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Using Semantic Web Technologies to Build a Community-Driven Knowledge Curation Platform for the Skeletal Dysplasia Domain [chapter]

Tudor Groza, Andreas Zankl, Yuan-Fang Li, Jane Hunter
2011 Lecture Notes in Computer Science  
In this paper we report on our on-going efforts in building SKELETOME -a community-driven knowledge curation platform for the skeletal dysplasia domain.  ...  Because SKELE-TOME is built on Drupal 7, we discuss the limitations of some of its embedded Semantic Web components and describe a set of new modules, developed to handle these limitations (which will  ...  The authors would like to thank Hasti Ziamatin and Razan Paul for their implementation support. Special thanks go to Tania Tudorache for her comprehensive and useful feed-back.  ... 
doi:10.1007/978-3-642-25093-4_6 fatcat:2ei5szrkjbdjllx76mdb4yygy4

DC Proposal: Decision Support Methods in Community-Driven Knowledge Curation Platforms [chapter]

Razan Paul
2011 Lecture Notes in Computer Science  
We aim to develop decision support methods in the skeletal dysplasia domain by applying uncertainty reasoning over Semantic Web data.  ...  Semantic Web technologies can, however, provide the appropriate means for encoding the knowledge and hence enabling complex forms of reasoning.  ...  The work presented in this paper is supported by the Australian Research Council (ARC) under the Linkage grant SKELETOME -LP100100156.  ... 
doi:10.1007/978-3-642-25093-4_26 fatcat:odrqyckyevb2ljysbw2awv76nu

State of the art and open challenges in community-driven knowledge curation

Tudor Groza, Tania Tudorache, Michel Dumontier
2013 Journal of Biomedical Informatics  
SysBorg uses the Liferay infrastructure (http://www.liferay.com/) as a backbone and Semantic Web technologies to represent and share knowledge.  ...  A skeletal dysplasia ontology [20] has, firstly, been developed and then used to generate the collaborative knowledge curation platform -as opposed to the other examples discussed above that usually  ... 
doi:10.1016/j.jbi.2012.11.007 pmid:23219718 fatcat:odppdhmlkrgqfk67zhphysoa5m

Getting Ready for the Human Phenome Project: The 2012 Forum of the Human Variome Project

William S. Oetting, Peter N. Robinson, Marc S. Greenblatt, Richard G. Cotton, Tim Beck, John C. Carey, Sandra C. Doelken, Marta Girdea, Tudor Groza, Carol M. Hamilton, Ada Hamosh, Berit Kerner (+11 others)
2013 Human Mutation  
Acknowledgments The 2012 Meeting of the Human Variome Project was chaired by Peter Robinson from Charité Universitätsmedizin Berlin.  ...  The sessions were chaired by Peter Robinson, Marc Greenblatt, and Richard Cotton.  ...  To begin this session, Andreas Zankl of the University of Queensland's Centre for Clinical Research presented "The 'Skeletome' platform, a knowledge-base for skeletal dysplasias."  ... 
doi:10.1002/humu.22293 pmid:23401191 pmcid:PMC4130157 fatcat:olvqoha4mrcstgbq23cpufuhka

The Human Phenotype Ontology

PN Robinson, S Mundlos
2010 Clinical Genetics  
algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and  ...  ACKNOWLEDGEMENTS The authors are grateful for the work of Miranda Jarnot and Tammy Powell at the National Library of Medicine for leading the work to import the HPO into the UMLS.  ... 
doi:10.1111/j.1399-0004.2010.01436.x pmid:20412080 fatcat:ltjtumlbpnfqdkp6vjahbzu35u

The Human Phenotype Ontology in 2017

Sebastian Köhler, Nicole A. Vasilevsky, Mark Engelstad, Erin Foster, Julie McMurry, Ségolène Aymé, Gareth Baynam, Susan M. Bello, Cornelius F. Boerkoel, Kym M. Boycott, Michael Brudno, Orion J. Buske (+47 others)
2016 Nucleic Acids Research  
algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition  ...  The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and  ...  ACKNOWLEDGEMENTS The authors are grateful for the work of Miranda Jarnot and Tammy Powell at the National Library of Medicine for leading the work to import the HPO into the UMLS.  ... 
doi:10.1093/nar/gkw1039 pmid:27899602 pmcid:PMC5210535 fatcat:55iggw3tzvei7ispy3gu6rwqum

Health—exploring complexity: an interdisciplinary systems approach HEC2016

Eva Grill, Martin Müller, Ulrich Mansmann
2016 European Journal of Epidemiology  
Methods We take a knowledge management approach, using semantic web technologies, to model the social cognition theory constructs, Canadian diabetes guidelines and BM protocols used locally, in terms of  ...  Semantic web technologies have been used to develop a SCT ontology and SWRL rules to infer personalized self-management plans based on a given patient profile.  ...  In this context, a focused crawler uses techniques from the field of machine learning to estimate the relevance of a webpage for the domain of interest [5,6].  ... 
doi:10.1007/s10654-016-0183-1 pmid:27522353 fatcat:dcl3nbpygvh5fg7keri74h55ie

Human genome meeting 2016

A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson, R. Polimanti, J. Gelernter, X. Lin (+828 others)
2016 Human Genomics  
Further, targeted quantitative analysis of a subset of discriminating metabolites using tandem mass spectrometry provided a reliable laboratory method to detect children with ASD.  ...  The new genetic/genomic technologies of the past decade have not been as productive as originally anticipated in unveiling the mysteries of autism.  ...  Acknowledgements Funding for research and development is acknowledged for Project: "Research Oriented Data Management and Analysis" at the Ucar Lab by The Jackson Laboratory, USA.  ... 
doi:10.1186/s40246-016-0063-5 pmid:27294413 pmcid:PMC4896275 fatcat:ycjj53ixrbauvnusibuz76y7bm

HGM 2010 Programme / Abstract

2010 The HUGO Journal  
The identification of an EYS mutation in a dog affected with retinal progressive atrophy would provide a useful model for establishing future therapies for retinitis pigmentosa.  ...  ACKNOWLEDGEMENTS HGM 2010 has received financial support from the following organisations. We would like to extend our utmost appreciation to them for all of their support.  ...  the technology to the scientific community.  ... 
doi:10.1007/s11568-010-9143-0 fatcat:oykxd6u7snfi5o7m6tst7wi6yq

Abstracts from the Human Genome Meeting 2018

2018 Human Genomics  
indicate our deep gratitude to the family for their participation in this study.  ...  Acknowledgments We are grateful to all members of the Laboratory for Autoimmune Diseases for their expert technical assistance Acknowledgements The study was supported by the Russian Science Foundation  ...  Finally, the system is constantly modified and improved by experimental validation to build a robust annotation platform for vlincRNAs.  ... 
doi:10.1186/s40246-018-0138-6 fatcat:nl6xhsuchzgbxik4pjwjvbbkie

Contents list

2018 Soft Matter  
To identify genetic loci accounting for these differences, we took advantage of a set of Interspecific Recombinant Congenic Strains (IRCS) resulting from crosses between C57BL/6 and SEG/Pas.  ...  Each of the 55 IRCS carries up to seven SEG/Pas chromosomal segments with an average size of 13.4 Mb, totalizing 1.26% of the genome. The complete series covers 38% of the SEG/Pas genome.  ...  Therefore, we developed a web-based database application -MausDB -for the GMC that serves as a central data platform accessible by all GMC users.  ... 
doi:10.1039/c8sm90107d fatcat:tko5byj5izccvgfzmdsssx4mgm

Presented Abstracts from the Thirty Fifth Annual Education Conference of the National Society of Genetic Counselors (Seattle, WA, September 2016)

2016 Journal of Genetic Counseling  
Abstract Awards Best Full Member Abstract Adapting evidenced based strategies for effective communication in cancer genetic counseling  ...  While the video may not be the initial method of communication, many endorsed using the video as a supplemental tool and noted multiple advantages to the web-based video platform.  ...  Initial cost of the program is dependent on the devices and technology platforms used, as well as the potential need for licensing genetic counselors in multiple states.  ... 
doi:10.1007/s10897-016-0027-x pmid:27730413 fatcat:go5fglrpsjdz7cwyt6jttvm4yq

American Association of Neuropathologists, Inc. Abstracts of the 93rd Annual Meeting June 8–11, 2017 Garden Grove, CA

2017 Journal of Neuropathology and Experimental Neurology  
Using the web-based platform Oncoscape as a tool, which currently utilizes The Cancer Genome Atlas (TCGA) datasets, we apply multidimensional scaling-derived molecular clusters to the 2D visualization  ...  functional domain of RAVER1 to form a hybrid TDP-RAVER1 protein.  ...  To our knowledge, lymphatic malformations are not known to occur within the CNS, and we believe this to be the first case report.  ... 
doi:10.1093/jnen/nlx029 fatcat:u42r2fehzfdrned7itfhkchpza

Development and evaluation of software for applied clinical genomics

Casper Shyr
2016
As with any new large-scale data, a need has emerged for mechanisms to translate knowledge from computationally oriented informatics specialists to the clinically oriented users who interact with it.  ...  Through a combination of usability methodologies across multiple distinct clinical user groups, the thesis highlights reoccurring domain-specific challenges and introduces ways to overcome the roadblo  ...  Web access A web access version of the final model is in progress. A downloadable version is in development and is planned for a future release.  ... 
doi:10.14288/1.0300436 fatcat:tfyub3u3pzbq3ejxzprgguygr4

Predicting the Evolutionary and Medical Significance of Human Genetic Variations with Machine Learning [article]

Arnab Saha Mandal, University Of Calgary, A. P. Jason De Koning
2019
The advent of inexpensive and high-throughput genome sequencing technologies has facilitated the acquisition of patient exome and genome sequences at a vast scale.  ...  Over the last two decades, many approaches have been proposed for VIP, which utilize data from patterns of evolutionary conservation, population genomics, protein structures and other sources to inform  ...  0002652 failure to thrive No Direct Match Abnormality of the vertebral column No Direct Match Short stature HP:0004322 skeletal dysplasia HP:0002652 .  ... 
doi:10.11575/prism/36479 fatcat:r5yq4sytnncotelxlfwyvqfnjq