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OnEX: Exploring changes in life science ontologies.

Hartung M, Kirsten T, Gross A, Rahm E - BMC Bioinformatics (2009)

Bottom Line: The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application.Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany. hartung@izbi.uni-leipzig.de

ABSTRACT

Background: Numerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.

Results: We present OnEX (Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, OnEX provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.

Conclusion: OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at http://www.izbi.de/onex.

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OnEX architecture. Three-tier architecture of the OnEX system.
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Figure 1: OnEX architecture. Three-tier architecture of the OnEX system.

Mentions: The OnEX system is based on a three-tier architecture displayed in Figure 1. The backend of the system consists of a data server (MySQL database) for storage and management of numerous ontology versions and corresponding statistics. Import modules allow the integration of ontology versions in various formats. A middleware component implemented in Java provides a common API to applications or visualization components. The middleware utilizes core functions such as query methods which use SQL calls to access the ontology version repository. The web application itself is platform-independent (usable in different web browsers) and is based on the Google Web Toolkit [37] as well as the Ext GWT library [38] for building rich internet applications. The modular architecture could also support additional applications besides the online tool presented herein. In particular, web services could be added for programmatic access to the change analysis primitives as well as the ontology versions.


OnEX: Exploring changes in life science ontologies.

Hartung M, Kirsten T, Gross A, Rahm E - BMC Bioinformatics (2009)

OnEX architecture. Three-tier architecture of the OnEX system.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2746816&req=5

Figure 1: OnEX architecture. Three-tier architecture of the OnEX system.
Mentions: The OnEX system is based on a three-tier architecture displayed in Figure 1. The backend of the system consists of a data server (MySQL database) for storage and management of numerous ontology versions and corresponding statistics. Import modules allow the integration of ontology versions in various formats. A middleware component implemented in Java provides a common API to applications or visualization components. The middleware utilizes core functions such as query methods which use SQL calls to access the ontology version repository. The web application itself is platform-independent (usable in different web browsers) and is based on the Google Web Toolkit [37] as well as the Ext GWT library [38] for building rich internet applications. The modular architecture could also support additional applications besides the online tool presented herein. In particular, web services could be added for programmatic access to the change analysis primitives as well as the ontology versions.

Bottom Line: The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application.Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Interdisciplinary Centre for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany. hartung@izbi.uni-leipzig.de

ABSTRACT

Background: Numerous ontologies have recently been developed in life sciences to support a consistent annotation of biological objects, such as genes or proteins. These ontologies underlie continuous changes which can impact existing annotations. Therefore, it is valuable for users of ontologies to study the stability of ontologies and to see how many and what kind of ontology changes occurred.

Results: We present OnEX (Ontology Evolution EXplorer) a system for exploring ontology changes. Currently, OnEX provides access to about 560 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an ontology version repository, a middleware component and the OnEX web application. Interactive workflows allow a systematic and explorative change analysis of ontologies and their concepts as well as the semi-automatic migration of out-dated annotations to the current version of an ontology.

Conclusion: OnEX provides a user-friendly web interface to explore information about changes in current life science ontologies. It is available at http://www.izbi.de/onex.

Show MeSH