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Accelerating Knowledge Discovery through Community Data Sharing and Integration

Y.L. Yip
2009 IMIA Yearbook of Medical Informatics  
Enabling technologies, either Semantic Web or other solutions, are expected to play an increasingly important role in generating new knowledge in the foreseeable future.  ...  to play an important role in heterogeneous data integration.  ...  Acknowledgement I would like to acknowledge the support of Martina Hutter and the reviewers in the selection process of the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1638650 fatcat:dmird6o2g5buldu7pnhbfirvoi

PhenoHM: human–mouse comparative phenome–genome server

Divya Sardana, Suresh Vasa, Nishanth Vepachedu, Jing Chen, Ranga Chandra Gudivada, Bruce J. Aronow, Anil G. Jegga
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We acknowledge the help of Ron Bryson, Technical Writer, Division of Biomedical Informatics, CCHMC, OH, USA, in editing the article.  ...  We used an online version of MetaMap, available as part of the Semantic Knowledge Representation project (, which aims to provide a framework for exploiting the UMLS knowledge resources  ...  the concept of reciprocally mapped comparative genomics and phenomics.  ... 
doi:10.1093/nar/gkq472 pmid:20507906 pmcid:PMC2896149 fatcat:trb2tkybvvedrasjh6ob6j7a4e

A visual and curatorial approach to clinical variant prioritization and disease gene discovery in genome-wide diagnostics

Regis A. James, Ian M. Campbell, Edward S. Chen, Philip M. Boone, Mitchell A. Rao, Matthew N. Bainbridge, James R. Lupski, Yaping Yang, Christine M. Eng, Jennifer E. Posey, Chad A. Shaw
2016 Genome Medicine  
Conclusions: Our integrative paradigm can improve efficiency and, potentially, the quality of genomic medicine by more effectively utilizing available phenotype information, catalog data, and genomic knowledge  ...  The tool also implements an adaptive approach for disease gene discovery based on patient phenotypes.  ...  The BCM Whole Genome Laboratory is part of the BMGL and performs fee-for-service clinical diagnostic testing. CAS, JRL, CE, YY, and MB are partially supported by this entity.  ... 
doi:10.1186/s13073-016-0261-8 pmid:26838676 pmcid:PMC4736244 fatcat:eycovdvsrzgrxithmnx6byyi5u


Emilia Zawadzka-Gosk, Krzysztof Wolk
2018 Computer Science  
variant as a causal one or the inability to identify a causal gene.  ...  NGS provides a list of all mutations in a genome, so identifying the one that causes a disease is not trivial.  ...  Knowledge about genes and DNA is broadly used for genetic disease diagnostics.  ... 
doi:10.7494/csci.2018.19.2.2319 fatcat:ithcup2rufbdlmbi6mfvym5oy4

Toward knowledge support for analysis and interpretation of complex traits

Nigel Collier, Anika Oellrich, Tudor Groza
2013 Genome Biology  
The systematic description of complex traits, from the organism to the cellular level, is important for hypothesis generation about underlying disease mechanisms.  ...  Acknowledgements The authors would like to thank Damian Smedley for providing the general idea of  ...  Phenomizer [41] , for example, uses a semantic scoring mechanism that calculates the similarity of a phenotype with the signs and symptoms of a disease.  ... 
doi:10.1186/gb-2013-14-9-214 pmid:24079802 pmcid:PMC4053827 fatcat:7xbr4o274vetlhziueou2dl42e

Mining human phenome to investigate modularity of complex disorders

Ranga C Gudivada, Yun Fu, Anil G Jegga, Xiaoyan A Qu, Eric K Neumann, Bruce J Aronow
2008 Summit on translational bioinformatics  
associations among disease entities such as shared protein domains and pathway and ontology functions of associated causal genes.  ...  To test the hypothesis that phenotypic similarities and differences among diseases and disease subvariants may represent differential activation of correlated feature "disease phenotype modules", we systematically  ...  We are currently working towards in combining these phenome networks obtained from clustering to integrated genome networks using SW standards and applying centrality analysis based ranking algorithms  ... 
pmid:21347123 pmcid:PMC3041520 fatcat:p4nzsyus2vhx7paogblwjfod3y

As Ontologies Reach Maturity, Artificial Intelligence Starts Being Fully Efficient: Findings from the Section on Knowledge Representation and Management for the Yearbook 2018

Jean Charlet, Ferdinand Dhombres
2018 IMIA Yearbook of Medical Informatics  
Additionally, among the 15 preselected papers, two aspects of KRM are in the spotlight: the design of knowledge bases and new challenges in using ontologies.  ...  Objectives: To select, present, and summarize the best papers published in 2017 in the field of Knowledge Representation and Management (KRM).  ...  Acknowledgements We would like to thank Martina Hutter and Adrien Ugon for their support and the reviewers for their participation in the selection process of best papers for the IMIA Yearbook.  ... 
doi:10.1055/s-0038-1667078 pmid:30157517 fatcat:otwpqzgeang5to4l7xfpiaf6ra

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

Roland Barriot, Jeroen Breckpot, Bernard Thienpont, Sylvain Brohée, Steven Van Vooren, Bert Coessens, Leon-Charles Tranchevent, Peter Van Loo, Marc Gewillig, Koenraad Devriendt, Yves Moreau
2010 Genome Medicine  
Description: We built on the recent advances in Wiki-based technologies to develop a collaborative knowledge base and gene prioritization portal aimed at mapping genes and genomic regions, and untangling  ...  Going beyond knowledge gathering, integrative data analysis strategies have been proposed recently for the prioritization of genes potentially involved in a given biological process, phenotype, or disease  ...  Acknowledgements We gratefully acknowledge Professor JE Lock (Cardiovascular program, Department of Cardiology, Children's Hospital Boston, MA, USA) for providing cartoons of heart defects.  ... 
doi:10.1186/gm137 pmid:20193066 pmcid:PMC2873794 fatcat:uwdxak5uafbmnoclveb4edbkwu

Data integration and genomic medicine

Brenton Louie, Peter Mork, Fernando Martin-Sanchez, Alon Halevy, Peter Tarczy-Hornoch
2007 Journal of Biomedical Informatics  
This presents daunting informatic challenges such as representation of data that is suitable for computational inference (knowledge representation), and linking heterogeneous data sets (data integration  ...  Genomic medicine aims to revolutionize health care by applying our growing understanding of the molecular basis of disease.  ...  The integration of these genetic, clinical, environmental and lifestyle data will facilitate the unravelling of polygenetic disease causality and complex gene-environment interactions existent in disease  ... 
doi:10.1016/j.jbi.2006.02.007 pmid:16574494 fatcat:mndnwkzzpzcu5ayqyg2ohyc75u

Semantic mashup of biomedical data

Kei-Hoi Cheung, Vipul Kashyap, Joanne S. Luciano, Huajun Chen, Yimin Wang, Susie Stephens
2008 Journal of Biomedical Informatics  
Ted Shortliffe (Editor-in-Chief of JBI) for his editorial review and guidance.  ...  Acknowledgments We thank the many reviewers who contributed their time and expertise to evaluation and revision of papers in this issue. We also thank Dr.  ...  [9] describes how to use RDF to represent a semantic network of genomic and phenomic data. On the basis of this network representation, casual relationships are inferred.  ... 
doi:10.1016/j.jbi.2008.08.003 pmid:18703163 pmcid:PMC3742004 fatcat:utdd2zyj6zfklh5etnhe4gbwwq

Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships

Xiaoyan A Qu, Ranga C Gudivada, Anil G Jegga, Eric K Neumann, Bruce J Aronow
2009 BMC Bioinformatics  
The uniform application of Semantic Web methodology to problems in data integration, knowledge representation, and analysis provides an efficient and potentially powerful means to allow mining of drug  ...  Further improvements in semantic representation of mechanistic relationships will provide a fertile basis for accelerated drug repositioning, reasoning, and discovery across the spectrum of human disease  ...  By using a specific scenario involved in drug development, we have provided anecdotal evidence for the benefit of such semantic knowledge integration and representation in identifying and ranking drug  ... 
doi:10.1186/1471-2105-10-s5-s4 pmid:19426461 pmcid:PMC2679404 fatcat:y5a36ldx4zdrtlgzmwz7l2vj7u

Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy

Aravind Venkatesan, Gildas Tagny Ngompe, Nordine El Hassouni, Imene Chentli, Valentin Guignon, Clement Jonquet, Manuel Ruiz, Pierre Larmande, Le Zhang
2018 PLoS ONE  
We present some integration results of the project, which initially focused on genomics, proteomics and phenomics.  ...  The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies.  ...  In particular, OpenPHACTS serves as a good example of what can be achieved by using Semantic Web knowledge bases.  ... 
doi:10.1371/journal.pone.0198270 pmid:30500839 pmcid:PMC6269127 fatcat:cje75vraa5c7bbyq6ei23cfogm

Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy [article]

Aravind Venkatesan, Gildas Tagny Ngompe, Nordine El Hassouni, Imene Chentli, Valentin Guignon, Clement Jonquet, Manuel Ruiz, Pierre Larmande
2018 bioRxiv   pre-print
We present some integration results of the project, which initially focused on genomics, proteomics and phenomics.  ...  The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies.  ...  Acknowledgments Authors thank the technical staffs of the South Green Bioinformatics platform for their support. Authors thank the providers of databases listed in  ... 
doi:10.1101/325423 fatcat:57xxtwu3uvc55jflrjmycsw2ja

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

Keywan Hassani-Pak, Christopher Rawlings
2017 Journal of Integrative Bioinformatics  
AbstractGenetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden.  ...  Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential  ...  It produces tables of ranked candidate genes or evidence summaries, and allows users to explore the knowledge networks using interactive web-based tools.  ... 
doi:10.1515/jib-2016-0002 pmid:28609292 pmcid:PMC6042805 fatcat:5n6hsndt5fecpkolgctalg4oca

Phenotype-driven strategies for exome prioritization of human Mendelian disease genes

Damian Smedley, Peter N. Robinson
2015 Genome Medicine  
Whole exome sequencing has altered the way in which rare diseases are diagnosed and disease genes identified.  ...  Disease-associated gene discovery and genomic diagnostics It seems fair to say that next-generation sequencing (NGS)-based diagnostics are revolutionizing the way that rare diseases are diagnosed and researched  ...  This work was supported by grants from the Bundesministerium für Bildung und Forschung (BMBF 0313911) and from the European Commission's Seventh Framework Program (SYBIL, 602300) and by core infrastructure  ... 
doi:10.1186/s13073-015-0199-2 pmid:26229552 pmcid:PMC4520011 fatcat:ukxzq4yj5zfzplqb6awrxapqtm
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