Ontology Based Data Management Systems for Post-Genomic Clinical Trials within a European Grid Infrastructure for Cancer Research

Weiler, Gabriele; Brochhausen, Mathias; Graf, Norbert; Schera, Fatima; Hoppe, Alexander; Kiefer, Stephan

doi:10.1109/iembs.2007.4353829

Cited by 19 publications

(6 citation statements)

References 4 publications

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“…ObTiMA [56] is an Ontology-based Trial Management Application intended to help design and conduct clinical trials in an end-user-friendly way. To support the whole life cycle of a clinical trial, it utilizes the features provided by the ACGT-MO and the ACGT-SM.…”

Section: Exploitation Of the Mo In The Acgt Projectmentioning

confidence: 99%

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

Brochhausen

Spear

Cocos

et al. 2011

Journal of Biomedical Informatics

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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 infra-structure (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.

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Section: Exploitation Of the Mo In The Acgt Projectmentioning

confidence: 99%

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

Brochhausen

Spear

Cocos

et al. 2011

Journal of Biomedical Informatics

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“…Additional information includes the content of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and protein-protein interaction networks [9]. Comprehensive meta-data describing the semantics of the heterogeneous and complex data are needed to leverage it for further research [12]. To address this issue, efforts exist for describing the data in a comprehensive way by domain specific ontologies [13].…”

Section: A Data Sourcesmentioning

confidence: 99%

Towards an environment for data mining based analysis processes in bioinformatics & personalized medicine

Wegener

Rossi

Buffa

et al. 2011

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

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Bioinformatics and data mining procedures are collaborating to implement and evaluate tools and procedures for prediction of disease recurrence and progression, response to treatment, as well as new insights into various oncogenic pathways [1], [2], [3], [4] by taking into account the user needs and their heterogeneity. Based on these advances, medicine is undergoing a revolution that is even transforming the nature of health care from reactive to proactive [5]. The p-medicine (www.p-medicine.eu) consortium is creating a biomedical platform to facilitate the translation from current practice to a predictive, personalized, preventive, participatory and psycho-cognitive medicine by integrating VPH models, clinical practice, imaging and omics data. In this paper, we present the challenges for data mining based analysis in bioand medical informatics and our approach towards a data mining environment addressing these requirements in the pmedicine platform.

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“…ACGT aims to provide solutions that demonstrate the possibility of creating data in an ontologygoverned way. To explore this approach, an Ontology-based Trial Management System (ObTiMA) is under development that enables those who undertake clinical trials to set up patient data management systems with comprehensive metadata by using the ACGT-MO [32]. This allows seamless integration of data collected in these systems into the ACGT mediator architecture.…”

Section: Exploitation Of the Ontology In A Clinical Trial Management mentioning

confidence: 99%

Applications of the ACGT Master Ontology on Cancer

Brochhausen

Weiler

Martín

et al. 2008

On the Move to Meaningful Internet Systems: OTM 2008 Workshops

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Abstract. In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within the ACGT project thus far.

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Ontology Based Data Management Systems for Post-Genomic Clinical Trials within a European Grid Infrastructure for Cancer Research

Cited by 19 publications

References 4 publications

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

Towards an environment for data mining based analysis processes in bioinformatics & personalized medicine

Applications of the ACGT Master Ontology on Cancer

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