Region Evolution eXplorer – A tool for discovering evolution trends in ontology regions

Journal of Biomedical Semantics

Anika Groß²  Michael Hartung²  Victor Christen¹ 

[1] Department of Computer Science, Universität Leipzig, Augustusplatz 10, Leipzig, Germany;Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstr. 16 - 18, Leipzig, Germany

关键词: Ontologies;    Ontology visualization;    Ontology evolution;   

Others  :  1209181
DOI  :  10.1186/s13326-015-0020-6

 received in 2014-09-30, accepted in 2015-04-17,  发布年份 2015

【 摘 要 】

Background

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.

Results

Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods.

Conclusion

REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex webcite.

【 授权许可】

   
2015 Christen et al.; licensee BioMed Central.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

Figure 6.

Figure 7.

Figure 8.

【 参考文献 】

• [1]Bodenreider O, Stevens R: Bio-ontologies: current trends and future directions. Brief Bioinform 2006, 7(3):256-74.
• [2]Lambrix P, Tan H, Jakoniene V, Strömbäck L. Biological ontologies. In: Semantic Web. Springer: 2007. p. 85–99. http://link.springer.com/chapter/10.1007\%2F978-0-387-48438-9_5.
• [3]Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al.: Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 1554, 102(43):5-50.
• [4]Hartung M, Terwilliger JF, Rahm E. Recent advances in schema and ontology evolution. In: Schema matching and mapping. Springer: 2011. p. 149–90. http://link.springer.com/chapter/10.1007/978-3-642-16518-4_6.
• [5]Malone J, Stevens R: Measuring the level of activity in community built bio-ontologies. J Biomed Inform 2013, 46:5-14.
• [6]Tudorache T, Noy NF, Tu S, Musen MA. Supporting collaborative ontology development in Protégé. In: The Semantic Web-ISWC. Springer: 2008. p. 17–32. http://link.springer.com/chapter/10.1007/978-3-540-88564-1_2.
• [7]Groza T, Tudorache T, Dumontier M: Commentary: State of the art and open challenges in community-driven knowledge curation. J Biomed Inform 2013, 46:1-4.
• [8]Sioutos N, Coronado Sd, Haber MW, Hartel FW, Shaiu WL, Wright LW: NCI Thesaurus: a semantic model integrating cancer-related clinical and molecular information. J Biomed Inform 2007, 40:30-43.
• [9]Gross A, Hartung M, Prüfer K, Kelso J, Rahm E: Impact of ontology evolution on functional analyses. Bioinformatics 2012, 28(20):2671-77.
• [10]Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, et al.: AmiGO: online access to ontology and annotation data. Bioinformatics 2009, 25(2):288-9.
• [11]Binns D, Dimmer E, Huntley R, Barrell D, O’Donovan C, Apweiler R: QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics 2009, 25(22):3045-46.
• [12]Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, et al.: BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res 2009, 37(suppl 2):W170-3.
• [13]Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, et al.: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-5.
• [14]Park YR, Park CH, Kim JH: GOChase: correcting errors from Gene Ontology-based annotations for gene products. Bioinformatics 2005, 21(6):829-31.
• [15]Park JC, Kim Te, Park J: Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability. BMC Bioinformatics 2008, 9(Suppl 3):S7. BioMed Central Full Text
• [16]Hartung M, Kirsten T, Gross A, Rahm E: OnEX: Exploring changes in life science ontologies. BMC Bioinformatics 2009, 10:250. BioMed Central Full Text
• [17]Hartung M, Gross A, Rahm E: CODEX: exploration of semantic changes between ontology versions. Bioinformatics 2012, 28(6):895-6.
• [18]Christen V, Gross A, Hartung M. REX - A Tool for Discovering Evolution Trends in Ontology Regions. In: Proceedings of the 10th International Conference on Data Integration in the Life Sciences (DILS). Springer: 2014. p. 96–103. http://link.springer.com/chapter/10.1007.
• [19]Hartung M, Gross A, Kirsten T, Rahm E. Discovering Evolving Regions in Life Science Ontologies. In: Proceedings of the 7th International Conference on Data Integration in the Life Sciences (DILS). Springer: 2010. p. 19–34. http://link.springer.com/chapter/10.1007/978-3-642-15120-0_3.
• [20]Hartung M, Gross A, Rahm E: COnto–Diff: generation of complex evolution mappings for life science ontologies. J Biomed Inform 2013, 46:15-32.
• [21]Noy NF, Musen MA. PROMPTDIFF: a fixed-point algorithm for comparing ontology versions. In: AAAI/IAAI. American Association for Artificial Intelligence: 2002. p. 744–50. http://dl.acm.org/citation.cfm?id=777092.777207.
• [22]Google Web Toolkit. http://developers.google.com/web-toolkit/.
• [23]InfoVis Toolkit. http://philogb.github.io/jit/.
• [24]Pesquita C, Faria D, Falcao AO, Lord P, Couto FM: Semantic similarity in biomedical ontologies. PLoS Comput Biol 2009, 5(7):e1000443.
• [25]Huntley RP, Sawford T, Mutowo-Meullenet P, Shypitsyna A, Bonilla C, Martin MJ, et al.: The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res 2015, 43(D1):D1057-D63.
• [26]Noy NF, Sintek M, Decker S, Crubézy M, Fergerson RW, Musen MA: Creating semantic web contents with protege-2000. IEEE Intell Syst 2001, 16(2):60-71.
• [27]Day-Richter J, Harris MA, Haendel M: Gene Ontology OBO-Edit Working Group, Lewis S. OBO-Edit – an ontology editor for biologists. Bioinformatics 2007, 23(16):2198-200.
• [28]Min H, Perl Y, Chen Y, Halper M, Geller J, Wang Y: Auditing as part of the terminology design life cycle. J Am Med Inform Assoc 2006, 13(6):676-90.