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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  
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.  ...  The project, now completed after four years of work, involved the development of both a set of methodological approaches as well as tools and services and its testing in the context of real-world clinico-genomic  ...  The vision of the Advancing Clinico-Genomic Trials on Cancer (ACGT) project (www.eu-acgt.org) was to tackle the above issues by developing a semantically rich grid infrastructure platform in support of  ... 
pmid:21893844 fatcat:m5qggzte4vhvjbdxo44ie3axwu

Post-genomic clinical trials - the perspective of ACGT

Norbert Graf
2009 ecancermedicalscience  
Acknowledgement The authors would like to thank all members of the ACGT consortium who are actively contributing to addressing the R&D challenges faced.  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support.  ...  These clinico-genomic trials are scenario based and driven by clinicians. Today, two main clinico-genomic trials and an in silico experiment are interconnected within the ACGT project.  ... 
doi:10.3332/ecms.2008.66 pmid:22275963 pmcid:PMC3234044 fatcat:vdjnfxvaenbebit4hmgnusltde

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  
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.  ...  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  ...  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

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  
The objective of the ACGT (Advancing Clinico-Genomic Trials on Cancer: Open Grid Services for improving Medical Knowledge Discovery, www.eu-acgt.org) project that has recently concluded successfully was  ...  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

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  
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  ...  scientific workflows in the context of multi-centric, post-genomic clinical trials.  ...  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

Section 7: Bioinformatics: Bioinformatics Linkage of Heterogeneous Clinical and Genomic Information in Support of Personalized Medicine

V. Maojo, J. A. Mitchell, L. J. Frey
2007 IMIA Yearbook of Medical Informatics  
These in turn will enable the faster advancement of personalized medicine.  ...  In order to achieve this, heterogeneous clinical and genomic data source must be integrated in scientifically meaningful and productive systems.  ...  for discussions on the cancer data standards repository.  ... 
doi:10.1055/s-0038-1638533 fatcat:m47yswixvzb2vjoznsfdtdbgxq

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

2008 Proceedings of the First International Conference on Health Informatics   unpublished
In this work, we describe the set of tools comprising the Data Access Infrastructure within Advancing Clinico-genomic Trials on Cancer (ACGT), a R&D Project funded in part by the European.  ...  Two experiments have been carried out in order to test the suitability of the selected approach, integrating clinical and DICOM image databases.  ...  ACKNOWLEDGEMENTS The authors would like to thank all members of the ACGT consortium who are actively contributing to addressing the R&D challenges faced.  ... 
doi:10.5220/0001045503010306 fatcat:bjrwg42bqbe4xkep5o662dhrze

Metadata extraction using text mining

Shivani Seth, Stefan Rüping, Stefan Wrobel
2009 Studies in Health Technology and Informatics  
In particular, we investigate the semi-automatic conversion of functions of the statistical environment R into Grid services as implemented by the GridR tool by the generation of appropriate metadata.  ...  In this paper, we investigate how relevant metadata can be extracted from a semi-structured textual documentation of the algorithm that is underlying the service, by the use of text mining methods.  ...  This is the aim of the Advancing Clinico-Genomics Trials on Cancer (ACGT) project.  ... 
pmid:19593048 fatcat:pr73olvlwbbz3k3m7lr5ywfbxq

p-Medicine: From data sharing and integration via VPH models to personalized medicine

S Rossi, Ml Christ-Neumann, S Rüping, Fm Buffa, D Wegener, G McVie, Pv Coveney, N Graf, M Delorenzi
2011 ecancermedicalscience  
oncologist to researchers, industrial partners, and tools developers; a famous patient was present: Janelle Hail, a 30-year breast cancer survivor, founder and CEO of the National Breast Cancer Foundation  ...  3rd symposium (Paris, 6-8 July 2011) to discussion on gateways to increase the efficacy of cancer diagnostics and therapeutics (http://www.winconsortium.org/symposium.html).Speakers ranged from clinical  ...  ) heterogeneous data management and experience gained during the ACGT project (http://www.eu-acgt.org/) in the field of quality assurance.  ... 
doi:10.3332/ecancer.2011.218 pmid:22276060 pmcid:PMC3223941 fatcat:y4dgvllw4nbzrbls6nwye7q7ce

Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment

Barry Smith, Mathias Brochhausen
2008 Studies in Health Technology and Informatics  
An example of such harmonization within the ACGT project is described, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.  ...  The authors argue that one key foundation for both ontology evaluation and harmonization is the adoption of a realist paradigm in ontology development.  ...  One such initiative financed by the European Union within its 6th Framework Programme is the Advancing Clinico-Genomic Trials on Cancer (ACGT) project.  ... 
pmid:18376049 fatcat:vjsdk2yfzzdodf4p4zeaemtg5e

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics [article]

Mahnoor Naseer Gondal, Safee Ullah Chaudhary
2021 bioRxiv   pre-print
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases  ...  Cancer systems biology models built on top of this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis  ...  Evolution of multiscale modeling software for abstracting and simulating the spatiotemporal biomolecular complexity. ) such as Advancing Clinico-Genomic Trials on Cancer (ACGT) (312), Clinically Oriented  ... 
doi:10.1101/2021.05.17.444410 fatcat:vbfvmtb5irdapglgkmh5na73je

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  
To test the method, experiments were carried out with four biomedical databases -containing rheumatoid arthritis, gene expression patterns, biological processes and breast cancer patients-proving the performance  ...  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  ...  They were developed and used by the authors in the context of two projects funded by the European Commission, the INFOBIOMED Network of Excellence and the ACGT project -Advanced Clinico-Genomic Trials  ... 
doi:10.1109/cbms.2008.71 dblp:conf/cbms/AnguitaPCM08 fatcat:74m6eocqgremzl2ohfhuozwjpi

Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid

Chun-Hsi Huang, Akihiko Konagaya, Vincenzo Lanza, Peter M. A. Sloot
2008 IEEE Transactions on Information Technology in Biomedicine  
limited to, the following: 1) computational genomics; computational proteomics; 2) systems biology, biological information integration; 3) storage of biomedical information; 4) retrieval of distributed  ...  The power of the grids lies not only in the aggregate computing ability, data storage, and network bandwidth that can readily be brought to bear on a particular problem, but also on its ease of use.  ...  Article [27] reports on original results of the Advancing Clinico Genomic Trials (ACGT) integrated project focusing on the design and development of a European Biomedical Grid infrastructure in support  ... 
doi:10.1109/titb.2008.918585 pmid:18416025 fatcat:tmlicpixnbeljbaut7mhays2zm

biomarkers (clinical)

2009 Annals of Oncology  
The underlying motivation of the EU-funded Advancing Clinico-Genomic Clinical Trials on Cancer project (ACGT; www.eu-acgt.org) is to provide researchers and clinicians with optimal computational, IT, legal  ...  and ethical, as well as security means and resources to facilitate clinico-genomic research, with a particular focus on breast cancer and nephroblastoma.  ... 
doi:10.1093/annonc/mdp103 fatcat:megr7qvczrfmzbpqqqwfd7ndby

Article Commentary: Dealing with Diversity in Computational Cancer Modeling

David Johnson, Steve McKeever, Georgios Stamatakos, Dimitra Dionysiou, Norbert Graf, Vangelis Sakkalis, Konstantinos Marias, Zhihui Wang, Thomas S. Deisboeck
2013 Cancer Informatics  
Human initiative projects on cancer.  ...  We briefly review current interoperability efforts drawing upon our experiences with the development of in silico models for predictive oncology within a number of European Commission Virtual Physiological  ...  Acknowledgements The authors would like to thank the participating institutions of the project consortium and its members.  ... 
doi:10.4137/cin.s11583 pmid:23700360 pmcid:PMC3653811 fatcat:gr2li3oeynarxpgc422bd5p6iu
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