Protégé-2000: an open-source ontology-development and knowledge-acquisition environment
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Updated: Aug 29, 2026

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Natalya F Noy1, Monica Crubezy, Ray W Fergerson
1Standford Medical Informatics, Stanford University School Medicine, CA 94305, USA. http://protege.stanford.edu
Abstract:
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 ontologies. Numerous plugins provide alternative visualization mechanisms, enable management of multiple ontologies, allow the use of interference engines and problem solvers with Protégé ontologies, and provide other functionality. The Protégé user community has more than 7000 members.
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