BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse (2009)
Patricia L. Whetzel, Nigam H. Shah, Natalya F. Noy, Benjamin Dai, Michael Dorf, Nicholas Griffith, ...
BioPortal ("http://bioportal.bioontology.org":http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies...
Web-Protégé: A Lightweight OWL Ontology Editor for the Web (2009)
Tania Tudorache, Jennifer Vendetti, Natalya F. Noy
Abstract. In this paper, we present Web-Protégé—a web-based lightweight ontology editor. Web-Protégé is open source, uses the Google Web Toolkit (GWT) for the user interface, and Protégé for...
BioPortal: A Web Repository for Biomedical Ontologies and Data Resources [Demonstration] (2009)
Natalya F. Noy, Nigam H. Shah, Benjamin Dai, Michael Dorf, Nicholas Griffith, Clement Jonquet, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, naturallanguage processing, and decision support. The National Center for...
Collaborative Protégé: Enabling Community-based Authoring of Ontologies [Demonstration] (2009)
Tania Tudorache, Natalya F. Noy, Mark A. Musen
Ontologies are becoming so large in their coverage that no single person or a small group of people can develop them effectively and ontology development becomes a community-based enterprise. We...
Sean M. Falconer, Natalya F. Noy, Margaret-anne Storey
understanding the needs of cognitive support
Ontology Mapping- A User Survey (2009)
Sean M. Falconer, Natalya F. Noy, Margaret-anne Storey
Abstract. Ontology mapping is the key to data interoperability in the semantic web vision. Computing mappings is the first step to applications such as query rewriting, instance sharing, web-service...
BioPortal: ontologies and integrated data resources at the click of a mouse (2009)
Noy, Natalya F., Shah, Nigam H., Whetzel, Patricia L., Dai, Benjamin, Dorf, Michael, Griffith, Nicholas, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal...
Harith Alani, Nigel Shadbolt, Natalya F. Noy, Mark A. Musen, Nigam Shah
As more ontologies become publicly available, finding the “right ” ontologies becomes much harder. In this paper, we address the problem of ontology search: finding a collection of ontologies...
The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction (2008)
Steffen Staab, Natalya F. Noy, Abhita Chugh Yahoo
Web 2.0’s great success is fueled mainly by an infrastructure that lets users easily create, share, tag, and connect content and knowledge. In general, the knowledge created in today’s...
Making Biomedical Ontologies and Ontology Libraries Work (2008)
Natalya F. Noy, Daniel Rubin, Mark A. Musen
Today, it is impossible to contemplate successful biomedical research in the absence of canonical data structures. From primary databases (such as those found in GenBank 1 and MEDLINE) to meta-data...
The Protégé OWL Experience (2008)
Holger Knublauch, Matthew Horridge, Mark Musen, Alan Rector, Robert Stevens, Nick Drummond, ...
Abstract. Protégé is one of the most widely used development platforms for ontology-based systems. We report on our experiences with the development of OWL support for Protégé, and on the...
Ontology Mapping- A User Survey (2008)
Sean M. Falconer, Natalya F. Noy, Margaret-anne Storey
Abstract. Ontology mapping is the key to data interoperability in the semantic web vision. Computing mappings is the first step to applications such as query rewriting, instance sharing, web-service...
Protégé: A Tool for Managing and Using Terminology in Radiology Applications (2008)
Daniel L. Rubin, Natalya F. Noy, Mark A. Musen
The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The...
The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction (2008)
Natalya F. Noy, Abhita Chugh, Harith Alani
The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured...
Using PROMPT Ontology-Comparison Tools in the EON Ontology Alignment Contest (2008)
Abstract. Objective evaluation and comparison of knowledge-based tools has so far been mostly an elusive goal for researchers and developers. Objective experiments are difficult to perform and...
EZPAL: Environment for Composing Constraint Axioms by Instantiating Templates (2008)
Abstract: Many ontology-development tools allow users to supplement frame-based representations with arbitrary logical sentences. However, few users actually take advantage of this opportunity. For...
Biomedical ontologies: a functional perspective (2008)
Rubin, Daniel L., Shah, Nigam H., Noy, Natalya F.
The information explosion in biology makes it difficult for researchers to stay abreast of current biomedical knowledge and to make sense of the massive amounts of online information....
Natalya F. Noy, Michel Klein, De Boelelaan A
Abstract. As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between...
The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction (2007)
Noy, Natalya F, Chugh, Abhita, Alani, Harith
The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured...
The CKC Challenge: Exploring Tools for Collaborative Knowledge Construction (2007)
Noy, Natalya F, Chugh, Abhita, Alani, Harith
The great success of Web 2.0 is mainly fuelled by an infrastructure that allows web users to create, share, tag, and connect content and knowledge easily. The tools for developing structured...
Rubin, Daniel L., Lewis, Suzanna E., Mungall, Chris J., Misra, Sima, Westerfield, Monte, Ashburner, Michael, ...
The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to...
Musen M.: A Framework for Ontology Evolution in Collaborative Environments (2006)
Natalya F. Noy, Abhita Chugh, William Liu, Mark A. Musen
Abstract. With the wider use of ontologies in the Semantic Web and as part of production systems, multiple scenarios for ontology maintenance and evolution are emerging. For example, successive...
Topic-Specific Trust and Open Rating Systems: An Approach for Ontology Evaluation (2006)
Holger Lewen, Kaustubh Supekar, Natalya F. Noy, Mark A. Musen
To achieve better interoperability among intelligent applications, and to relieve knowledge engineers from the burden of developing ontologies from scratch, it is critical to reuse ontologies....
Ontology mapping discovery with uncertainty (2005)
Prasenjit Mitra, Natalya F. Noy, Anuj R. Jaiswal
Abstract. Resolving semantic heterogeneity among information sources is a central problem in information interoperation, information integration, and information sharing among websites. Ontologies...
User Ratings of Ontologies: Who will Rate the Raters (2005)
Natalya F. Noy, Ramanathan Guha, Mark A. Musen
The number of ontologies and knowledge bases covering different domains and available on the World-Wide Web is steadily growing. As more ontologies are available, it is becoming harder, and not...
Natalya F. Noy, Deborah L. Mcguinness
1 ¿Por qué desarrollar una ontología? 3 2 ¿Qué es una ontología? 5 3 Una simple metodología de ingeniería del conocimiento 6 4 Definición de las clases y de la jerarquía de clases 15
Tracking Changes During Ontology Evolution (2004)
Natalya F. Noy, Hya Kunnatur, Michel Klein, Mark A. Musen
Abstract. As ontology development becomes a collaborative process, developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code or versions of...
Editing description logic ontologies with the protégé OWL plugin (2004)
Holger Knublauch, Holger Knublauch, Ray W. Fergerson, Natalya F. Noy, Natalya F. Noy, Mark A. Musen, ...
We will demonstrate the OWL Plugin [1,2,3], a Semantic Web extension of the Protégé ontology development platform. The OWL Plugin can be used to edit ontologies in the Web Ontology Language (OWL),...
Ontology Versioning in an Ontology Management Framework (2004)
A uniform framework for managing ontology versions will help developers work more effectively with existing ontologies and create new ones. O n t o l o g i e s
Semantic Integration: A Survey Of Ontology-Based Approaches (2004)
Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontologies. This paper provides a brief survey of the approaches to semantic...
Semantic Integration: A Survey Of Ontology-Based Approaches (2004)
Semantic integration is an active area of research in several disciplines, such as databases, information-integration, and ontologies. This paper provides a brief survey of the approaches to semantic...
Ontology evolution: Not the same as schema evolution (2004)
As ontology development becomes a more ubiquitous and collaborative process, ontology versioning and evolution becomes an important area of ontology research. The many similarities between...
Accessing and Manipulating Ontologies Using Web Services (2004)
Olivier Dameron, Natalya F. Noy, Holger Knublauch, Mark A. Musen
Abstract. Ontologies and Semantic Web Services are the two core technologies of the Semantic Web. The Semantic Web hinges on the ability of computer programs to perform some task involving the...
OMEN: A Probabilistic Ontology Mapping Tool (2004)
Prasenjit Mitra, Natalya F. Noy, Anuj R. Jaiswal
Abstract. Most existing ontology mapping tools do not provide exact mappings. Rather, there is usually some degree of uncertainty. We describe a framework to improve existing ontology mappings using...
The Protégé OWL plugin: An open development environment for semantic web applications (2004)
Holger Knublauch, Ray W. Fergerson, Natalya F. Noy, Mark A. Musen
Abstract. We introduce the OWL Plugin, a Semantic Web extension of the Protégé ontology development platform. The OWL Plugin can be used to edit ontologies in the Web Ontology Language (OWL), to...
The prompt suite: Interactive tools for ontology merging and mapping (2003)
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. This distributed nature of ontology development has led to a large number of ontologies...
Ontology versioning as an element of an ontology-management framework (2003)
As ontology development becomes a more ubiquitous and collaborative process, the developers face the problem of managing multiple ontologies: comparing, aligning, and merging them, maintaining...
A Component-Based Framework for Ontology Evolution (2003)
Support for ontology evolution becomes extremely important in distributed development and use of ontologies. Information about change...
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO) (2003)
Iwei Yeh, Peter D. Karp, Natalya F. Noy, Russ B. Altman
Motivation: Acritical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO;...
Tracking complex changes during ontology evolution (2003)
For the Semantic Web to succeed, it will require the development and integration of numerous ontologies. As ontology development becomes a more ubiquitous and collaborative process, support for...
Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO) (2003)
Yeh, Iwei, Karp, Peter D., Noy, Natalya F., Altman, Russ B.
Motivation: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO;...
Pushing the envelope: Challenges in a frame-based representation of human anatomy (2002)
Natalya F. Noy, Mark A. Musen, Cornelius Rosse
One of the main threads in the history of knowledge-representation formalisms is the trade-off between the expressiveness of first-order logic on the one hand and the tractability and ease-of-use of...
PROMPTDIFF: A fixed-point algorithm for comparing ontology versions (2002)
As ontology development becomes a more ubiquitous and collaborative process, the developers face the problem of maintaining versions of ontologies akin to maintaining versions of software code in...
A template-based approach toward acquisition of logical sentences (2002)
Abstract: Ontology-development languages may allow users to supplement frame-based representations with arbitrary logical sentences. In the case of the Ontolingua ontology library, only 10 % of the...
Evaluating ontology-mapping tools: Requirements and experience (2002)
Abstract. The appearance of a large number of ontology tools may leave a user looking for an appropriate tool overwhelmed and uncertain on which tool to choose. Thus evaluation and comparison of...
The Evolution of Protégé: An Environment for Knowledge-Based Systems Development (2002)
John H. Gennari, Mark A. Musen, Ray W. Fergerson, William E. Grosso, Monica Crubézy, Henrik Eriksson, ...
The Protégé project has come a long way since Mark Musen first built the Protégé metatool for knowledge-based systems in 1987. The original tool was a small application, aimed at building...
Evaluating ontology-mapping tools: Requirements and experience (2002)
Abstract. The appearance of a large number of ontology tools may leave a user looking for an appropriate tool overwhelmed and uncertain on which tool to choose. Thus evaluation and comparison of...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Ontology Development 101: A Guide to Creating Your First Ontology (2001)
Natalya F. Noy, Deborah L. Mcguinness
In recent years the development of ontologies—explicit formal specifications of the terms in the domain and relations among them (Gruber 1993)—has been moving from the realm of...
Anchor-PROMPT: Using non-local context for semantic matching (2001)
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the World-Wide Web where they provide...
Creating semantic web contents with (2001)
Natalya F. Noy, Michael Sintek, Stefan Decker, Monica Crubézy, Ray W. Fergerson, Mark A. Musen
T h e S e m a n t i c W e b As researchers continue to create new languages in the hope of developing a Semantic Web, they still lack consensus on a standard. The authors describe how...
Ontology Development 101: A Guide to Creating Your First Ontology (2001)
Natalya F. Noy, Deborah L. Mcguinness
In recent years the development of ontologies—explicit formal specifications of the terms in the domain and relations among them (Gruber 1993)—has been moving from the realm of...
Component-Based Support for Building Knowledge-Acquisition Systems (2000)
Mark A. Musen, Ray W. Fergerson, William E. Grosso, Natalya F. Noy, Monica Crubézy, John H. Gennari
During the past decade, there has been increasing consensus within the knowledge-based–systems community on appropriate conceptual components for building intelligent computer programs. Intelligent...
Noy, Natalya F., Crubézy, Monica, Fergerson, Ray W., Knublauch, Holger, Tu, Samson W., Vendetti, Jennifer, ...
Protégé-2000 is an open-source tool that assists users in the construction of large electronic knowledge bases. It has an intuitive user interface that enables developers to create and edit domain...
Noy, Natalya F., Crubézy, Monica, Fergerson, Ray W., Knublauch, Holger, Tu, Samson W., Vendetti, Jennifer, ...
Protégé-2000 is an open-source tool that assists users in the construction of large electronic knowledge bases. It has an intuitive user interface that enables developers to create and edit domain...
Protégé: A Tool for Managing and Using Terminology in Radiology Applications
Rubin, Daniel L., Noy, Natalya F., Musen, Mark A.
The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The...
Representation of Structural Relationships in the Foundational Model of Anatomy
Mejino, José L.V., Noy, Natalya F., Musen, Mark A., Brinkley, James F., Rosse, Cornelius
We propose an ontology of anatomical relationships in the Digital Anatomist Foundational Model. Our purpose is to generate a sharable resource that can support inference about the structural...
Developing Biomedical Ontologies Collaboratively
Noy, Natalya F., Tudorache, Tania, De Coronado, Sherri, Musen, Mark A.
The development of ontologies that define entities and relationships among them has become essential for modern work in biomedicine. Ontologies are becoming so large in their coverage that no single...
BioPortal: ontologies and integrated data resources at the click of a mouse
Noy, Natalya F., Shah, Nigam H., Whetzel, Patricia L., Dai, Benjamin, Dorf, Michael, Griffith, Nicholas, ...
Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal...