The ACGT Master Ontology and its applications - Towards an ontology-driven cancer research and management system

The ACGT Master Ontology and its applications - Towards an ontology-driven cancer research and management system,10.1016/j.jbi.2010.04.008,Journal of

The ACGT Master Ontology and its applications - Towards an ontology-driven cancer research and management system   (Citations: 2)
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Mathias Brochhausen, Andrew D. Spear, Cristian Cocos, Gabriele Weiler, Luis Martín, Alberto Anguita, Holger Stenzhorn, Evangelia Daskalaki, Fatima Schera, Ulf Schwarz, Stelios Sfakianakis, Stephan Kiefer
Objective: This paper introduces the objectives, methods and results of ontology development in the EU co-funded project Advancing Clinico-genomic Trials on Cancer – Open Grid Services for Improving Medical Knowledge Discovery (ACGT). While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems, category schemes and reporting methods on the part of different research groups. The goal of the ACGT project is to contribute to the resolution of these problems by developing an ontology-driven, semantic grid services infrastructure that will enable efficient execution of discovery-driven scientific workflows in the context of multi-centric, post-genomic clinical trials. The focus of the present paper is the ACGT Master Ontology (MO). Methods: ACGT project researchers undertook a systematic review of existing domain and upper-level ontologies, as well as of existing ontology design software, implementation methods, and end-user interfaces. This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts and clinicians. Results: To date, the results of the ACGT project include (i) the development of a master ontology (the ACGT-MO) based on clearly defined principles of ontology development and evaluation; (ii) the development of a technical infrastructure (the ACGT Platform) that implements the ACGT-MO utilizing independent tools, components and resources that have been developed based on open architectural standards, and which includes an application updating and evolving the ontology efficiently in response to end-user needs; and (iii) the development of an Ontology-based Trial Management Application (ObTiMA) that integrates the ACGT-MO into the design process of clinical trials in order to guarantee automatic semantic integration without the need to perform a separate mapping process.
Journal: Journal of Biomedical Informatics - JBI , vol. 44, no. 1, pp. 8-25, 2011
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    • ...Many recent biomedical research projects [3, 7, 8, 11, 16] employed this approach, but also required huge efforts to adopt semantic technologies...
    • ...While traditional information modeling methodologies produce large and detailed domain-specific models [3, 8], the two-level modeling paradigm does not specify a predefined set of attributes that can be represented...
    • ...Alike to the already mentioned projects, the ACGT semantic data integration framework was based on a domain ontology and corresponding mappings to the actual database schemes (annotations), which in turn was also experienced as challenging cross-domain collaboration [8]...
    • ...The semantic enrichment of data sources with these annotations is by itself a significant undertaking, and can become a major bottleneck to the practical applicability of those mediation approaches that are not specifically designed to address this issue [8, 14, 15]...

    Jesus Bisbalet al. Archetype-based semantic mediation: Incremental provisioning of data s...

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