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An evaluation of ontology exchange languages for bioinformatics

R McEntire, P Karp, N Abernethy, D Benton, G Helt, M DeJongh, R Kent, A Kosky, S Lewis, D Hodnett, E Neumann, F Olken (+4 others)
2000 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community.  ...  The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics.  ...  This paper reports on an effort among the authors to evaluate a number of alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community  ... 
pmid:10977085 fatcat:7otzi2snqba3resy4bzyzitz3q

BioXSD: the common data-exchange format for everyday bioinformatics web services

M. Kalas, P. Puntervoll, A. Joseph, E. Bartaseviciute, A. Topfer, P. Venkataraman, S. Pettifer, J. C. Bryne, J. Ison, C. Blanchet, K. Rapacki, I. Jonassen
2010 Bioinformatics  
However, efficient use of the resources is hampered by the lack of widely used, standard data-exchange formats for the basic, everyday bioinformatics data types.  ...  Results: BioXSD has been developed as a candidate for standard, canonical exchange format for basic bioinformatics data.  ...  ACKNOWLEDGEMENTS We thank Kjell Petersen, Peter Fischer Hallin and Torbjørn Lium for knowledgeable advice and extensive technical support. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq391 pmid:20823319 pmcid:PMC2935419 fatcat:z2dvwykkhnhvvjimg5zbw245rq

Ontology Language XOL Used for Cross-Application Communication [chapter]

Jinta Weng, Jing Qiu, Ying Gao
2020 Ontology in Information Science [Working Title]  
As for effective exchange of the different ontology messages in different applications, US bioinformatic community and researcher develop a XML-based ontology language.  ...  The 2000s may be the flourishing time of the topic of ontology. Specialists and scholars concentrated to define ontology effectively and formulated uniform ontology protocol.  ...  11 Ontology Language XOL Used for Cross-Application Communication DOI: http://dx.doi.org/10.5772/intechopen.91385  ... 
doi:10.5772/intechopen.91385 fatcat:3j6ceadvuzaufomo27a4knzbjy

Evaluation of ontology development tools for bioinformatics

P. Lambrix, M. Habbouche, M. Perez
2003 Bioinformatics  
We continue, however, with an overview of related work. Abstract Introduction Related Work Gene Ontology Ontology . . . Evaluation Set-Up Results and . . .  ...  They can be used for making the content in information sources explicit and serve as an index to a repository of information.  ...  We also acknowledge the financial support of the Center for Industrial Information Technology.  ... 
doi:10.1093/bioinformatics/btg194 pmid:12912838 fatcat:xk5pmi4kxvgvxo5dum6wyqro6y

Ontology Engineering Techniques for Biological Data

Asma Fardoos, Jamshaid Iqbal Janjua, Amjad Farooq
2014 Journal of Computers  
The dire need to deal with such type of issues has demanded the construction of a large number of ontologies for these domains.  ...  In this paper our main focus is integration of biological data in single ontology which will be developed using an efficient engineering algorithm.  ...  Ontologies In Bioinformatics Bioinformatics is an emerging field.  ... 
doi:10.4304/jcp.9.9.2151-2158 fatcat:dckwvugrhnguxdgoqnohbbukqe

Ontology-based knowledge representation for bioinformatics

R. Stevens
2000 Briefings in Bioinformatics  
An ontology is the concrete form of a conceptualisation of a community's knowledge of a domain. This paper aims to introduce the reader to the use of ontologies within bioinformatics.  ...  A description of the type of knowledge held in an ontology will be given.  ...  Acknowledgements: Robert Stevens is supported by a grant from the BBSRC/EPSRC under the bioinformatics initiative (34/BIO12090); Sean Bechhofer is supported by a grant from the EPSRC under the DIM initiative  ... 
doi:10.1093/bib/1.4.398 pmid:11465057 fatcat:gfi2yhajmjfkvpl7zwfbumiqsq

XML-based approaches for the integration of heterogeneous bio-molecular data

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2009 BMC Bioinformatics  
The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but  ...  Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes.  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 12, 2009: Bioinformatics Methods for Biomedical Complex System Applications.  ... 
doi:10.1186/1471-2105-10-s12-s7 pmid:19828083 pmcid:PMC2762072 fatcat:n4tvxjx3ifadjbo4x7jbpx5zfa

XML-Based Approaches for the Integration of Heterogeneous Bio-Molecular Data [chapter]

Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga-Llavori, Paolo Perlasca, Giorgio Valentini, David Manset
2011 Recent Advances in Biochemistry  
Abstract Background: The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics  ...  Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes.  ...  This article has been published as part of BMC Bioinformatics Volume 10 Supplement 12, 2009: Bioinformatics Methods for Biomedical Complex System Applications.  ... 
doi:10.1201/b13131-13 fatcat:ytu7u4pcbzgbflpblij6x3wwky

Introduction to semantic e-Science in biomedicine

Huajun Chen, Yimin Wang, Zhaohui Wu
2007 BMC Bioinformatics  
This special issue is intended to give an introduction of the state-of-the-art of Semantic Web technologies and describe how such technologies would be used to build the e-Science infrastructure for biomedical  ...  Six papers have been selected and included, featuring different approaches and experiences in a variety of biomedical domains.  ...  Acknowledgements We thank all of the program committee members of SeS2006 for their dedication and efforts to peer review the manuscripts submitted by the attendees.  ... 
doi:10.1186/1471-2105-8-s3-s1 fatcat:ajgvbuqndjb55hk7uw3bqq6jda

The development of non-coding RNA ontology

Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin (+11 others)
2016 International Journal of Data Mining and Bioinformatics  
On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field.  ...  Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade.  ...  Acknowledgments Funding for J. Huang was provided in part by the National Cancer Institute (NCI) at the National Institutes of Health (NIH), under the Award Number U01CA180982. Funding for G.M.  ... 
doi:10.1504/ijdmb.2016.077072 pmid:27990175 pmcid:PMC5156483 fatcat:i62jsm2cdze23pdoevo3gtxnjq

Evaluation of ontology merging tools in bioinformatics

P Lambrix, A Edberg
2003 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
Tools have been developed for ontology merging, but they have not been evaluated for their use in bioinformatics.  ...  In this paper we evaluate two of the most well-known ontology merging tools with a bioinformatics perspective. As test ontologies we have used Gene Ontology and Signal-Ontology.  ...  languages for bioinformatics McE00 .  ... 
pmid:12603060 fatcat:4trttj6mynfsvhnexjz22ypytq

Knowledge-Based Bioinformatics - From analysis to interpretation. * Edited by Gil Alterovitz and Marco Ramoni

S. Kim
2010 Briefings in Bioinformatics  
This chapter examines KR languages for building bio-ontologies such as the Resource Description Framework (RDF), the Web Ontology Language (OWL) and the Open Biomedical Ontologies (OBO) format, and summarizes  ...  features of each KR language.  ... 
doi:10.1093/bib/bbq070 fatcat:af44dwyq2ndqrem5rmqwf6eh2y

Advancing Post-Genome Data and System Integration through Machine Learning

Francisco Azuaje
2002 Comparative and Functional Genomics  
This paper discusses a number of issues on intelligent systems for the integration of bioinformatic resources.  ...  Research on biological data integration has traditionally focused on the development of systems for the maintenance and interconnection of databases.  ...  Three relevant integration problems Mining XML data and metadata XML has become an important choice for data representation and exchange in the biotechnology sector.  ... 
doi:10.1002/cfg.129 pmid:18628880 pmcid:PMC2447240 fatcat:ticxny3dxfhaxigb5hu7f3bwwy

EVALUATION OF ONTOLOGY MERGING TOOLS IN BIOINFORMATICS

P. LAMBRIX, A. EDBERG
2002 Biocomputing 2003  
One of the issues in ontology research is the aligning and merging of ontologies. Tools have been developed for ontology merging, but they have not been evaluated for their use in bioinformatics.  ...  In this paper we e v aluate two of the most well-known ontology merging tools with a bioinformatics perspective. As test ontologies we have used Gene Ontology and Signal-Ontology.  ...  languages for bioinformatics McE00 .  ... 
doi:10.1142/9789812776303_0055 fatcat:ix6a6tgirfhapl2yphuk7ixpf4

Linking genotype to phenotype: the International Rice Information System (IRIS)

R. M. Bruskiewich, A. B. Cosico, W. Eusebio, A. M. Portugal, L. M. Ramos, Ma. T. Reyes, M. A. B. Sallan, V. J. M. Ulat, X. Wang, K. L. McNally, R. Sackville Hamilton, C. G. McLaren
2003 Bioinformatics  
the management and integration of global information on genetic resources and germplasm improvement for any crop.  ...  The International Rice Information System (IRIS, http://www.iris.irri.org) is the rice implementation of the International Crop Information System (ICIS, http://www.icis.cgiar.org), a database system for  ...  ACKNOWLEDGEMENTS ICIS/IRIS development is supported from core funding of the International Rice Research Institute. X. Wang is funded by a Rockefeller Foundation dissertation fellowship.  ... 
doi:10.1093/bioinformatics/btg1006 pmid:12855438 fatcat:ulf3lkthc5dkpevqmvps5npxpu
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