Results 1 - 10 of 114

BioPortal: A Web Repository for Biomedical Ontologies and Data Resources [Demonstration]

by Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, Michael J. Montegut, Daniel L. Rubin, Cherie Youn, Mark A. Musen
"... Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, naturallanguage processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a Web-based system that serves as a repository for biomed ..."
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Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, naturallanguage processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a Web-based system that serves as a repository

Using SPARQL to Query BioPortal

by Manuel Salvadores, Matthew Horridge, Paul R. Alex, Ray W. Fergerson, Mark A. Musen, Natalya F. Noy
"... edu Abstract. BioPortal is a repository of biomedical ontologies—the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other languages, as well as a large number of medical terminologies that the US National Library of Me ..."
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edu Abstract. BioPortal is a repository of biomedical ontologies—the largest such repository, with more than 300 ontologies to date. This set includes ontologies that were developed in OWL, OBO and other languages, as well as a large number of medical terminologies that the US National Library

Reusing the NCBO BioPortal technology for agronomy to build AgroPortal

by Clément Jonquet , Anne Toulet , Elizabeth Arnaud , Sophie Aubin , Esther Dzalé Yeumo , Vincent Emonet , John Graybeal , Mark A Musen , Cyril Pommier , Pierre Larmande
"... Abstract-Many vocabularies and ontologies are produced to represent and annotate agronomic data. By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain. We plan to turn that prototype into a real service t ..."
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Abstract-Many vocabularies and ontologies are produced to represent and annotate agronomic data. By reusing the NCBO BioPortal technology, we have already designed and implemented an advanced prototype ontology repository for the agronomy domain. We plan to turn that prototype into a real service

The national center for biomedical ontology

by Mark A. Musen, Natasha F. Noy, Nigam H. Shah, Christopher G. Chute, Margaret-anne Storey, Barry Smith, The Ncbo Team - Journal of American Medical Informatics Association , 2012
"... The National Center for Biomedical Ontology (NCBO) is now in its seventh year. The goals of this National Center for Biomedical Computing are to create and maintain a repository of biomedical ontologies and terminologies; to build tools and Web services to enable the use of ontologies and terminolog ..."
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. The centerpiece of the NCBO is a Web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world’s biomedical ontologies and terminologies, and supports a wide range of Web services that enable investigators to use the ontologies to annotate

Proposed SKOS Extensions for BioPortal Terminology Services

by Cui Tao, Natalya F. Noy, Harold R. Solbrig, Nigam H. Shah, Mark A. Musen, Christopher G. Chute
"... Abstract. 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. One of our missions is to align lexical features (i.e., textual definitions) that are commonly used in ..."
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on the Semantic Web. The BioPortal is in the process of adopting SKOS in the backend representation for its content. During this process, we discovered that there exists a set of commonly-used lexical features shared by the biomedical ontologies that SKOS does not yet represent. In this paper, we discuss our

Harnessing the Power of the Community in a Library of Biomedical Ontologies

by Natalya F. Noy, Michael Dorf, Nicholas Griffith, Csongor Nyulas, Mark A. Musen
"... Abstract. Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a web-based library of biomedical ontologies. ..."
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Abstract. Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing, and decision support. The National Center for Biomedical Ontology is developing BioPortal, a web-based library of biomedical ontologies

N.F.: The quad economy of a semantic web ontology repository

by Manuel Salvadores, Paul R Alex, Mark A. Musen, Natalya F. Noy - In: The 7th International Workshop on Scalable Semantic Web Knowledge Base Systems (SSWS2011
"... Abstract. Quad stores have a number of features that make them very attractive for Semantic Web applications. Quad stores use Named Graphs to give contextual information to RDF graphs. Developers can use these contexts to incorporate meta-data such as provenance and versioning. The OWL language spec ..."
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imports and versioning. We have performed the experiments in the context of storing ontologies from the BioPortal ontology repository. This repository has 304 ontologies, with multiple versions for many of them. We extract metrics on the levels of imports, and the storage and performance requirements

Updates to the AberOWL ontology repository

by Miguelángel Rodríguez-García , Luke T Slater , Imene Boudellioua , Paul N Schofield , Georgios V Gkoutos , Robert Hoehndorf
"... ABSTRACT A large number of ontologies have been developed in the biological and biomedical domains, which are mostly expressed in the Web Ontology Language (OWL). These ontologies form a logical foundation for our knowledge in these domains, and they are in widespread use to annotate biomedical and ..."
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ABSTRACT A large number of ontologies have been developed in the biological and biomedical domains, which are mostly expressed in the Web Ontology Language (OWL). These ontologies form a logical foundation for our knowledge in these domains, and they are in widespread use to annotate biomedical

Musen M: What Four Million Mappings Can Tell You About Two Hundred Ontologies

by Amir Ghazvinian, Natalya F. Noy, Clement Jonquet, Nigam Shah, Mark A. Musen - In 8th International Semantic Web Conference (ISWC 2009). Volume 5823/2009
"... Abstract. The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal— an open community-based repository of biomedical ontologies. We ana ..."
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Abstract. The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal— an open community-based repository of biomedical ontologies. We

The open ontology repository initiative: Requirements and research challenges

by Kenneth Baclawski, Todd Schneider - In Proceedings of Workshop on Collaborative Construction,Management and Linking of Structured Knowledge, ISWC , 2009
"... Very large data sets are increasingly common both in science and industry. However, incorporating multiple data types from multiple sources to solve major problems is a significant interoperability challenge. Furthermore, documents and other artifacts created in the past can be as important as recen ..."
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and diversity. An initial OOR server based on BioPortal has been deployed, and further development will emphasize technological solutions that build on existing ontology repositories as well as proven architectures and standards. Nevertheless, many research challenges remain to achieve the requirements
Results 1 - 10 of 114