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)

Web-Protege: A Lightweight OWL Ontology Editor for the Web. - Tania Tudorache; Jennifer Vendetti; Natalya Fridman Noy (OWLED, 2008)

Introducing WebProtégé 2 as a Collaborative Platform for Editing Biomedical Ontologies. - Matthew Horridge; Jonathan Mortensen; Tania Tudorache; Jennifer Vendetti; Csongor Nyulas; Mark A. Musen; Natalya Fridman Noy (ICBO, 2013)

Simplified OWL Ontology Editing for the Web: Is WebProtégé Enough? - Matthew Horridge; Tania Tudorache; Jennifer Vendetti; Csongor Nyulas; Mark A. Musen; Natalya Fridman Noy (ISWC (1), 2013)

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies. - Matthew Horridge; Tania Tudorache; Csongor Nyulas; Jennifer Vendetti; Natalya Fridman Noy; Mark A. Musen (Bioinform., 2014)

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)

Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. - Marcos Martínez Romero; Martin J. O'Connor; Michael Dorf; Jennifer Vendetti; Debra Willrett; Attila L. Egyedi; John B. Graybeal; Mark A. Musen (ICBO, 2017)

Ontology Repositories and Semantic Artefact Catalogues with the OntoPortal Technology. - Clément Jonquet; John B. Graybeal; Syphax Bouazzouni; Michael Dorf; Nicola Fiore; Xeni Kechagioglou; Timothy Redmond; Ilaria Rosati; Alex Skrenchuk; Jennifer Vendetti; Mark A. Musen (ISWC, 2023)

A change language for ontologies and knowledge graphs. - Harshad Hegde; Jennifer Vendetti; Damien Goutte-Gattat; J. Harry Caufield; John B. Graybeal; Nomi L. Harris; Naouel Karam; Christian Kindermann; Nicolas Matentzoglu; James A. Overton; Mark A. Musen; Christopher J. Mungall (Database J. Biol. Databases Curation, 2025)