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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  ...  The focus of the present paper is the ACGT Master Ontology (MO).  ...  The ACGT project (FP6-2005-IST-026996) is partly funded by the EC and the authors are grateful for this support. The authors thank two anonymous reviewers for valuable comments.  ... 
doi:10.1016/j.jbi.2010.04.008 pmid:20438862 pmcid:PMC5755590 fatcat:r5o5r66xazh7dfxh4pfzchb46m

Applications of the ACGT Master Ontology on Cancer [chapter]

Mathias Brochhausen, Gabriele Weiler, Luis Martín, Cristian Cocos, Holger Stenzhorn, Norbert Graf, Martin Dörr, Manolis Tsiknakis, Barry Smith
2008 Lecture Notes in Computer Science  
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.  ...  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  ...  The ACGT Master Ontology Technical Details of the ACGT MO The intention of the ACGT MO [4] is to represent the domain of cancer research and management in a computationally tractable manner.  ... 
doi:10.1007/978-3-540-88875-8_132 fatcat:wuovugba2rdxdkfflrxohgxprm

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

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, project that has recently concluded successfully was  ...  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  ...  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

Ontologies for clinical and translational research: Introduction

Barry Smith, Richard H. Scheuermann
2011 Journal of Biomedical Informatics  
We are grateful for the support of the National Institutes of Health and of the National Human Genome Research Institute through the NIH Roadmap for Medical Research Grant 1 U 54 HG004028 and through conference  ...  Acknowledgments The majority of the contributions to this issue are based on papers presented at the first International Conference on Biomedical Ontology held in Buffalo, NY in July 2009.  ...  Original research ''The ACGT Master Ontology and Its Applications -Towards an Ontology-Driven Cancer Research and Management System'' [4] .  ... 
doi:10.1016/j.jbi.2011.01.002 pmid:21241822 pmcid:PMC4896064 fatcat:27z33vylvrcrbaqcadzvnbjjvu

Transformation of Health and Social Care Systems—An Interdisciplinary Approach Toward a Foundational Architecture

Bernd Blobel, Frank Oemig, Pekka Ruotsalainen, Diego M. Lopez
2022 Frontiers in Medicine  
To represent architectural elements consistently, an aligned system of ontologies is used.ResultsThe system-oriented, architecture-centric, and ontology-based generic reference model allows for re-engineering  ...  the existing and emerging knowledge representations, models, and standards, also considering the real-world business processes and the related development process of supporting IT systems for the sake  ...  ACKNOWLEDGMENTS The authors are indebted not only to Mathias Brochhausen, Little Rock, and Dipak Kalra, Brussels, but also colleagues from ISO/TC215 for their valuable advice and cooperation.  ... 
doi:10.3389/fmed.2022.802487 pmid:35402446 pmcid:PMC8992002 fatcat:wqolixcknfd2videfdhtn6cbii

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
This review, besides surveying the current state-of-the-art, will also provide a road map for future research and open questions.  ...  ]) BioGrid Application Development Toolkits (section 2.2.3 [78-83]) Grid-based Problem Solving Environments (section 2.2.4 [84-85]) Grid-based Workflow Management Systems (section 2.2.5 [86-87]) Grid-based  ...  Advancing Clinico-Genomic Trials on Cancer (ACGT) ACGT is a Europe wide integrated biomedical grid for post-genomic research on cancer (http://www. [115] .  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Machine Learning Applications for Therapeutic Tasks with Genomics Data [article]

Kexin Huang, Cao Xiao, Lucas M. Glass, Cathy W. Critchlow, Greg Gibson, Jimeng Sun
2021 arXiv   pre-print
This survey overviews recent research at the intersection of machine learning, genomics, and therapeutic development.  ...  In this survey, we review the literature on machine learning applications for genomics through the lens of therapeutic development.  ...  Models With advances in high-throughput technologies and data management systems, we now have vast and hetero- geneous datasets in the field of biomedicine.  ... 
arXiv:2105.01171v1 fatcat:d2nbrjt4tvak7momoxxjlmqk2m

A Concept of a Patient-centered Healthcare System Based on the Virtualized Networking and Information Infrastructure

Artur Binczewski, Krzysztof Kurowski, Cezary Mazurek, Maciej Stroinski
In the paper we introduce and discuss the concept of an architecture of a patient-centered eHealth ecosystem.  ...  The environment of this kind is natural for storing, management of and access to personal health records.  ...  Smart EHR The most important role in data integration is played by a Master Ontology developed for ACGT.  ... 

New statistical algorithms for the analysis of mass spectrometry time-of- flight mass data with applications in clinical diagnostics [article]

Tim Conrad, Universitätsbibliothek Der FU Berlin, Universitätsbibliothek Der FU Berlin
The ongoing progress in terms of more sensitive machines and improved data analysis algorithms led to a constant expansion of its fields of applications.  ...  To prove the platform's practical relevance it has been utilized in several clinical studies two of which are presented in this thesis. In these studies it could be shown that our platform is [...]  ...  Some Remarks on Blood During the previous years in proteomics driven cancer research much emphasis has been given to blood analysis.  ... 
doi:10.17169/refubium-14645 fatcat:rdto5m4wg5ffjgadfn2fho3tju

94th Annual Meeting, Virginia Academy of Science, 2016: Proceedings

Virginia Academy Of Science
Full proceedings of the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.  ...  We compared biomechanical properties of the dentaries for the 4 species, and used discriminant functions analysis to discriminate between the species in a jaw-function space.  ...  Although the skulls and dentaries of S. carolinensis and S. vulgaris differ morphologically, they are functionally similar.  ... 
doi:10.25778/8ave-wp88 fatcat:c6ilaqpp2nhnjehq74ggooc5sa

Functional Characterization of the Binding Properties of the Hematopoietic Transcription Factor PU.1

Julia Minderjahn
How this master transcription factor gains access to its binding sites in the context of chromatin is only partially understood yet.  ...  Here, I analyzed its motif cooperativeness and epigenetic regulation and used a transient mRNA-transfection model to study the de novo binding of PU.1 in the lymphatic leukemia cell line CTV-1 that neither  ...  Closed chromatin domains lastly, represent an opportunity for PU.1 binding likely driven by its association with the SWI/SNF remodeler complex as summarized in Figure 6 -1.  ... 
doi:10.5283/epub.38126 fatcat:f2xjsnstxrestibqnixfca4myy

Genomic imprinting in human stem cells and human peripheral blood leukocytes

Jennifer May Frost, Lesley Regan
Imprinting can be transient and tissue specific, indicative of its role in specific developmental regimes. Placental specific imprinting has been found to be non-conserved between humans and mice.  ...  biallelic expression of several imprinted genes, to an extent consistent between both types of stem cell.  ...  and the swimmers of Saxon Crown Masters squad.  ... 
doi:10.25560/4661 fatcat:xa2wmzxrknchjaqk6ovgs6wyge

Genome-Wide Characterization of the Roles of Transcription Factors GAF and HSF in the Transcriptional Heat Shock Response

Fabiana De Melo Duarte
In eukaryotes, RNA polymerase II (Pol II) is responsible for the transcription of all protein-coding genes, and regulation of its activity is fundamental for cellular homeostasis and the programmed development  ...  When studying mechanisms of transcription regulation, inducible systems are an invaluable resource: regulatory processes can be triggered instantaneously, enabling the tracking of ordered mechanistic events  ...  an effective model system to discover and study mechanisms of transcription and its regulation .  ... 
doi:10.7298/x4pz56xm fatcat:frtqxm2uajbzxa74ljp76my6ba