Analyzing the Evolution of Life Science Ontologies and Mappings

Ontologies are heavily developed and used in life sciences and undergo continuous changes. However, the evolution of life science ontologies and references to them (e.g., annotations) is not well understood and has received little attention so far. We therefore propose a generic framework for analyzing both the evolution of ontologies and the evolution of ontology-related mappings, in particular annotations referring to ontologies and similarity (match) mappings between ontologies. We use our framework for an extensive comparative evaluation of evolution measures for 16 life science ontologies. Moreover, we analyze the evolution of annotation mappings and ontology mappings for the Gene Ontology.

[1]  Michel C. A. Klein,et al.  Change Management for Distributed Ontologies , 2004 .

[2]  Michel C. A. Klein,et al.  Ontology versioning on the Semantic Web , 2001, SWWS.

[3]  Olivier Bodenreider,et al.  Non-Lexical Approaches to Identifying Associative Relations in the Gene Ontology , 2004, Pacific Symposium on Biocomputing.

[4]  Zhe Yang,et al.  Ontology Analysis on Complexity and Evolution Based on Conceptual Model , 2006, DILS.

[5]  Andreas Prlic,et al.  Ensembl 2007 , 2006, Nucleic Acids Res..

[6]  Lawrence Hunter,et al.  Pacific symposium on biocomputing 2006 , 2005, PSB 2016.

[7]  Olivier Bodenreider,et al.  Linking the Gene Ontology to other biological ontologies , 2005 .

[8]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[9]  Andreas Thor,et al.  Instance-Based Matching of Large Life Science Ontologies , 2007, DILS.

[10]  Frank van Harmelen,et al.  A Framework for Handling Inconsistency in Changing Ontologies , 2005, SEMWEB.

[11]  Boris Motik,et al.  Ontology Evolution within Ontology Editors , 2002, EON.

[12]  Mark A. Musen,et al.  A Framework for Ontology Evolution in Collaborative Environments , 2006, SEMWEB.

[13]  Michel C. A. Klein,et al.  Ontology Evolution: Not the Same as Schema Evolution , 2004, Knowledge and Information Systems.

[15]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[16]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[17]  Boris Motik,et al.  User-Driven Ontology Evolution Management , 2002, EKAW.

[18]  Ljiljana Stojanovic,et al.  Methods and tools for ontology evolution , 2004 .

[19]  Sherri de Coronado,et al.  NCI Thesaurus: A semantic model integrating cancer-related clinical and molecular information , 2007, J. Biomed. Informatics.