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

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

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

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

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

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

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

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

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

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

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". (Version 1) - Herr, Bruce William, II; Hardi, Josef; Quardokus, Ellen M.; Bueckle, Andreas; Caron, Anita R.; Chen, Lu; Wang, Fusheng; Osumi-Sutherland, David; Musen, Mark A.; Börner, Katy (Zenodo, 2022)

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". (Version 2) - Herr, Bruce William, II; Hardi, Josef; Quardokus, Ellen M.; Bueckle, Andreas; Caron, Anita R.; Chen, Lu; Wang, Fusheng; Osumi-Sutherland, David; Musen, Mark A.; Börner, Katy (Zenodo, 2022)

Tables for "Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas". (Version 3) - Herr, Bruce William, II; Hardi, Josef; Quardokus, Ellen M.; Bueckle, Andreas; Caron, Anita R.; Chen, Lu; Wang, Fusheng; Osumi-Sutherland, David; Musen, Mark A.; Börner, Katy (Zenodo, 2022)

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

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

A Simple Standard for Sharing Ontological Mappings (SSSOM). - Matentzoglu, Nicolas; Balhoff, James P.; Bello, Susan M.; Bizon, Chris; Brush, Matthew H.; Callahan, Tiffany J.; Chute, Christopher G.; Duncan, William D.; Evelo, Chris T. A.; Gabriel, Davera; Graybeal, John B.; Gray, Alasdair J. G.; et al. (CoRR, 2021)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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