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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 knowledge-acquisition tools for a few specialized programs in medical planning. From this initial tool, the Protégé system has evolved into a durable, exten-sible platform(More)
Researchers in the ontology-design field have developed the content for ontologies in many domain areas. Recently, ontologies have become increasingly common on the WorldWide Web where they provide semantics for annotations in Web pages. This distributed nature of ontology development has led to a large number of ontologies covering overlapping domains. In(More)
Knowledge-based systems have become ubiquitous in recent years. The WorldWide Web consortium is developing the Resource Description Framework (RDF)—a system for annotating even Web pages with knowledge elements. Knowledge-base developers need to be able to share and reuse knowledge bases that they build. Therefore, interoperability among different(More)
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 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(More)
Functional brain networks detected in task-free ("resting-state") functional magnetic resonance imaging (fMRI) have a small-world architecture that reflects a robust functional organization of the brain. Here, we examined whether this functional organization is disrupted in Alzheimer's disease (AD). Task-free fMRI data from 21 AD subjects and 18 age-matched(More)
B ecause we can process only a tiny fraction of information available on the Web, we must turn to machines for help in processing and analyzing its contents. With current technology, machines cannot understand and interpret the meaning of the information in natural-language form, which is how most Web information is represented today. We need a Semantic Web(More)
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(More)
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,(More)
P rovision of, automated support for planning protocol-directed therapy requires a computer program to take as input clinical data stored in an electronic patient-record system and to generate as output recommendations for therapeutic interventions and laboratory testing that are defined by applicable protocols. This paper presents a synthesis of research(More)