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The ACGT project in retrospect: Lessons learned and future outlook
2011
Procedia Computer Science
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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
2011
Journal of Biomedical Informatics
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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
2008
Studies in Health Technology and Informatics
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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
2015
ecancermedicalscience
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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
2007
ecancermedicalscience
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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]
2012
Lecture Notes in Computer Science
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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
2013
BioMed Research International
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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
english
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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
2010
Studies in Health Technology and Informatics
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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]
2012
Health Informatics Series
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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
2014
Journal of Medicine and Life
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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
2013
Zenodo
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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
2010
Pediatric Research
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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]
Handbook of Research on Social Dimensions of Semantic Technologies and Web Services
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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]
Handbook of Research on Social Dimensions of Semantic Technologies and Web Services
Preserved Fulltext
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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