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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  ...  the development of a semantically rich infrastructure facilitating seamless and secure access and analysis, of multi-level clinical and genomic data enriched with high-performing knowledge discovery operations  ...  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

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  
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.  ...  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  ...  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

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  
Moreover, Information Retrieval techniques must consider heterogeneities present in databases, initially belonging to different domains-e.g. clinical and genetic data.  ...  One of the goals, among others, of the ACGT European is to provide seamless and homogeneous access to integrated databases.  ...  The classical role of ontologies in database integration is acting as a general description of the domain the different data belong to -e.g. clinical, genetic and image data, in the case of ACGT.  ... 
pmid:18487699 fatcat:osmnats6kragrm5qvjd7hjr7wu

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

M Tsiknakis
2015 ecancermedicalscience  
Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the  ...  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  
Post-genomic CTs use multi-level clinical and genomic data and advanced computational analysis and visualization tools to test hypotheses in trying to identify the molecular reasons for a disease and the  ...  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

Challenges for Future Platforms, Services and Networked Applications [chapter]

Krzysztof Kurowski
2012 Lecture Notes in Computer Science  
New development tools, easy-to-program powerful mobile devices, interactive panels, etc. enable users to prototype new IT systems with much better interfaces, to quickly setup collaborative environments  ...  in the future.  ...  To achieve syntactic integration, data access services first need to provide uniform and secure data access interfaces.  ... 
doi:10.1007/978-3-642-31095-9_2 fatcat:xjcz3sp7bveonbasjw4iecqjg4

Translational Biomedical Informatics in the Cloud: Present and Future

Jiajia Chen, Fuliang Qian, Wenying Yan, Bairong Shen
2013 BioMed Research International  
Next generation sequencing and other high-throughput experimental techniques of recent decades have driven the exponential growth in publicly available molecular and clinical data.  ...  The scale and dimensionality of data, however, pose obvious challenges in data mining, storage, and integration.  ...  For example, the ACGT project [41] launched by the European Union developed a set of methodological approaches as well as tools and services for semantic integration of distributed multilevel databases  ... 
doi:10.1155/2013/658925 pmid:23586054 pmcid:PMC3613081 fatcat:dmpe2jfwxvaoxoagpkhwu4gnnu

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.  ...  This infrastructure aims at improving Post-genomic clinical trials by providing seamless access to integrated clinical, genetic, and image databases.  ...  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

The DebugIT core ontology: semantic integration of antibiotics resistance patterns

Daniel Schober, Martin Boeker, Jessica Bullenkamp, Csaba Huszka, Kristof Depraetere, Douglas Teodoro, Nadia Nadah, Remy Choquet, Christel Daniel, Stefan Schulz
2010 Studies in Health Technology and Informatics  
Massive amounts of clinical data are being collected and stored in proprietary and unconnected systems in heterogeneous format.  ...  The semantic glue for this endeavor is DCO, an application ontology that enables data miners to query distributed clinical information systems in a semantically rich and content driven manner.  ...  We acknowledge Hans Cools who has significantly contributed to the DebugIT ontology development and Djamila Raufie who helped curating DCO.  ... 
pmid:20841846 fatcat:57ekm26fcbhifbgxd5fxcz44bu

Knowledge Representation and Ontologies [chapter]

Kin Wah Fung, Olivier Bodenreider
2012 Health Informatics Series  
For example, the first distinction made among the semantic types in the UMLS Semantic Network [9] is between Entity and Event, roughly equivalent to the distinction between continuants and occurrents in  ...  We then show how ontologies are integrated in and made accessible through knowledge repositories, and illustrate their role in clinical research.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1007/978-1-84882-448-5_14 fatcat:r7e2fbulcrcddpxh7jo6lu77wa

Solutions for medical databases optimal exploitation

I Branescu, V L Purcarea, R Dobrescu
2014 Journal of Medicine and Life  
The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, "multimodel" federated system for extending OLAP querying  ...  to external object databases.  ...  The EPR is supposed to be the only (or at least the primary) tool that the clinical user is using in the daily work, so there is a great need to have access to all data, also lab results, etc., through  ... 
pmid:24653769 pmcid:PMC3956088 fatcat:u4hwqx6lbbcvvdbc7iy6zt5dnu

D33.2 Earth Science metadata, semantics and ontology harmonization report

Yannis Marketakis, Yannis Tzitzikas
2013 Zenodo  
The purpose of this deliverable is to summarize and analyze the results of the surveys conducted in WP15, identify the needs and gaps between communities based also on the results of the user requirements  ...  Particular focus is given in the part of the survey concerning metadata, semantics and ontologies.  ...  ACGT Semantic Mediator The European project ACGT included in its tasks the development of a semantic mediation layer for accessing data from clinical trials [17] .  ... 
doi:10.5281/zenodo.3275163 fatcat:auuz2aiqabh47jdipeewa7wr2e

Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine

Victor Maojo, Fernando Martin-Sanchez, Casimir Kulikowski, Alfonso Rodriguez-Paton, Martin Fritts
2010 Pediatric Research  
Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine  ...  Nanoinformatics can accelerate the introduction of nano-related research and applications into clinical practice, leading to an area that could be called "translational nanoinformatics."  ...  To effectively and efficiently manage all these data, new informatics tools must be implemented to archive, access, and annotate the relevant data, to couple that data to new computational methods, and  ... 
doi:10.1203/pdr.0b013e3181d6245e pmid:20118825 fatcat:wcrx72ih5nd3bfabxpgujd6ade

Web Services Automation [chapter]

L. Koumakis, V. Moustakis, G. Potamias
Handbook of Research on Social Dimensions of Semantic Technologies and Web Services  
Put it simply, web services come in small pieces of software, which can be put together to address complex tasks over heterogeneous and distribute data sources.  ...  Web service semantics are linked with natural language processing capabilities to empower users to write descriptions in their own language and in the sequel to have these descriptions mapped automatically  ...  Finally the association rules mining service generate associations between clinical and genomics data and stores them to the file system.  ... 
doi:10.4018/978-1-60566-650-1.ch012 fatcat:mcl3spgtovcxrgesr7brdmdlwe

Web Services Automation [chapter]

L. Koumakis, V. Moustakis, G. Potamias
Handbook of Research on Social Dimensions of Semantic Technologies and Web Services  
Put it simply, web services come in small pieces of software, which can be put together to address complex tasks over heterogeneous and distribute data sources.  ...  Web service semantics are linked with natural language processing capabilities to empower users to write descriptions in their own language and in the sequel to have these descriptions mapped automatically  ...  Finally the association rules mining service generate associations between clinical and genomics data and stores them to the file system.  ... 
doi:10.4018/9781605666501.ch012 fatcat:vv5kmufcavee3l4iwj3kf66fce