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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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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]
2008
Lecture Notes in Computer Science
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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
2006
Studies in Health Technology and Informatics
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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
2011
Procedia Computer Science
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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 ...
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
2011
Journal of Biomedical Informatics
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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
2022
Frontiers in Medicine
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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
2008
Current Bioinformatics
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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. eu-acgt.org) [115] . ...
doi:10.2174/157489308783329850
fatcat:thpj6eywwvg5tfdqvbw5nch3ty
Machine Learning Applications for Therapeutic Tasks with Genomics Data
[article]
2021
arXiv
pre-print
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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
unpublished
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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. ...
fatcat:3em6i2sawvdk3n6g7ilrf4bluy
New statistical algorithms for the analysis of mass spectrometry time-of- flight mass data with applications in clinical diagnostics
[article]
2008
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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
2016
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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
2019
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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
2010
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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
2017
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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