CARO - The Common Anatomy Reference Ontology. - Melissa A. Haendel; Fabian Neuhaus; David Osumi-Sutherland; Paula M. Mabee; José L. V. Mejino Jr.; Chris Mungall; Barry Smith 001 (Anatomy Ontologies for Bioinformatics, 2008)

FlyBase: enhancing Drosophila Gene Ontology annotations. - Susan Tweedie; Michael Ashburner; Kathleen Falls; Paul C. Leyland; Peter McQuilton; Steven J. Marygold; Gillian H. Millburn; David Osumi-Sutherland; Andrew J. Schroeder; Ruth L. Seal; Haiyan Zhang (Nucleic Acids Res., 2009)

Modularization for the Cell Ontology. - Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl (ICBO, 2011)

FUNCARO: A Functional Extension to CARO. - David Osumi-Sutherland (ICBO, 2011)

CARO 2.0. - David Osumi-Sutherland (ICBO, 2011)

The Virtual Fly Brain browser and query interface. - Nestor Milyaev; David Osumi-Sutherland; Simon Reeve; Nicholas Burton; Richard A. Baldock; J. Douglas Armstrong (Bioinform., 2012)

A strategy for building neuroanatomy ontologies. - David Osumi-Sutherland; Simon Reeve; Christopher J. Mungall; Fabian Neuhaus; Alan Ruttenberg; Gregory S. X. E. Jefferis; J. Douglas Armstrong (Bioinform., 2012)

The Drosophila anatomy ontology. - Marta Costa; Simon Reeve; Gary Grumbling; David Osumi-Sutherland (J. Biomed. Semant., 2013)

The Drosophila phenotype ontology. - David Osumi-Sutherland; Steven J. Marygold; Gillian H. Millburn; Peter McQuilton; Laura Ponting; Raymund Stefancsik; Kathleen Falls; Nicholas H. Brown; Georgios V. Gkoutos (J. Biomed. Semant., 2013)

Use of OWL within the Gene Ontology. - Chris Mungall; Heiko Dietze; David Osumi-Sutherland (OWLED, 2014)

Virtual Fly Brain - Using OWL to Support the Mapping and Genetic Dissection of the Drosophila Brain. - David Osumi-Sutherland; Marta Costa; Robert Court; Cahir O'Kane (OWLED, 2014)

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. - Wasila M. Dahdul; Hong Cui; Paula M. Mabee; Christopher J. Mungall; David Osumi-Sutherland; Ramona L. Walls; Melissa A. Haendel (J. Biomed. Semant., 2014)

TermGenie - A web application for pattern-based ontology class generation. - Heiko Dietze; Tanya Z. Berardini; Rebecca E. Foulger; David P. Hill; Jane Lomax; David Osumi-Sutherland; Paola Roncaglia; Christopher J. Mungall (J. Biomed. Semant., 2014)

Improvements to the Drosophila anatomy ontology. - Marta Costa; David Osumi-Sutherland; Steven J. Marygold; Nick Brown 001 (ICBO, 2015)

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

Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary. - David Osumi-Sutherland; Enrico Ponta; Mélanie Courtot; Helen E. Parkinson; Laura Badi (SWAT4LS, 2015)

PhenoImageShare: an image annotation and query infrastructure. - Solomon Adebayo; Kenneth McLeod; Ilinca Tudose; David Osumi-Sutherland; Tony Burdett; Richard A. Baldock; Albert Burger; Helen E. Parkinson (J. Biomed. Semant., 2016)

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. - Alexander D. Diehl; Terrence F. Meehan; Yvonne M. Bradford; Matthew H. Brush; Wasila M. Dahdul; David S. Dougall; Yongqun He; David Osumi-Sutherland; Alan Ruttenberg; Sirarat Sarntivijai; Ceri E. Van Slyke; Nicole A. Vasilevsky; et al. (J. Biomed. Semant., 2016)

Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. - Nicole A. Vasilevsky; James P. Balhoff; Christopher J. Mungall; David Osumi-Sutherland; Sebastian Köhler 001; Susan M. Bello; Cynthia L. Smith; Peter N. Robinson; Melissa A. Haendel (ICBO, 2017)

Dead simple OWL design patterns. - David Osumi-Sutherland; Mélanie Courtot; James P. Balhoff; Christopher J. Mungall (J. Biomed. Semant., 2017)

Cell ontology in an age of data-driven cell classification. - David Osumi-Sutherland (BMC Bioinform., 2017)

Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework. - Nicolas Matentzoglu; David Osumi-Sutherland (ICBO, 2018)

Human Cell Atlas Ontology. - Danielle Welter; Simon Jupp; David Osumi-Sutherland (ICBO, 2018)

Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. - David Osumi-Sutherland; Enrico Ponta; Mélanie Courtot; Helen E. Parkinson; Laura Badi (J. Biomed. Semant., 2018)

Where Does an Ontology Start? - Henriette Harmse; Mélanie Courtot; Warren Read; Nicolas Matentzoglu; David Osumi-Sutherland; Simon Jupp (ICBO, 2019)

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. - Sebastian Köhler 001; Leigh Carmody; Nicole A. Vasilevsky; Julius O. B. Jacobsen; Daniel Danis; Jean-Philippe F. Gourdine; Michael A. Gargano; Nomi L. Harris; Nicolas Matentzoglu; Julie A. McMurry; David Osumi-Sutherland; Valentina Cipriani; et al. (Nucleic Acids Res., 2019)

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)

OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - Rebecca C. Jackson; Nicolas Matentzoglu; James A. Overton; Randi Vita; James P. Balhoff; Pier Luigi Buttigieg; Seth Carbon; Mélanie Courtot; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Nomi L. Harris; et al. (Database J. Biol. Databases Curation, 2021)

Ubergraph: Integrating OBO Ontologies into a Unified Semantic Graph. - James P. Balhoff; Ugur Bayindir; Anita R. Caron; Nicolas Matentzoglu; David Osumi-Sutherland; Christopher J. Mungall (ICBO, 2022)

OBO Academy: Training Materials for Bioontologists. - James A. Overton; Rebecca C. Jackson; Sabrina Toro; Shawn Zheng Kai Tan; Bradley Varner; David Osumi-Sutherland; Nicolas Matentzoglu; Nicole A. Vasilevsky (ICBO, 2022)

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Nicolas Matentzoglu; James P. Balhoff; Susan M. Bello; Chris Bizon; Matthew H. Brush; Tiffany J. Callahan; Christopher G. Chute; William D. Duncan; Chris T. A. Evelo; Davera Gabriel; John B. Graybeal; Alasdair J. G. Gray; et al. (Database J. Biol. Databases Curation, 2022)

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (Database J. Biol. Databases Curation, 2022)

The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. - Malcolm E. Fisher; Erik Segerdell; Nicolas Matentzoglu; Mardi J. Nenni; Joshua D. Fortriede; Stanley Chu; Troy J. Pells; David Osumi-Sutherland; Praneet Chaturvedi; Christina James-Zorn; Nivitha Sundararaj; Vaneet S. Lotay; et al. (BMC Bioinform., 2022)

Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. - Nicolas Matentzoglu; Damien Goutte-Gattat; Shawn Zheng Kai Tan; James P. Balhoff; Seth Carbon; Anita R. Caron; William D. Duncan; Joe E. Flack; Melissa A. Haendel; Nomi L. Harris; William R. Hogan; Charles Tapley Hoyt; et al. (CoRR, 2022)

Expression Atlas update: gene and protein expression in multiple species. - Pablo A. Moreno; Silvie Fexova; Nancy George; Jonathan R. Manning; Zhichao Miao; Suhaib Mohammed; Alfonso Muñoz-Pomer Fuentes; Anja Füllgrabe; Yalan Bi; Natassja Bush; Haider Iqbal; Upendra Kumbham; et al. (Nucleic Acids Res., 2022)

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". - Bruce William Herr II; Josef Hardi; Ellen M. Quardokus; Andreas Bueckle; Anita R. Caron; Lu Chen; Fusheng Wang 001; David Osumi-Sutherland; Mark A. Musen; Katy Börner (Zenodo, 2022)

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". - Bruce William Herr II; Josef Hardi; Ellen M. Quardokus; Andreas Bueckle; Anita R. Caron; Lu Chen; Fusheng Wang 001; David Osumi-Sutherland; Mark A. Musen; Katy Börner (Zenodo, 2022)

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". - Bruce William Herr II; Josef Hardi; Ellen M. Quardokus; Andreas Bueckle; Anita R. Caron; Lu Chen; Fusheng Wang 001; David Osumi-Sutherland; Mark A. Musen; Katy Börner (Zenodo, 2022)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - Sabrina Toro; Anna V. Anagnostopoulos; Sue Bello; Kai Lewis Blumberg; Rhiannon Cameron; Leigh Carmody; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Petra Fey; Pascale Gaudet; Nomi L. Harris; et al. (CoRR, 2023)

COVoc and COVTriage: novel resources to support literature triage. - Déborah Caucheteur; Zoë May Pendlington; Paola Roncaglia; Julien Gobeill; Luc Mottin; Nicolas Matentzoglu; Donat Agosti; David Osumi-Sutherland; Helen E. Parkinson; Patrick Ruch (Bioinform., 2023)

The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. - Elliot Sollis; Abayomi Mosaku; Ala Abid; Annalisa Buniello; Maria Cerezo; Laurent Gil; Tudor Groza; Osman Nuri Günes; Peggy Hall; James D. Hayhurst; Arwa Ibrahim; Yue Ji; et al. (Nucleic Acids Res., 2023)

Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). - Sabrina Toro; Anna V. Anagnostopoulos; Susan M. Bello; Kai Lewis Blumberg; Rhiannon Cameron; Leigh Carmody; Alexander D. Diehl; Damion M. Dooley; William D. Duncan; Petra Fey; Pascale Gaudet; Nomi L. Harris; et al. (J. Biomed. Semant., 2024)

The Cell Ontology in the age of single-cell omics. - Shawn Zheng Kai Tan; Aleix Puig-Barbe; Damien Goutte-Gattat; Caroline Eastwood; Brian D. Aevermann; Alida Avola; James P. Balhoff; Ismail Ugur Bayindir; Jasmine Belfiore; Anita R. Caron; David S. Fischer; Nancy George; et al. (CoRR, 2025)

Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework. - Yasemin Bridges; Vinicius de Souza; Katherina G. Cortes; Melissa A. Haendel; Nomi L. Harris; Daniel R. Korn; Nikolaos M. Marinakis; Nicolas Matentzoglu; James A. McLaughlin; Christopher J. Mungall; Aaron Odell; David Osumi-Sutherland; et al. (BMC Bioinform., 2025)