Abstract
A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution Explorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies and is available at http://www.izbi.de/rex .
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References
Bodenreider, O., Stevens, R.: Bio-ontologies: current trends and future directions. Briefings in Bioinformatics 7(3) (2006)
Groß, A., Hartung, M., Prüfer, K., et al.: Impact of ontology evolution on functional analyses. Bioinformatics 28(20) (2012)
Groza, T., Tudorache, T., Dumontier, M.: Commentary: State of the art and open challenges in community-driven knowledge curation. Journal of Biomedical Informatics 46(1) (2013)
Hartung, M., Gross, A., Kirsten, T., Rahm, E.: Discovering Evolving Regions in Life Science Ontologies. In: Lambrix, P., Kemp, G. (eds.) DILS 2010. LNCS, vol. 6254, pp. 19–34. Springer, Heidelberg (2010)
Hartung, M., Gross, A., Rahm, E.: CODEX: exploration of semantic changes between ontology versions. Bioinformatics 28(6) (2012)
Hartung, M., Kirsten, T., Gross, A., Rahm, E.: OnEX: Exploring changes in life science ontologies. BMC Bioinformatics 10(1) (2009)
Hartung, M., Terwilliger, J.F., Rahm, E.: Recent Advances in Schema and Ontology Evolution. In: Schema Matching and Mapping. Springer, Heidelberg (2011)
Lambrix, P., Tan, H., Jakoniene, V., Strömbäck, L.: Biological ontologies. In: Semantic Web. Springer, Heidelberg (2007)
Malone, J., Stevens, R.: Measuring the level of activity in community built bio-ontologies. Journal of Biomedical Informatics 46(1) (2013)
Noy, N.F., Shah, N.H., Whetzel, P., et al.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Research 37(suppl. 2) (2009)
Park, J.C., Kim, T., Park, J.: Monitoring the evolutionary aspect of the gene ontology to enhance predictability and usability. BMC Bioinformatics 9 (2008)
Park, Y.R., Park, C.H., Kim, J.H.: GOChase: correcting errors from Gene Ontology-based annotations for gene products. Bioinformatics 21(6) (2005)
Sioutos, N., De Coronado, S., Haber, M.W., et al.: NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. Journal of Biomedical Informatics 40(1) (2007)
Smith, B., Ashburner, M., Rosse, C., et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology 25(11) (2007)
Subramanian, A., Tamayo, P., Mootha, V.K., et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102(43) (2005)
Tudorache, T., Noy, N.F., Tu, S., Musen, M.A.: Supporting collaborative ontology development in protégé. In: Sheth, A.P., Staab, S., Dean, M., Paolucci, M., Maynard, D., Finin, T., Thirunarayan, K. (eds.) ISWC 2008. LNCS, vol. 5318, pp. 17–32. Springer, Heidelberg (2008)
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Christen, V., Groß, A., Hartung, M. (2014). REX – A Tool for Discovering Evolution Trends in Ontology Regions. In: Galhardas, H., Rahm, E. (eds) Data Integration in the Life Sciences. DILS 2014. Lecture Notes in Computer Science(), vol 8574. Springer, Cham. https://doi.org/10.1007/978-3-319-08590-6_9
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DOI: https://doi.org/10.1007/978-3-319-08590-6_9
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-08589-0
Online ISBN: 978-3-319-08590-6
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