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ontoCAT: an R package for ontology traversal and search

N. Kurbatova, T. Adamusiak, P. Kurnosov, M. A. Swertz, M. Kapushesky
2011 Bioinformatics  
The ontoCAT package supports a number of traversal and search functions on a single ontology, as well as searching for ontology terms across multiple ontologies and in major ontology repositories.  ...  We present ontoCAT-an R package to access ontologies in widely used standard formats, stored locally in the filesystem or available online.  ...  INTRODUCTION The R package ontoCAT was created to support basic operations on ontologies: traversal and search, uniform access to ontologies in OWL (Lacy, 2005) and OBO (Barry et al., 2007) formats  ... 
doi:10.1093/bioinformatics/btr375 pmid:21697126 fatcat:r4bd4tzeffautad7eiofo4wplq

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen Parkinson, Morris A Swertz
2011 BMC Bioinformatics  
Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal  ...  Conclusions: OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly  ...  Acknowledgements The authors would like to thank Eamonn Maguire for designing the OntoCAT logo, James Malone  ... 
doi:10.1186/1471-2105-12-218 pmid:21619703 pmcid:PMC3129328 fatcat:gql53crntrbv7idta5wy24acsi

Building a Custom Sentiment Analysis Tool based on an Ontology for Twitter Posts

K. Vithiya Ruba, D. Venkatesan
2015 Indian Journal of Science and Technology  
The thoughts of the people vary according to the domain and also the opinion may contain both positive and negative words which are called as opinion words and are given in the form of dictionary called  ...  The sentiment analysis done without feature extraction fails to give the deep result about the users opinion but in our proposed approach , features of the domain are extracted by building ontology which  ...  This package was created to support basic operations in an ontology which also includes the traversing and searching the terms.  ... 
doi:10.17485/ijst/2015/v8i13/61464 fatcat:2oo2fqx3erdfzfd62h4pxb6rxa

Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments

M. Kapushesky, T. Adamusiak, T. Burdett, A. Culhane, A. Farne, A. Filippov, E. Holloway, A. Klebanov, N. Kryvych, N. Kurbatova, P. Kurnosov, J. Malone (+10 others)
2011 Nucleic Acids Research  
treatments and other biological/ experimental conditions.  ...  The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive and the European Nucleotide Archive.  ...  and Nikolay Kolesnikov for help with ArrayExpress Archive interface.  ... 
doi:10.1093/nar/gkr913 pmid:22064864 pmcid:PMC3245177 fatcat:qi4tj2jmszh3zdkwmbwotggyo4

KneeTex: an ontology–driven system for information extraction from MRI reports

Irena Spasić, Bo Zhao, Christopher B. Jones, Kate Button
2015 Journal of Biomedical Semantics  
Methods: As an ontology-driven information extraction system, KneeTex makes active use of an ontology to strongly guide and constrain text analysis.  ...  Results: We adopted an existing ontology, TRAK (Taxonomy for RehAbilitation of Knee conditions), for use within KneeTex.  ...  Acknowledgements We would like to thank Thomas Edwards and David Rogers for their assistance in testing the software.  ... 
doi:10.1186/s13326-015-0033-1 pmid:26347806 pmcid:PMC4561435 fatcat:ucu5vkafgncg5ppslbpsvwduom

Methods for Determining the Genetic Causes of Rare Diseases

Daniel Greene, Apollo-University Of Cambridge Repository, Apollo-University Of Cambridge Repository, Ernest Turro, Sylvia Richardson, Willem Ouwehand
2018
I developed a suite of software packages dubbed 'ontologyX' in order to simplify analysis and visualisation of such ontologically encoded data, and enable them to be incorporated into complex analysis  ...  It does so by evaluating support for a model under which the probability that a person carries rare alleles in a locus depends on the similarity between the person's ontologically encoded phenotype and  ...  Software for working with ontological data The ontoCAT R package enables simple querying and traversal of ontologies, but many of its key functions are slow and dependency on Java hinders its portability  ... 
doi:10.17863/cam.17443 fatcat:edfiw335lrecxefa3inveewosq

Dynamic Composition of Service Specific Overlay Networks

Yousif Al Ridhawi, Université D'Ottawa / University Of Ottawa, Université D'Ottawa / University Of Ottawa
2013
The H-SON permits fast and efficient searches for component services that meet client functional and quality expectations.  ...  The H-SON is a dynamic hybrid overlay dedicated to service composition for multimedia delivery in dynamic networks.  ...  OntoCAT exists in a number of flavors including stand-alone database and browser, REST services, and OntoCAT R package.  ... 
doi:10.20381/ruor-2920 fatcat:r66ugsskhvai3icnd3qohwlc5i

Development and evaluation of software for applied clinical genomics

Casper Shyr
2016
In the genomics field, the complexity of the data, combined with the gap in perspectives and skills between computational biologists and clinicians, present an unsolved grand challenge for bioinformaticians  ...  The Human Genome Project published its first draft of the human genome in 2000 at an enormous cost of 3 billion dollars, and was an international collaborative effort that spanned more than a decade.  ...  each tree was built based on a hierarchical structure using the hie-ran-forest package in R 3.2.0 to assure the compositions of scores were accounted for.  ... 
doi:10.14288/1.0300436 fatcat:tfyub3u3pzbq3ejxzprgguygr4