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ONTOLOGY BASED INTEGRATION OF DISTRIBUTED AND HETEROGENEOUS DATA SOURCES IN ACGT
english

2008 Proceedings of the First International Conference on Health Informatics   unpublished
A data access layer, based on OGSA-DAI, has been developed in order to cope with syntactic heterogeneities in databases.  ...  The semantic problems present in data sources with different nature are tackled by two core tools, namely the Semantic Mediator and the Master Ontology on Cancer.  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ... 
doi:10.5220/0001045503010306 fatcat:bjrwg42bqbe4xkep5o662dhrze

Building a European biomedical grid on cancer: the ACGT Integrated Project

M Tsiknakis, D Kafetzopoulos, G Potamias, A Analyti, K Marias, A Manganas
2006 Studies in Health Technology and Informatics  
The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable  ...  This paper presents the needs and requirements that led to the formation of the ACGT (Advancing Clinico Genomic Trials) integrated project, its vision and methodological approaches of the project.  ...  Acknowledgements The authors wish to express their gratitude to the whole of the ACGT consortium for their contributions with various ideas on which the ACGT project was developed.  ... 
pmid:16823143 fatcat:y5z67zykjfeydiemgb6emr5oou

An ontology based method to solve query identifier heterogeneity in post-genomic clinical trials

Alberto Anguita, Luis Martín, José Crespo, Manolis Tsiknakis
2008 Studies in Health Technology and Informatics  
One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases.  ...  Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains-e.g. clinical and genetic data.  ...  OntoQueryClean is the evolution of OntoDataClean, a tool for data preprocessing also based on ontologies, and which forms part of the ONTOFUSION system for integration of distributed and heterogeneous  ... 
pmid:18487699 fatcat:osmnats6kragrm5qvjd7hjr7wu

ACGT: advancing clinico-genomic trials on cancer - four years of experience

Luis Martin, Alberto Anguita, Norbert Graf, Manolis Tsiknakis, Mathias Brochhausen, Stefan Rüping, Anca Bucur, Stelios Sfakianakis, Thierry Sengstag, Francesca Buffa, Holger Stenzhorn
2011 Studies in Health Technology and Informatics  
The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with  ...  Advancing Clinico-Genomic Trials (ACGT) was a European Commission funded Integrated Project that aimed at providing tools and methods to enhance the efficiency of clinical trials in the -omics era.  ...  Strong security features such as credential-based data access were added to all platform tools and services thus achieving security in the context of large, distributed data processing.  ... 
pmid:21893844 fatcat:m5qggzte4vhvjbdxo44ie3axwu

Developing a European grid infrastructure for cancer research: vision, architecture, and services

M Tsiknakis
2015 ecancermedicalscience  
Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D.  ...  This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ... 
doi:10.3332/ecancer.2007.56 fatcat:c4imtkihsrh3djksxu6frunesu

Developing a European Grid Infrastructure for Cancer Research: Vision, Architecture, and Services

M Tsiknakis
2007 ecancermedicalscience  
Data integration across heterogeneous data sources and data aggregation across different aspects of the biomedical spectrum, therefore, is at the centre of current biomedical and pharmaceutical R&D.  ...  This paper reports on original results from the ACGT integrated project, focusing on the design and development of a European Biomedical Grid infrastructure in support of multi-centric, post-genomic clinical  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ... 
doi:10.3332/ecms.2007.56 pmid:22275955 pmcid:PMC3223975 fatcat:w5drhkauzneafiwiuhzaeavtfa

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

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 (+3 others)
2011 Journal of Biomedical Informatics  
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  ...  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  ...  Acknowledgments The authors thank all members of the ACGT consortium who are actively contributing to addressing the R&D challenges faced.  ... 
doi:10.1016/j.jbi.2010.04.008 pmid:20438862 pmcid:PMC5755590 fatcat:r5o5r66xazh7dfxh4pfzchb46m

The ACGT project in retrospect: Lessons learned and future outlook

Anca Bucur, Stefan Ruping, Thierry Sengstag, Stelios Sfakianakis, Manolis Tsiknakis, Dennis Wegener
2011 Procedia Computer Science  
In this paper we describe the way the ACGT consortium has approached important challenges in the design and the execution of the clinical trials such as the issues of data integration, semantics based  ...  and services in support of multicentric, post-genomic clinical trials.  ...  Acknowledgements The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996.  ... 
doi:10.1016/j.procs.2011.04.119 fatcat:ls5emmpmrrfwnhnkscbpazorge

An Ontology for Clinical Trial Data Integration

Ratnesh Sahay, Dimitrios Ntalaperas, Eleni Kamateri, Panagiotis Hasapis, Oya Deniz Beyan, Marie-Pierre F. Strippoli, Christiana A. Demetriou, Thomai Gklarou-Stavropoulou, Matthias Brochhausen, Konstantinos Tarabanis, Thanassis Bouras, David Tian (+5 others)
2013 2013 IEEE International Conference on Systems, Man, and Cybernetics  
We address two key challenges in developing an ontology-based clinical terminology (1) an ontology building methodology for clinical terminologies that are separated in global and local layers; and (2)  ...  data, schema, and medical codes.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of NCATS or NIH. Authors acknowledge Helena F.  ... 
doi:10.1109/smc.2013.553 dblp:conf/smc/SahayNKHBSDGBTBTAAGHD13 fatcat:tdbj7lsyczfjvmu5kn7dawdcb4

Automatic Generation of Integration and Preprocessing Ontologies for Biomedical Sources in a Distributed Scenario

Alberto Anguita, David Pérez-Rey, José Crespo, Víctor Maojo
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
In this scenario, the authors have developed various methods and tools in the area of database integration, using an ontological approach.  ...  Access to a large number of remote data sources has boosted research in biomedicine, where different biological and clinical research projects are based on collaborative efforts among international organizations  ...  Distributed and Ontology-Based KDD Approach This paper is the extension of two ontology-based systems previously developed by the authors to address the integration and preprocessing of distributed data  ... 
doi:10.1109/cbms.2008.71 dblp:conf/cbms/AnguitaPCM08 fatcat:74m6eocqgremzl2ohfhuozwjpi

Post-genomic clinical trials - the perspective of ACGT

Norbert Graf
2009 ecancermedicalscience  
The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ...  Acknowledgement The authors would like to thank all members of the ACGT consortium who are actively contributing to addressing the R&D challenges faced.  ...  ontologies and metadata for the semantic integration of heterogeneous data (clinical imaging genomic proteomic metabolomic and other as well as open source data from the web); 4. develop an Ontology-Based  ... 
doi:10.3332/ecms.2008.66 pmid:22275963 pmcid:PMC3234044 fatcat:vdjnfxvaenbebit4hmgnusltde

Supporting Parallel R Code in Clinical Trials: A Grid-Based Approach

Dennis Wegener, Thierry Sengstag, Stelios Sfakianakis, Stefan Rüping
2008 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications  
The GridR service and its extension are developed as components of the ACGT platform, one aim of which is to facilitate the data mining of clinical trials involving large datasets.  ...  The ACGT GridR service is extended by a component that uses a set of preprocessor-like directives to organize and distribute calculations.  ...  Acknowledgments The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996. References  ... 
doi:10.1109/ispa.2008.29 dblp:conf/ispa/WegenerSSR08 fatcat:a42ukhvvsvet7cyxr7levl54si

Querying phenotype-genotype associations across multiple knowledge bases using Semantic Web technologies

Oya Deniz Beyan, Aftab Iqbal, Yasar Khan, Athos Antoniades, John Keane, Panagiotis Hasapis, Christos Georgousopoulos, Myrto Ioannidi, Stefan Decker, Ratnesh Sahay
2013 13th IEEE International Conference on BioInformatics and BioEngineering  
Biomedical and genomic data are inherently heterogeneous and their recent proliferation over the Web has demanded innovative querying methods to help domain experts in their clinical and research studies  ...  In this paper we present the use of Semantic Web technologies in querying diverse phenotype-genotype associations for supporting personalized medicine and potentially helping to discover new associations  ...  As our semantic model is an ontology, it has the advantage of the representation of data from various knowledge sources in a consistent manner.  ... 
doi:10.1109/bibe.2013.6701573 dblp:conf/bibe/BeyanIKAKHGIDS13 fatcat:awszdzb6sfg6hiu45ivkhklyjy

Archetype-based semantic mediation: Incremental provisioning of data services

Jesus Bisbal, Gerhard Engelbrecht, Alejandro Frangi
2010 2010 IEEE 23rd International Symposium on Computer-Based Medical Systems (CBMS)  
Modern organizations need to exploit the information stored in heterogeneous and interrelated data sources, but often have no means to integrate them in a principled fashion.  ...  In this paper we propose a novel application of semantic and mediation technologies, which leads to an incremental and on-demand definition of data mediation services.  ...  Introduction The growing amount of heterogeneous and distributed information in e-Science infrastructures exceeds the current capacity of enterprise data management and data integration platforms, which  ... 
doi:10.1109/cbms.2010.6042628 dblp:conf/cbms/BisbalEF10 fatcat:eormuwl4b5eppnbihesyxtjggu

Adapting Clinical Ontologies in Real-World Environments

Holger Stenzhorn, Stefan Schulz, Martin Boeker, Barry Smith
2008 Journal of universal computer science (Online)  
However, the use of the term 'ontology' has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models.  ...  The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years.  ...  The work of Stenzhorn, Schulz, and Boeker on this publication has been carried out jointly within the @neurIST and the ACGT integrated projects funded by the European Commission (IST-027703 and IST-026996  ... 
doi:10.3217/jucs-014-22-3767 pmid:20390048 pmcid:PMC2853050 fatcat:auptzitrcjh7zi4aghxnrjfcje
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