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BioPortal: A Web Repository for Biomedical Ontologies and Data Resources

Natalya Fridman Noy, Nigam Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clément Jonquet, Michael Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen
2008 International Semantic Web Conference  
The National Center for Biomedical Ontology is developing BioPortal, a Web-based system that serves as a repository for biomedical ontologies.  ...  BioPortal enables ontology users to learn what biomedical ontologies exist, what a particular ontology might be good for, and how individual ontologies relate to one another.  ...  This work was supported by the National Center for Biomedical Ontology, under roadmap-initiative grant U54 HG004028 from the National Institutes of Health.  ... 
dblp:conf/semweb/NoySDDGJMRYM08 fatcat:ypca3crzgbcufbisppzxljda3a

Roadmap for a Multilingual BioPortal

Clément Jonquet, Vincent Emonet, Mark A. Musen
2015 Extended Semantic Web Conference  
We propose a set of representations to support multilingualism in the portal and to enable a complete use of the functionalities and services for any kind of ontologies and data.  ...  We are currently deploying and implementing these representations in a local instance of BioPortal for French ontologies.  ...  We thanks the National Center for Biomedical Ontology (NCBO) for latest information about BioPortal.  ... 
dblp:conf/esws/JonquetEM15 fatcat:tdxmgym7prhl3doixausf55zqu

Reusing the NCBO BioPortal Technology for Agronomy to Build AgroPortal

Clément Jonquet, Anne Toulet, Elizabeth Arnaud, Sophie Aubin, Esther Dzalé Yeumo Kaboré, Vincent Emonet, John Graybeal, Mark A. Musen, Cyril Pommier, Pierre Larmande
2016 International Conference on Biomedical Ontology  
By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain.  ...  Many vocabularies and ontologies are produced to represent and annotate agronomic data.  ...  We also thank the National Center for Biomedical Ontologies for help and time spent with us in deploying the AgroPortal.  ... 
dblp:conf/icbo/JonquetTAAKEGMP16 fatcat:qa4gvttf7rffppch64bk5q67hu

Proposed SKOS Extensions for BioPortal Terminology Services [chapter]

Cui Tao, Natalya F. Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute
2012 Lecture Notes in Computer Science  
The National Center for Biomedical Ontology (NCBO) Bio-Portal provides common access for browsing and querying a large set of ontologies that are commonly used in biomedical communities.  ...  The Simple Knowledge Organization System (SKOS) is a recommendation of the World-Wide-Web Consortium (W3C) for a common data model for sharing and linking knowledge organization systems on the Semantic  ...  Acknowledgement This research is partially supported by the National Center for Biomedical Ontology (NCBO) under the NIH Grant #N01-HG04028 and the NSF under Grant #0937060 to the Computing Research Association  ... 
doi:10.1007/978-3-642-29923-0_23 fatcat:dt6q7urtu5cghphdnqaijft6l4

Using SPARQL to Query BioPortal Ontologies and Metadata [chapter]

Manuel Salvadores, Matthew Horridge, Paul R. Alexander, Ray W. Fergerson, Mark A. Musen, Natalya F. Noy
2012 Lecture Notes in Computer Science  
In our laboratory, we have developed BioPortal, a community-based ontology repository for biomedical ontologies [11] .  ...  BioPortal is a repository of biomedical ontologies-the largest such repository, with more than 300 ontologies to date.  ...  This work was supported by the National Center for Biomedical Ontology, under grant U54 HG004028 from the National Institutes of Health.  ... 
doi:10.1007/978-3-642-35173-0_12 fatcat:ooklwzs3xff3vjwujrrav35bpu

BioPortal: ontologies and integrated data resources at the click of a mouse

N. F. Noy, N. H. Shah, P. L. Whetzel, B. Dai, M. Dorf, N. Griffith, C. Jonquet, D. L. Rubin, M.-A. Storey, C. G. Chute, M. A. Musen
2009 Nucleic Acids Research  
BioPortal (http:// bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Proté  ...  Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety  ...  BioPortal not only provides investigators, clinicians and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also integrates data from various biomedical resources.  ... 
doi:10.1093/nar/gkp440 pmid:19483092 pmcid:PMC2703982 fatcat:lbiqy5zoszaadkullyg46a76zi

Partitioning of BioPortal Ontologies: An Empirical Study

Alsayed Algergawy, Birgitta König-Ries
2019 Workshop on Semantic Web Applications and Tools for Life Sciences  
BioPortal is a leading repository of biomedical ontologies developed in different formats such as OWL and OBO.  ...  This has sparked a number of studies analyzing different aspects of BioPortal ontologies, such as their quality and reuse.  ...  Since its deployment, the National Center for Biomedical Ontologies (NCBO) BioPortal has evolved to become the prevalent repository of biomedical ontologies and terminologies [17, 32] .  ... 
dblp:conf/swat4ls/AlgergawyK19 fatcat:4kqkszzhufhphaer6nknoyyquq

BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse

Patricia Whetzel, Clement Jonquet, Barry Smith, Cherie Youn, Margaret-Anne Storey, Adrien Coulet, Christopher Chute, Chris Callendar, Mark Musen, Nigam Shah, Natalya Noy, Benjamin Dai (+3 others)
2009 Nature Precedings  
Acknowledgements BioPortal is developed by the National Center for Biomedical Ontology (NCBO), one of seven National Centers for Biomedical Computing under the NIH Roadmap.  ...  For more information on NCBO and working with the Center, visit http://bioontology.org/ or email support@bioontology.org. BioPortal Web Services •!  ...  The National Center for Biomedical Ontology, one of the seven National Centers for Biomedical Computing created under the NIH Roadmap, is developing BioPortal, a Webbased system that serves as a repository  ... 
doi:10.1038/npre.2009.3868.1 fatcat:j3mywcp5orb6jl67z25dnuc24y

How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal Usage Logs [article]

Simon Walk, Lisette Espín-Noboa, Denis Helic, Markus Strohmaier, Mark Musen
2016 arXiv   pre-print
Towards that goal, the National Center for Biomedical Ontology (NCBO) has developed BioPortal---an online repository designed to support users in exploring and finding more than 500 existing biomedical  ...  Thus, a crucial prerequisite for ontology adoption and reuse is effective support for exploring and finding existing ontologies.  ...  biomedical ontology and taxonomy repositories on the Web.  ... 
arXiv:1610.09160v2 fatcat:leadapaqqfb37d6re6qzujoxzy

BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse

Patricia Whetzel, Patricia Whetzel, Nigam Shah, Natalya Noy, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Cherie Youn, Adrien Coulet, Chris Callendar, Daniel Rubin (+4 others)
2009 Nature Precedings  
Acknowledgements BioPortal is developed by the National Center for Biomedical Ontology (NCBO), one of seven National Centers for Biomedical Computing under the NIH Roadmap.  ...  For more information on NCBO and working with the Center, visit http://bioontology.org/ or email support@bioontology.org. BioPortal Web Services •!  ...  The National Center for Biomedical Ontology, one of the seven National Centers for Biomedical Computing created under the NIH Roadmap, is developing BioPortal, a Webbased system that serves as a repository  ... 
doi:10.1038/npre.2009.3868 fatcat:znrxxhuw7nek5jmacsi5pp2siu

NCBO-Galaxy: bridging the BioPortal web services and the Galaxy platform

José Antonio Miñarro-Giménez, Mikel Egaña Aranguren, Jesualdo Tomás Fernández-Breis, Erick Antezana
2012 International Conference on Biomedical Ontology  
This work has been possible thanks to the funding of the Spanish Ministry of Science and Innovation through grant TIN2010-21388-C02-02.  ...  INTRODUCTION BioPortal (Noy et al. (2009) ) is a web-based application for searching, sharing, visualizing, and analyzing bio-ontologies.  ...  bio-ontology terms, • Recommend a bio-ontology depending on annotations of a text, • Search for terms in bio-ontologies depending on the text provided, • Search for resources matched up with terms in  ... 
dblp:conf/icbo/Minarro-GimenezAFA12 fatcat:3ue7xra6pzbnbfmolppn2cvcem

BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF

Manuel Salvadores, Paul R Alexander, Mark A Musen, Natalya F Noy
2013 Semantic Web Journal  
BioPortal is a repository of biomedical ontologies-the largest such repository, with more than 300 ontologies to date.  ...  the class names and provenance data.  ...  Acknowledgments This work was supported by the National Center for Biomedical Ontology, under grant U54 HG004028 from the National Institutes of Health.  ... 
pmid:25214827 pmcid:PMC4159173 fatcat:i6j4zckcs5dwdd7h45avi46kcm

OntoMaton: a Bioportal powered ontology widget for Google Spreadsheets

E. Maguire, A. Gonzalez-Beltran, P. L. Whetzel, S.-A. Sansone, P. Rocca-Serra
2012 Bioinformatics  
Results: OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web  ...  Motivation: Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices,  ...  Conflict of Interest: none declared. (2) create a standard Google Spreadsheet and install OntoMaton within that; or (3) as part of the ISA suite, export an Excel template from ISAconfigurator and upload  ... 
doi:10.1093/bioinformatics/bts718 pmid:23267176 pmcid:PMC3570217 fatcat:cc7ygvclnngjzdrymrotxdsqwi

Analysis of Advanced Complexity Metrics of Biomedical Ontologies in the Bioportal Repository

Yannick Kazela Kazadi, Jean Vincent Fonou-Dombeu
2017 International Journal of Bioscience Biochemistry and Bioinformatics  
A set of 100 biomedical ontologies from the BioPortal repository was collected.  ...  This study analyses and discusses the advanced complexity features of the biomedical ontologies stored in the BioPortal repository.  ...  The BioPortal repository includes 491 biomedical ontologies and provides tools and services for browsing the ontologies.  ... 
doi:10.17706/ijbbb.2017.7.1.20-32 fatcat:urriith6qrh7rgo32x5kh2nqxi

A Survey of Multilingual OWL Ontologies in BioPortal

Frances Gillis-Webber, C. Maria Keet
2022 Workshop on Semantic Web Applications and Tools for Life Sciences  
As OWL ontologies are widely used in the biomedical domain, the survey was limited to those ontologies in NCBO BioPortal, a biomedical repository.  ...  The internationalisation goal for OWL sought to offer support for multilingual ontologies. User-displayable labels were suggested as a way to realise this, by means of rdfs:label.  ...  In the context of a global pandemic, there are requirements for biomedical and healthcare tools, as well as data integration at the national level.  ... 
dblp:conf/swat4ls/Gillis-WebberK22 fatcat:mo2nooqbhbewlndumxdr4vbp3u
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