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2002 Biocomputing 2003  
Since the purpose of GO is to capture the information about the role of gene products, we propose that the mapping of GO's established ontological concepts to a molecular imaging terminology will provide  ...  The Gene Ontology (GO) Consortium seeks to provide a set of structured terminologies for the conceptual annotation of gene product function, process and location in databases.  ...  Acknowledgments We wish to acknowledge our colleague, Neil Sarkar, for his helpful comments and insightful discussions. Travel support provided by Columbia University Corporate Affiliates Program.  ... 
doi:10.1142/9789812776303_0057 fatcat:ehherdnwz5ajrlumjhlq64ojwq

Get GO! Retrieving GO Data Using AmiGO, QuickGO, API, Files, and Tools [chapter]

Monica Munoz-Torres, Seth Carbon
2016 Msphere  
The Gene Ontology Consortium (GOC) produces a wealth of resources widely used throughout the scientifi c community.  ...  from the command line, including the ability to restrict the data being retrieved to subsets with only certain attributes.  ...  In order to best represent the Ontology complexity of these classes, along with the approximately 27 million associations that connect them to each molecular entity (genes or gene products), members  ... 
doi:10.1007/978-1-4939-3743-1_11 pmid:27812941 fatcat:tzenvai4zndmfimw5en3guu4hq

GONOME: measuring correlations between GO terms and genomic positions

Stefan M Stanley, Timothy L Bailey, John S Mattick
2006 BMC Bioinformatics  
Current methods to find significantly under- and over-represented gene ontology (GO) terms in a set of genes consider the genes as equally probable "balls in a bag", as may be appropriate for transcripts  ...  By explicitly considering gene size, GONOME avoids a systematic bias toward GO terms linked to large genes.  ...  These regions are linked to the GO terms associated with the gene's GO terms (If a gene has no associated GO terms, its regions are associated with the "placeholder" term "NO_GO").  ... 
doi:10.1186/1471-2105-7-94 pmid:16504139 pmcid:PMC1413564 fatcat:utwafhszrreazixtktklgulwkq

Going Digital: A Survey on Digitalization and Large Scale Data Analytics in Healthcare [article]

Volker Tresp, J. Marc Overhage, Markus Bundschus, Shahrooz Rabizadeh, Peter A. Fasching, Shipeng Yu
2016 arXiv   pre-print
We discuss the recent political initiatives designed to shift care delivery processes from paper to electronic, with the goals of more effective treatments with better outcomes; cost pressure is a major  ...  Finally we discuss recent initiatives towards a personalized medicine, based on advances in molecular medicine, data management, and data analytics.  ...  ACKNOWLEDGMENT Volker Tresp acknowledges support by the German Federal Ministry for Economic Affairs and Energy, technology program "Smart Data" (grant 01MT14001).  ... 
arXiv:1606.08075v3 fatcat:aenoicczojfvjfzktbuhklqeiy

Integrating Bio-ontologies and Controlled Clinical Terminologies: From Base Pairs to Bedside Phenotypes [chapter]

Spiros C. Denaxas
2016 Msphere  
Analogous to the Gene Ontology, controlled clinical terminologies were created to facilitate the standardization and integration of medical concepts and knowledge and enable their subsequent use for translational  ...  This chapter will introduce several of the main controlled clinical terminologies used to record diagnoses, surgical procedures, laboratory results and medications.  ...  The biological process and molecular functions of the gene product are annotated using the Gene Ontology: double-strand break repair via homologous recombination(GO:0000724), DNA Repair (GO:0006281), cytokinesis  ... 
doi:10.1007/978-1-4939-3743-1_20 pmid:27812950 fatcat:j43wxtcsyjgn3o7t4c6fwzhbly

Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers

Andrew J. Buckler, M. Ouellette, J. Danagoulian, G. Wernsing, Tiffany Ting Liu, Erica Savig, Baris E. Suzek, Daniel L. Rubin, David Paik
2013 Journal of digital imaging  
We use an ontology to represent, integrate, and harmonize heterogeneous knowledge across the domain of imaging biomarkers.  ...  We have demonstrated that QIBO can be used to annotate imaging experiments with standardized terms in the ontology and to generate hypotheses for novel imaging biomarker-disease associations.  ...  We would also like to acknowledge Yi Liu of the Biomedical Informatics Program at Stanford University annotating linked terms in QIBO shared with Disease Ontology.  ... 
doi:10.1007/s10278-013-9599-2 pmid:23589184 pmcid:PMC3705004 fatcat:czuz7iswincb7bf2dump4whrca

InterMOD: integrated data and tools for the unification of model organism research

Julie Sullivan, Kalpana Karra, Sierra A. T. Moxon, Andrew Vallejos, Howie Motenko, J. D. Wong, Jelena Aleksic, Rama Balakrishnan, Gail Binkley, Todd Harris, Benjamin Hitz, Pushkala Jayaraman (+12 others)
2013 Scientific Reports  
This conservation of function combined with the rapidly increasing availability of new genome sequences and functional genomic data means that cross-species research promises to contribute to the molecular  ...  In recent years, genomic analysis has provided extensive evidence of widespread conservation of gene sequence and function amongst eukaryotes, allowing insights from model organisms to help decipher gene  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the funding bodies.  ... 
doi:10.1038/srep01802 pmid:23652793 pmcid:PMC3647165 fatcat:ylyyacmxdbeclgtk6u5jzqsizy

The Gene Ontology in 2010: extensions and refinements

2009 Nucleic Acids Research  
The Gene Ontology (GO) Consortium (http://www (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and  ...  Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains.  ...  ACKNOWLEDGEMENTS The GO Consortium thanks the community researchers who have participated in content-related meetings or provided valuable feedback on ontology content and annotations.  ... 
doi:10.1093/nar/gkp1018 pmid:19920128 pmcid:PMC2808930 fatcat:coftgdrxfbad7imo4qgcgxgp6q

Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features

Anandhi Iyappan, Erfan Younesi, Alberto Redolfi, Henri Vrooman, Shashank Khanna, Giovanni B. Frisoni, Martin Hofmann-Apitius
2017 Journal of Alzheimer's Disease  
Therefore, the Neuro-Imaging Feature Terminology (NIFT) was developed to organize the knowledge domain of measured brain features in association with neurodegenerative diseases by imaging technologies.  ...  Existing imaging ontologies capture general aspects of the imaging domain as a whole such as methodological concepts or calibrations of imaging instruments.  ...  ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimer's Asso-  ... 
doi:10.3233/jad-161148 pmid:28731430 pmcid:PMC5611802 fatcat:jb7h3ikqfrhddasmq6b2kymd4q

Visualising A Skeletal Dysplasia Knowledgebase

Ingrid B Jakobsen, Theodor G Wyeld, David P Hansen, Andreas Zankl
2007 International Conference on Medical Information Visualisation - BioMedical Visualisation (MediVis 2007)  
Once established, the terms used can be linked to an existing database of exemplar x-ray images and explored interactively.  ...  The aim of this project is to assist clinicians to make more accurate diagnoses of skeletal dysplasias and to foster translational research.  ...  Acknowledgements This project is jointly funded by the University of Queensland, the Royal Children's Hospital Brisbane, the Queensland Facility for Advanced Bioinformatics, the E-Health Research Centre  ... 
doi:10.1109/medivis.2007.21 fatcat:winzhet7p5h33k2hcbhuq5ukim

Computational Approaches to Phenotyping: High-Throughput Phenomics

Y. A. Lussier, Y. Liu
2007 Proceedings of the American Thoracic Society online  
Although altered phenotypes are among the most reliable manifestations of altered gene functions, research using systematic analysis of phenotype relationships to study human biology is still in its infancy  ...  of molecular-based strategies to more effectively prevent, diagnose, and treat these diseases.  ...  Acknowledgment : The authors thank Lee Sam for his advice on improving the manuscript.  ... 
doi:10.1513/pats.200607-142jg pmid:17202287 pmcid:PMC2647609 fatcat:gb4dc7uvkjg6tbg5epfudwlh3u

Data integration for spatio-temporal patterns of gene expression of zebrafish development: the GEMS database

Mounia Belmamoune, Fons J Verbeek
2008 Journal of Integrative Bioinformatics  
In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO) are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration  ...  At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development.  ...  Acknowledgments The authors would like to express gratitude to Dr. M.C. Welten, W. Spoor and A. Sels for their contributions by submitting experimental data to the system.  ... 
doi:10.2390/biecoll-jib-2008-92 pmid:20134060 fatcat:aeyoeaovafattonwa6hhestwb4

Biomedical ontologies: a functional perspective

D. L. Rubin, N. H. Shah, N. F. Noy
2007 Briefings in Bioinformatics  
The myriad of ontologies being created enables researchers not only to solve some of the problems in handling the data explosion but also introduces new challenges.  ...  As biomedical scientists begin to recognize the many different ways ontologies enable biomedical research, they will drive the emergence of new computer applications that will help them exploit the wealth  ...  Acknowledgements This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1093/bib/bbm059 pmid:18077472 fatcat:z3orlk75yzherjf37i3nehqlmm

From classification to epilepsy ontology and informatics

Guo-Qiang Zhang, Satya S. Sahoo, Samden D. Lhatoo
2012 Epilepsia  
The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular  ...  Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the NIH/NINDS Common Data Elements, the ICD systems and explicitly specifies all  ...  Acknowledgments The authors' epilepsy ontology development work is supported by NIH/NINDS (Grant P20-NS076965 -01-The PRISM Project)  ... 
doi:10.1111/j.1528-1167.2012.03556.x pmid:22765502 pmcid:PMC3398997 fatcat:ostorswpf5e7vafrg5wtb56z4a

Towards BioDBcore: a community-defined information specification for biological databases

P. Gaudet, A. Bairoch, D. Field, S.-A. Sansone, C. Taylor, T. K. Attwood, A. Bateman, J. A. Blake, C. J. Bult, J. M. Cherry, R. L. Chisholm, G. Cochrane (+26 others)
2011 Database: The Journal of Biological Databases and Curation  
experimental molecular reagents; functional genomics (gene expression); biochemical pathways; images of phenoty- pic mutants and gene expres- sion; links to other tools and other database resources  ...  Gene Ontology (Biological Process, Molecular Function, Cellular Component), GO annotations for proteins, func- tional RNAs and stable complexes.  ... 
doi:10.1093/database/baq027 pmid:21205783 pmcid:PMC3017395 fatcat:zfghil52nramtih22wxuqe2xqq
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