David Osumi-Sutherland

According to our database, David Osumi-Sutherland authored at least 42 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

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, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig-Barbe, Justin T. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

J. Biomed. Semant., December, 2024

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, Sajo John, Elizabeth Lewis, Jacqueline A. L. MacArthur, Aoife McMahon, David Osumi-Sutherland, Kalliope Panoutsopoulou, Zoë May Pendlington, Santhi Ramachandran, Raymund Stefancsik, Jonathan Stewart, Patricia L. Whetzel, Robert J. Wilson, Lucia Hindorff, Fiona Cunningham, Samuel A. Lambert, Michael Inouye, Helen E. Parkinson, Laura W. Harris

Nucleic Acids Res., January, 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., January, 2023

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, Marcin P. Joachimiak, Leila Kiani, Tiago Lubiana, Monica C. Munoz-Torres, Shawn T. O'Neil, David Osumi-Sutherland, Aleix Puig, Justin P. Reese, Leonore Reiser, Sofia M. C. Robb, Troy Ruemping, James Seager, Eric Sid, Raymund Stefancsik, Magalie Weber, Valerie Wood, Melissa A. Haendel, Christopher J. Mungall

CoRR, 2023

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, David Osumi-Sutherland, Mark A. Musen, Katy Börner

Dataset, September, 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, David Osumi-Sutherland, Mark A. Musen, Katy Börner

Dataset, September, 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, David Osumi-Sutherland, Mark A. Musen, Katy Börner

Dataset, September, 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, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou

Nucleic Acids Res., 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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

CoRR, 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, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov, Bradley I. Arshinoff, Kamran Karimi, Peter D. Vize, Aaron M. Zorn

BMC Bioinform., 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, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland

Database J. Biol. Databases Curation, 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 Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall

Database J. Biol. Databases Curation, 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

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

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

Proceedings of the International Conference on Biomedical Ontology 2022 (ICBO), Ann Arbor, Michigan, USA, September 25, 2022

2021

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, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters

Database J. Biol. Databases Curation, 2021

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, Susan M. Bello, Hannah Blau, Yvonne M. Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria G. Della Rocca, Nathan A. Dunn, Shahim Essaid, Petra Fey, Christian A. Grove, Jean-Philippe F. Gourdine, Ada Hamosh, Midori A. Harris, Ingo Helbig, Maureen E. Hoatlin, Marcin P. Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoë May Pendlington, Clare Pilgrim, Tim E. Putman, Vida Ravanmehr, Justin T. Reese, Erin Rooney Riggs, Sofia M. C. Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne E. Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland

Nucleic Acids Res., 2020

2019

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.

Sebastian Köhler, 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, James P. Balhoff, Tom Conlin, Hannah Blau, Gareth Baynam, Richard Palmer, Dylan Gratian, Hugh J. S. Dawkins, Michael Segal, Anna C. Jansen, Ahmed Muaz, Willie H. Chang, Jenna Bergerson, Stanley J. F. Laulederkind, Zafer Yüksel, Sergi Beltran, Alexandra F. Freeman, Panagiotis I. Sergouniotis, Daniel Durkin, Andrea L. Storm, Marc Hanauer, Michael Brudno, Susan M. Bello, Murat Sincan, Kayli Rageth, Matthew T. Wheeler, Renske Oegema, Halima Lourghi, Maria G. Della Rocca, Rachel Thompson, Francisco Castellanos, James Priest, Charlotte Cunningham-Rundles, Ayushi Hegde, Ruth C. Lovering, Catherine Hajek, Annie Olry, Luigi Notarangelo, Morgan Similuk, Xingmin Aaron Zhang, David Gómez-Andrés, Hanns Lochmüller, Hélène Dollfus, Sergio Rosenzweig, Shruti Marwaha, Ana Rath, Kathleen Sullivan, Cynthia L. Smith, Joshua D. Milner, Dorothée Leroux, Cornelius F. Boerkoel, Amy Klion, Melody C. Carter, Tudor Groza, Damian Smedley, Melissa A. Haendel, Chris Mungall, Peter N. Robinson

Nucleic Acids Res., 2019

Where Does an Ontology Start?

Henriette Harmse, Mélanie Courtot, Warren Read, Nicolas Matentzoglu, David Osumi-Sutherland, Simon Jupp

Proceedings of the 10th International Conference on Biomedical Ontology (ICBO 2019), Buffalo, New York, USA, July 30, 2019

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

Human Cell Atlas Ontology.

Danielle Welter, Simon Jupp, David Osumi-Sutherland

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework.

Nicolas Matentzoglu, David Osumi-Sutherland

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

Cell ontology in an age of data-driven cell classification.

David Osumi-Sutherland

BMC Bioinform., 2017

Dead simple OWL design patterns.

David Osumi-Sutherland, Mélanie Courtot, James P. Balhoff, Christopher J. Mungall

J. Biomed. Semant., 2017

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, Susan M. Bello, Cynthia L. Smith, Peter N. Robinson, Melissa A. Haendel

Proceedings of the 8th International Conference on Biomedical Ontology (ICBO 2017), Newcastle-upon-Tyne, United Kingdom, September 13th, 2017

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, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall

J. Biomed. Semant., 2016

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

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

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

ROBOT: A command-line tool for ontology development.

James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, Christopher J. Mungall

Proceedings of the International Conference on Biomedical Ontology, 2015

Improvements to the Drosophila anatomy ontology.

Marta Costa, David Osumi-Sutherland, Steven J. Marygold, Nick Brown

Proceedings of the International Conference on Biomedical Ontology, 2015

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

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

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

Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) co-located with 13th International Semantic Web Conference on (ISWC 2014), 2014

Use of OWL within the Gene Ontology.

Chris Mungall, Heiko Dietze, David Osumi-Sutherland

Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) co-located with 13th International Semantic Web Conference on (ISWC 2014), 2014

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

The Drosophila anatomy ontology.

Marta Costa, Simon Reeve, Gary Grumbling, David Osumi-Sutherland

J. Biomed. Semant., 2013

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 Virtual Fly Brain browser and query interface.

Nestor Milyaev, David Osumi-Sutherland, Simon Reeve, Nicholas Burton, Richard A. Baldock, J. Douglas Armstrong

Bioinform., 2012

2011

CARO 2.0.

David Osumi-Sutherland

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

FUNCARO: A Functional Extension to CARO.

David Osumi-Sutherland

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

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

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2009

FlyBase: enhancing <i>Drosophila</i> 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

2008

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

Proceedings of the Anatomy Ontologies for Bioinformatics, Principles and Practice, 2008