint Conference on Automated Reasoning (IJCAR-01), volume 2083 of Lecture Notes in Artificial Intelligence, Springer-Verlag, 701–705, 2001.
Baker C.J.O., Su X., Butler G., and Haarslev V. Ontoligent Interactive Query Tool. In Proceedings of the Canadian Semantic Web Working Symposium, June 6, 2006, Quebec City, Quebec, Canada, Series: Semantic Web and Beyond: Computing for Human Experience, Vol. 2, Springer Verlag, 2006, pp. 155–169, 2006a.
Shaban-Nejad A., Baker C.J.O., Haarslev V., and Butler G. The FungalWeb Ontology: Semantic Web Challenges in Bioinformatics and Genomics. In Semantic Web Challenge-Proceedings of the 4th International Semantic Web Conference, Nov. 6–10, Galway, Ireland, Springer-Verlag, LNCS, Vol. 3729, 2005, pp. 1063–1066, 2005. (2. Prize in the Semantic Web Challenges competition).
Baker C.J.O., Shaban-Nejad A., Su X., Haarslev V., and Butler G. Semantic Web Infrastructure for Fungal Enzyme Biotechnologists. Journal of Web Semantics, (4)3, 2006, 2006b.
Bechhofer S. Horrocks I., Turi D. The OWL Instance Store: System Description. Proceedings CADE-20, Lecture Notes in Computer Science, Springer-Verlag. (To appear.)
Mabey J.E., Anderson M.J., Giles P.F., Miller C.J., Attwood T.K., Paton N.W., Bornberg-Bauer E., Robson G.D., Oliver S.G., and Denning D.W.. CADRE: the Central Aspergillus Data REpository. Nucleic Acids Res 32:D401–405, 2004.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Springer Science+Business Media, LLC
About this chapter
Cite this chapter
Wolstencroft, K., Stevens, R., Haarslev, V. (2007). Applying OWL Reasoning to Genomic Data. In: Baker, C.J.O., Cheung, KH. (eds) Semantic Web. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-48438-9_12
Download citation
DOI: https://doi.org/10.1007/978-0-387-48438-9_12
Publisher Name: Springer, Boston, MA
Print ISBN: 978-0-387-48436-5
Online ISBN: 978-0-387-48438-9
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)