Natalya Fridman Noy

The evolution of Protégé: an environment for knowledge-based systems development

The Protege project has come a long way since Mark Musen first built the Protege meta-tool for knowledge-based systems in 1987. The original tool was a small application, aimed at building knowledge-acquisition tools for a few specialized programs in medical planning. From this initial tool, the Protege system has evolved into a durable, extensible platform for knowledge-based systems development and research. The current version, Protege-2000, can be run on a variety of platforms, supports customized user-interface extensions, incorporates the Open Knowledge-Base Connectivity (OKBC) knowledge model, interacts with standard storage formats such as relational databases, XML, and RDF, and has been used by hundreds of individuals and research groups. In this paper, we follow the evolution of the Protege project through three distinct re-implementations. We describe our overall methodology, our design decisions, and the lessons we have learned over the duration of the project. We believe that our success is one of infrastructure: Protege is a flexible, well-supported, and robust development environment. Using Protege, developers and domain experts can easily build effective knowledge-based systems, and researchers can explore ideas in a variety of knowledge-based domains.

Semantic integration: a survey of ontology-based approaches

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 integration developed by researchers in the ontology community. We focus on the approaches that differentiate the ontology research from other related areas. The goal of the paper is to provide a reader who may not be very familiar with ontology research with introduction to major themes in this research and with pointers to different research projects. We discuss techniques for finding correspondences between ontologies, declarative ways of representing these correspondences, and use of these correspondences in various semantic-integration tasks

Creating Semantic Web contents with Protege-2000

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 Protege-2000, a tool for ontology development and knowledge acquisition, can be adapted for editing models in different Semantic Web languages.

The protégé OWL plugin: an open development environment for semantic web applications

We introduce the OWL Plugin, a Semantic Web extension of the Protege ontology development platform. The OWL Plugin can be used to edit ontologies in the Web Ontology Language (OWL), to access description logic reasoners, and to acquire instances for semantic markup. In many of these features, the OWL Plugin has created and facilitated new practices for building Semantic Web contents, often driven by the needs of and feedback from our users. Furthermore, Proteges flexible open-source platform means that it is easy to integrate custom-tailored components to build real-world applications. This document describes the architecture of the OWL Plugin, walks through its most important features, and discusses some of our design decisions.

The PROMPT suite: interactive tools for ontology merging and mapping

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 covering overlapping domains. In order for these ontologies to be reused, they first need to be merged or aligned to one another. We developed a suite of tools for managing multiple ontologies. These suite provides users with a uniform framework for comparing, aligning, and merging ontologies, maintaining versions, translating between different formalisms. Two of the tools in the suite support semi-automatic ontology merging: IPROMPT is an interactive ontology-merging tool that guides the user through the merging process, presenting him with suggestions for next steps and identifying inconsistencies and potential problems. ANCHORPROMPT uses a graph structure of ontologies to find correlation between concepts and to provide additional information for IPROMPT.

The Knowledge Model of Protégé-2000: Combining Interoperability and Flexibility

Knowledge-based systems have become ubiquitous in recent years. Knowledge-base developers need to be able to share and reuse knowledge bases that they build. Therefore, interoperability among different knowledge-representation systems is essential. The Open Knowledge-Base Connectivity protocol (OKBC) is a common query and construction interface for frame-based systems that facilitates this interoperability. ProtEgE-2000 is an OKBC-compatible knowledge-base-editing environment developed in our laboratory. We describe ProtEgE-2000 knowledge model that makes the import and export of knowledge bases from and to other knowledge-base servers easy. We discuss how the requirements of being a usable and configurable knowledge-acquisition tool affected our decisions in the knowledge-model design. ProtEgE-2000 also has a flexible metaclass architecture which provides configurable templates for new classes in the knowledge base. The use of metaclasses makes ProtEgE-2000 easily extensible and enables its use with other knowledge models. We demonstrate that we can resolve many of the differences between the knowledge models of ProtEgE-2000 and Resource Description Framework (RDF)--a system for annotating Web pages with knowledge elements--by defining a new metaclass set. Resolving the differences between the knowledge models in declarative way enables easy adaptation of ProtEgE-2000 as an editor for other knowledge-representation systems.

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

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. 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 Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. 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 of biomedical resources.

Ontology Evolution: Not the Same as Schema Evolution

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 database-schema evolution and ontology evolution will allow us to build on the extensive research in schema evolution. However, there are also important differences between database schemas and ontologies. The differences stem from different usage paradigms, the presence of explicit semantics and different knowledge models. A lot of problems that existed only in theory in database research come to the forefront as practical problems in ontology evolution. These differences have important implications for the development of ontology-evolution frameworks: The traditional distinction between versioning and evolution is not applicable to ontologies. There are several dimensions along which compatibility between versions must be considered. The set of change operations for ontologies is different. We must develop automatic techniques for finding similarities and differences between versions.

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications

The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

The State of the Art in Ontology Design: A Survey and Comparative Review

In this article, we develop a framework for comparing ontologies and place a number of the more prominent ontologies into it. We have selected 10 specific projects for this study, including general ontologies, domain-specific ones, and one knowledge representation system. The comparison framework includes general characteristics, such as the purpose of an ontology, its coverage (general or domain specific), its size, and the formalism used. It also includes the design process used in creating an ontology and the methods used to evaluate it. Characteristics that describe the content of an ontology include taxonomic organization, types of concept covered, top-level divisions, internal structure of concepts, representation of part-whole relations, and the presence and nature of additional axioms. Finally, we consider what experiments or applications have used the ontologies. Knowledge sharing and reuse will require a common framework to support interoperability of independently created ontologies. Our study shows there is great diversity in the way ontologies are designed and the way they represent the world. By identifying the similarities and differences among existing ontologies, we clarify the range of alternatives in creating a standard framework for ontology design.