An Ontology for Gastrointestinal Endoscopy. - Shahim Essaid (ICBO, 2011)

Enabling semantic search in a bio-specimen repository. - Shahim Essaid; Carlo Torniai; Melissa A. Haendel (ICBO, 2013)

Finding common ground: integrating the eagle-i and VIVO ontologies. - Carlo Torniai; Shahim Essaid; Brian Lowe; Jon Corson-Rikert; Melissa A. Haendel (ICBO, 2013)

ROBOT: A command-line tool for ontology development. - James A. Overton; Heiko Dietze; Shahim Essaid; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2015)

Enhancing SciENcv through Semantic Research Profile Integration with the VIVO-ISF Ontology. - Marijane White; Matthew H. Brush; Shahim Essaid; Robin Champieux; Adrienne Zell; Melissa A. Haendel; Colin Grove; Syeda Momina Tabish; David Eichmann (ICBO/BioCreative, 2016)

OpenVIVO: Transparency in Scholarship. - Violeta Ilik; Michael Conlon 001; Graham Triggs; Marijane White; Muhammad Javed 002; Matthew H. Brush; Karen Gutzman; Shahim Essaid; Paul Friedman; Simon Porter 001; Martin Szomszor; Melissa Anne Haendel; et al. (Frontiers Res. Metrics Anal., 2017)

Mondo Disease Ontology: Harmonizing Disease Concepts Across the World (short paper). - Nicole A. Vasilevsky; Shahim Essaid; Nicolas Matentzoglu; Nomi L. Harris; Melissa A. Haendel; Peter N. Robinson; Christopher J. Mungall (ICBO/ODLS, 2020)

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. - Kent A. Shefchek; Nomi L. Harris; Michael A. Gargano; Nicolas Matentzoglu; Deepak R. Unni; Matthew H. Brush; Dan Keith; Tom Conlin; Nicole A. Vasilevsky; Xingmin Aaron Zhang; James P. Balhoff; Larry Babb; et al. (Nucleic Acids Res., 2020)

From Survey to Ontology, the Challenges and Opportunities in Ontologizing Questions and Answers. - Lauren E. Chan; Jimmy Phuong; Anne E. Thessen; Stephanie S. Hong; Shahim Essaid; Melissa A. Haendel (ICBO, 2022)