The Knowledge Model of Protégé-2000: Combining Interoperability and Flexibility. - Natalya Fridman Noy; Ray W. Fergerson; Mark A. Musen (EKAW, 2000)

Protege-2000: A Plug-in Architecture to Support Knowledge Acquisition, Knowledge Visualization, and the Semantic Web. - Mark A. Musen; Ray W. Fergerson; Natalya Fridman Noy; Monica Crubézy (AMIA, 2001)

Creating Semantic Web Contents with Protégé-2000. - Natalya Fridman Noy; Michael Sintek; Stefan Decker; Monica Crubézy; Ray W. Fergerson; Mark A. Musen (IEEE Intell. Syst., 2001)

Jambalaya: an interactive environment for exploring ontologies. - Margaret-Anne D. Storey; Natasha F. Noy; Mark A. Musen; Casey Best; Ray W. Fergerson; Neil A. Ernst (IUI, 2002)

Protégé-2000: An Open-Source Ontology-Development and Knowledge-Acquisition Environment: AMIA 2003 Open Source Expo. - Natalya Fridman Noy; Monica Crubézy; Ray W. Fergerson; Holger Knublauch; Samson W. Tu; Jennifer Vendetti; Mark A. Musen (AMIA, 2003)

The evolution of Protégé: an environment for knowledge-based systems development. - John H. Gennari; Mark A. Musen; Ray W. Fergerson; William E. Grosso; Monica Crubézy; Henrik Eriksson; Natalya Fridman Noy; Samson W. Tu (Int. J. Hum. Comput. Stud., 2003)

The Protégé OWL Plugin: An Open Development Environment for Semantic Web Applications. - Holger Knublauch; Ray W. Fergerson; Natalya Fridman Noy; Mark A. Musen (ISWC, 2004)

Protégé-OWL: Creating Ontology-Driven Reasoning Applications with the Web Ontology Language. - Daniel L. Rubin; Holger Knublauch; Ray W. Fergerson; Olivier Dameron; Mark A. Musen (AMIA, 2005)

The NCBO Annotator: Ontology-Based Annotation as a Web Service. - Patricia L. Whetzel; Clément Jonquet; Cherie Youn; Michael Dorf; Ray W. Fergerson; Mark A. Musen; Nigam Shah (ICBO, 2011)

Bioportal: Ontologies and Integrated Data Resources at the Click of a Mouse. - Patricia L. Whetzel; Natasha F. Noy; Nigam Shah; Paul R. Alexander; Michael Dorf; Ray W. Fergerson; Margaret-Anne D. Storey; Barry Smith 001; Christopher G. Chute; Mark A. Musen (ICBO, 2011)

Using SPARQL to Query BioPortal Ontologies and Metadata. - Manuel Salvadores; Matthew Horridge; Paul R. Alexander; Ray W. Fergerson; Mark A. Musen; Natalya Fridman Noy (ISWC (2), 2012)

Getting Lucky in Ontology Search: A Data-Driven Evaluation Framework for Ontology Ranking. - Natalya Fridman Noy; Paul R. Alexander; Rave Harpaz; Patricia L. Whetzel; Ray W. Fergerson; Mark A. Musen (ISWC (1), 2013)

Boosting RDF Adoption in Ruby with Goo. - Manuel Salvadores; Paul R. Alexander; Ray W. Fergerson; Natalya Fridman Noy; Mark A. Musen (WaSABi@ISWC, 2013)

NCBO BioPortal version 4. - Ray W. Fergerson; Paul R. Alexander; Michael Dorf; Rafael S. Gonçalves 001; Manuel Salvadores; Alex Skrenchuk; Jennifer Vendetti; Mark A. Musen (ICBO, 2015)