Ontology Guided Data Integration for Computational Prioritization of Disease Genes | SpringerLink
Skip to main content
Springer Nature Link
Log in

Ontology Guided Data Integration for Computational Prioritization of Disease Genes

  • Conference paper
On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops (OTM 2006)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 4277))

Abstract

In this paper we present our progress on a framework for collection and presentation of biomedical information through ontology-based mediation. The framework is built on top of a methodology for computational prioritization of candidate disease genes, called Endeavour. Endeavour prioritizes genes based on their similarity with a set of training genes while using a wide variety of information sources. However, collecting information from different sources is a difficult process and can lead to non-flexible solutions. In this paper we describe an ontology-based mediation framework for efficient retrieval, integration, and visualization of the information sources Endeavour uses. The described framework allows to (1) integrate the information sources on a conceptual level, (2) provide transparency to the user, (3) eliminate ambiguity and (4) increase efficiency in information display.

Research supported by: [Research Council KUL: GOA AMBioRICS, CoE EF/05/007 SymBioSys, IDO (Genetic networks), several PhD/postdoc & fellow grants]; [Flemish Government: FWO: PhD/postdoc grants, projects G.0407.02 (support vector machines), G.0413.03 (inference in bioi), G.0388.03 (microarrays for clinical use), G.0229.03 (Bonatema), G.0241.04 (Functional Genomics), G.0499.04 (Statistics), G.0232.05 (Cardiovascular), G.0318.05 (subfunctionalization), G.0553.06 (VitamineD), G.0302.07 (SVM/Kernel) research communities (ICCoS, ANMMM, MLDM); IWT: PhD Grants, GBOU-McKnow-E (Knowledge management algorithms), GBOU-SQUAD (quorum sensing), GBOU-ANA (biosensors), TAD-BioScope-IT, Silicos]; [Belgian Federal Science Policy Office: IUAP P5/22 (‘Dynamical Systems and Control: Computation, Identification and Modeling, 2002-2006)]; [EU-RTD: ERNSI: European Research Network on System Identification; FP6-NoE Biopattern; FP6-IP e-Tumours, FP6-MC-EST Bioptrain].

An erratum to this chapter can be found at http://dx.doi.org/10.1007/11915034_125.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Similar content being viewed by others

References

  1. Hernandez, T., Kambhampati, S.: Integration of biological sources: current systems and challenges ahead. ACM Sigmod Record 33(3), 51–60 (2004)

    Article  Google Scholar 

  2. Stein, L.: Creating a bioinformatics nation. Nature 417(6885), 119–120 (2002)

    Article  Google Scholar 

  3. Stonebraker, M.: Integrating Islands of Information. EAI Journal (September 1999), http://www.eaijournal.com/DataIntegration/IntegrateIsland.asp

  4. Sheth, A.: Changing Focus on Interoperability in Information Systems: From System, Syntax, Structure to Semantics. In: Goodchild, M.F., Egenhofer, M.J., Fegeas, R., Kottman, C.A. (eds.) Interoperating Geographic Information Systems, Kluwer Publishers, Dordrecht (1998)

    Google Scholar 

  5. Spyns, P., Oberle, D., Volz, R., Zheng, J., Jarrar, M., Sure, Y., Studer, R., Meersman, R.: OntoWeb - a Semantic Web Community Portal. In: Proc. Fourth International Conference on Practical Aspects of Knowledge Management (PAKM), Vienna, Austria (December 2002)

    Google Scholar 

  6. Context Browser: http://www.agilense.com/p_artifactmgt.html

  7. Dzbor, M., Domingue, J., Motta, E.: Magpie - Towards a Semantic Web Browser. In: Fensel, D., Sycara, K.P., Mylopoulos, J. (eds.) ISWC 2003. LNCS, vol. 2870, pp. 690–705. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  8. García, E., Sicilia, M.A.: User Interface Tactics in Ontology-Based Information Seeking. Psychnology e-journal 1(3), 243–256 (2003)

    Google Scholar 

  9. Birkland, A., Yona, G.: BIOZON: a system for unification, management and analysis of heterogeneous biological data. BMC Bioinformatics 7, 70–70 (2006)

    Article  Google Scholar 

  10. Etzold, T., Ulyanov, A., Argos, P.: SRS: information retrieval system for molecular biology data banks. Methods Enzymol 266, 114–128 (1996)

    Article  Google Scholar 

  11. Stevens, R., Baker, P., Bechhofer, S., Ng, G., Jacoby, A., Paton, N.W., Goble, C.A., Brass, A.: TAMBIS: transparent access to multiple bioinformatics information sources. Bioinformatics 16, 184–185 (2000)

    Article  Google Scholar 

  12. Davidson, S.B., Crabtree, J., Brunk, B.P., Schug, J., Tannen, V., Overton, G.C., Stoeckert, C.J.: K2/Kleisli and GUS: Experiments in integrated access to genomic data sources. IBM Systems Journal 40, 512–531 (2001)

    Article  Google Scholar 

  13. Haas, L.M., Schwarz, P.M., Kodali, P., Kotlar, E., Rice, J.E., Swope, W.C.: DiscoveryLink: A system for integrated access to life sciences data sources. IBM Systems Journal 40, 489–511 (2001)

    Article  Google Scholar 

  14. Wong, L.: The Collection Programming Language - Reference Manual. Technical Report Kent Ridge Digital Labs, 21 Heng Mui Keng Terrace, Singapore 119613

    Google Scholar 

  15. Alashqur, A.M., Su, S.Y.W., Lam, H.: OQL: A Query Language for Manipulating Object-oriented Databases. In: Proceedings of the Fifteenth International Conference on Very Large Data Bases, Amsterdam, The Netherlands, August 22-25, pp. 433–442 (1989)

    Google Scholar 

  16. Aerts, S., Lambrechts, D., Maity, S., Van Loo, P., Coessens, B., De Smet, F., Tranchevent, L.C., De Moor, B., Marynen, P., Hassan, B., Carmeliet, P., Moreau, Y.: Gene prioritization via genomic data fusion. Nat. Biotechnol. 24, 537–544 (2006)

    Article  Google Scholar 

  17. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG resources for deciphering the genome. Nucleic Acids Res. 32, D277–D280 (2004)

    Article  Google Scholar 

  18. The Gene Ontology Consortium: Gene Ontology: tool for the unification of biology. Nature Genet. 25, 25–29 (2000)

    Google Scholar 

  19. 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., Ponting, C.P., Quevillon, E., Selengut, J., Sigrist, C.J., Silventoinen, V., Studholme, D.J., Vaughan, R., Wu, C.H.: InterPro, progress and status in 2005. Nucleic Acids Res. 33, D201–205 (2005)

    Article  Google Scholar 

  20. Gilbert, D.: Biomolecular interaction network database. Brief Bioinform 6, 194–198 (2005)

    Article  Google Scholar 

  21. Reiter, R.: Towards a Logical Reconstruction of Relational Database Theory. In: Brodie, M., Mylopoulos, J., Schmidt, J. (eds.) On Conceptual Modelling, pp. 191–233. Springer, Heidelberg (1984)

    Google Scholar 

  22. Meersman, R.: The Use of Lexicons and Other Computer-Linguistic Tools in Semantics, Design and Cooperation of Database Systems. In: Zhang, Y., Rusinkiewicz, M., Kambayashi, Y. (eds.) Proceedings of the Conference on Cooperative Database Systems (CODAS 1999), pp. 1–14. Springer, Heidelberg (1999)

    Google Scholar 

  23. Meersman, R.: Ontologies and Databases: More than a Fleeting Resemblance. In: d’Atri, A., Missikoff, M. (eds.) OES/SEO 2001 Rome Workshop, Luiss Publications (2001)

    Google Scholar 

  24. Spyns, P., Meersman, R., Jarrar, M.: Data Modelling versus Ontology Engineering. SIGMOD Record: Special Issue on Semantic Web and Data Management 31(4), 12–17 (2002)

    Google Scholar 

  25. Guarino, N., Giaretta, P.: Ontologies and Knowledge Bases: Towards a Terminological Clarification. In: Mars, N. (ed.) Towards Very Large Knowledge Bases: Knowledge Building and Knowledge Sharing, pp. 25–32. IOS Press, Amsterdam

    Google Scholar 

  26. Kasprzyk, A., Keefe, D., Smedley, D., London, D., Spooner, W., Melsopp, C., Hammond, M., Rocca-Serra, P., Cox, T., Birney, E.: EnsMart: a generic system for fast and flexible access to biological data. Genome Res. 14, 160–169 (2004)

    Article  Google Scholar 

  27. Maglott, D., Ostell, J., Pruitt, K.D., Tatusova, T.: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33, 54–58 (2005)

    Article  Google Scholar 

  28. Meersman, R.: Semantic Web and Ontologies: Playtime or Business at the Last Frontier in Computing? In: NSF-EU Workshop on Database and Information Systems Research for Semantic Web and Enterprises, pp. 61–67 (2002)

    Google Scholar 

  29. De Leenheer, P., Meersman, R.: Towards a formal foundation of DOGMA ontology: part I. Technical Report STAR-2005-06, VUB STARLab (2005)

    Google Scholar 

  30. De Leenheer, P., de Moor, A., Meersman, R.: Context Dependency Management in Ontology Engineering. Technical Report STARLab, Brussel (2006)

    Google Scholar 

  31. Deray, T., Verheyden, P.: Towards a semantic integration of medical relational databases by using ontologies: a case study. In: Meersman, R., Tari, Z. (eds.) OTM-WS 2003. LNCS, vol. 2889, pp. 137–150. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  32. Verheyden, P., Deray, T., Meersman, R.: Semantic Mapping of Large and Complex Databases to Ontologies: Methods and Tools. Technical Report 25, STAR Lab, Brussel (2004)

    Google Scholar 

  33. Verheyden, P., De Bo, J., Meersman, R.: Semantically unlocking database content through ontology-based mediation. In: Bussler, C.J., Tannen, V., Fundulaki, I. (eds.) SWDB 2004. LNCS, vol. 3372, pp. 109–126. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  34. Trog, D., Vereecken, J.: Context-driven Visualization for Ontology Engineering. Master thesis, Vrije Universiteit Brussel (2006)

    Google Scholar 

  35. Halpin, T.: Information Modeling and Relational Databases. Morgan Kaufmann, San Francisco (2001)

    Google Scholar 

  36. Barriot, R., Poix, J., Groppi, A., Barré, A., Goffard, N., Sherman, D., Dutour, I., de Daruvar, A.: New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Res. 32(12), 3581–3589 (2004)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Electrical Engineering, Katholieke Universiteit Leuven,  

    Bert Coessens, Yves Moreau & Bart De Moor

  2. Semantics Technology and Applications Research Laboratory, Vrije Universiteit Brussel,  

    Stijn Christiaens, Ruben Verlinden & Robert Meersman

Authors
  1. Bert Coessens
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stijn Christiaens
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ruben Verlinden
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yves Moreau
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Robert Meersman
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bart De Moor
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. STARLab, Vrije Universiteit Brussel (VUB), Bldg G/10, Pleinlaan 2, 1050, Brussels, Belgium

    Robert Meersman

  2. School of Computer Science and Information Technology, RMIT University, Bld 10.10, 376-392 Swanston Street, 3001, Melbourne, VIC, Australia

    Zahir Tari

  3. Facultad de Informática, Universidad Politécnica de Madrid, Campus de Montegancedo S/N, 28660, Boadilla del Monte, Madrid, Spain

    Pilar Herrero

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Coessens, B., Christiaens, S., Verlinden, R., Moreau, Y., Meersman, R., De Moor, B. (2006). Ontology Guided Data Integration for Computational Prioritization of Disease Genes. In: Meersman, R., Tari, Z., Herrero, P. (eds) On the Move to Meaningful Internet Systems 2006: OTM 2006 Workshops. OTM 2006. Lecture Notes in Computer Science, vol 4277. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11915034_93

Download citation

  • DOI: https://doi.org/10.1007/11915034_93

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-48269-7

  • Online ISBN: 978-3-540-48272-7

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics