SNP-Converter: An Ontology-Based Solution to Reconcile Heterogeneous SNP Descriptions for Pharmacogenomic Studies

1. Kruglyak, L., Nickerson, D.: Variation is the spice of life. Nat. Genet. 27(3), 234–236 (2001)

   Article  Google Scholar 

2. Frawley, W., Piatetsky-Shapiro, G., Matheus, C.: Knowledge Discovery in databases: An Overview. In: Knowledge Discovery in Databases, pp. 1–30. AAAI/MIT Press (1991)

   Google Scholar 

3. Janetzko, D., Cherfi, H., Kennke, R., Napoli, A., Toussaint, Y.: Knowledge-based Selection of Association Rules for Text Mining. In: 16th European Conference on Artificial Intelligence, ECAI 2004, Valencia (2004)

   Google Scholar 

4. Vetere, G., Lenzerini, M.: Models for Semantic. Interoperability in Service Oriented Architectures. IBM Systems Journal 44 (2005)

   Google Scholar 

5. Gruber, T.R.: A Translation Approach to Portable Ontology Specifications. Knowledge Acquisition 5, 199–220 (1993)

   Article  Google Scholar 

6. Evans, W., Relling, M.: Pharmacogenomics: moving toward individualized medicine. Nature. 29, 464–468 (2004)

   Article  Google Scholar 

7. Klein, T., Chang, J., Cho, M., Easton, K., Fergerson, R., Hewett, M., Lin, Z., Liu, Y., Liu, S., Oliver, D., et al.: Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenom. J. 1, 167–170 (2001)

   Google Scholar 

8. Marsh, S., Kwok, P., McLeod, H.: SNP databases and pharmacogenetics: great start, but a long way to go. Hum. Mutat. 20(3), 174–179 (2002)

   Article  Google Scholar 

9. Coulet, A., Smaïl-Tabbone, M., Napoli, A., Benlian, P., Devignes, M.D.: SNPOntology for semantic integration of genomic variation data. In: ISMB 2006, Fortaleza (2006), https://hal.inria.fr/inria-00067863

10. Anand, S., Bell, D., Hughes, J.: The role of domain knowledge in data mining. In: Conference on Information and Knowledge Management CIKM 1995, Baltimore, USA (1995)

    Google Scholar 

11. Euler, T., Scholz, M.: Using Ontologies in a KDD workbench. In: ECML/PKDD 2004 Workshop on Knowledge Discovery and Ontologies (KDO 2004), Pisa (2004)

    Google Scholar 

12. Catarci, T., Lenzerini, M.: Representing and using inter-schema knowledge in cooperative information systems. Journal of Intelligent and Cooperative Information Systems 2, 375–398 (1993)

    Article  Google Scholar 

13. Levy, A.: Logic-Based Techniques in Data Integration Logic Based Artificial Intelligence. Jack Minker. Kluwer Publishers, Dordrecht (2000)

    Google Scholar 

14. den Dunnen, J., Antonarakis, S.: Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum. Mutat. 15, 7–12 (2000)

    Article  Google Scholar 

15. den Dunnen, J., Paalman, M.: Standardizing mutation nomenclature: why bother? Hum. Mutat. 22, 181–182 (2003)

    Article  Google Scholar 

16. Cotton, R.G.H., Kazazian, H.H.: Toward a human variome project. Hum. Mutat. 26(6), 499 (2005)

    Article  Google Scholar 

17. Sherry, S., Ward, M., Sirotkin, K.: dbSNP—Database for Single Nucleotide Polymorphisms and Other Classes of Minor Genetic Variation. Genome. Res. 9, 677–679 (1999)

    Google Scholar 

18. Fredman, D., Munns, G., Rios, D., Sjoholm, F., Siegfried, M., Lenhard, B., Lehvaslaiho, H., Brookes, A.: HGVbase: a curated resource describing human DNA variation and phenotype relationships. Nucleic Acids Res. 32, D516–519 (2004)

    Article  Google Scholar 

19. Hemminger, B., Saelim, B., Sullivan, P.: TAMAL: an integrated approach to chosing SNPs for genetics studies of human compex traits. Bioinformatics 22, 626–627 (2006)

    Article  Google Scholar 

20. Karchin, R., Diekhaux, M., Kelly, L., Thomas, D., Pieper, U., Eswar, N., Haussler, D., Sali, A.: LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814–2820 (2005)

    Article  Google Scholar 

21. Sugawara, H., Mizushima, H., Kano, T., Shigemoto, Y., Hashimoto, Y., Tomabechi, I., Sakagami, N., et al.: Polymorphism Markup Language (PML) for the interoperability of data on SNPs and other sequence variations. In: 19th International CODATA Conference (2004)

    Google Scholar 

22. OMG Single Nucleotide Polymorphisms specification (2005), http://www.omg.org/cgi-bin/doc/dtc/05-02-06.pdf

23. Oliver, D., Rubin, D., Stuart, J., Hewett, M., Klein, T., Altman, R.: Ontology development for a pharmacogenetics knowledge base. In: Pac. Symp. Biocomput., pp. 65–76 (2002)

    Google Scholar 

24. Horrocks, P., Patel-Schneider, F., van Harmelen, F.: From SHIQ and RDF to OWL: The making of a web ontology language. Journal of Web Semantics 1(1), 7–26 (2003)

    Google Scholar 

25. Noy, N., Sintek, M., Decker, S., et al.: Creating Semantic Web contents with Protege-2000. IEEE Intelligent Systems 16, 60–71 (2001)

    Article  Google Scholar 

26. W3C Web Ontology Working Group (WOWG), Owl web ontology language semantics and abstract syntax. W3C recommendation (2004), http://www.w3.org/TR/owl-ref/

27. 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 

28. Cheung, K.H., Kevin, Y., Yip, K.Y., Smith, A., de Knikker, R., Masiar, A., Gerstein, M.: YeastHub: a semantic web use case for integrating data in the life sciences domain. Bioinformatics 21(28), i85–i96 (2005)

    Article  Google Scholar 

Download references