David Osumi-Sutherland

Publication Activity (10 Years)

Years Active: 2009-2023
Publications (10 Years): 21

Top Topics

Ontology Development

Biomedical Ontologies

Design Patterns

Top Venues

J. Biomed. Semant.

Nucleic Acids Res.

Publications

Déborah Caucheteur, Zoë May Pendlington, Paola Roncaglia, Julien Gobeill, Luc Mottin, Nicolas Matentzoglu, Donat Agosti, David Osumi-Sutherland, Helen E. Parkinson, Patrick Ruch
COVoc and COVTriage: novel resources to support literature triage. Bioinform. 39 (1) (2023)
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
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res. 51 (D1) (2023)
Sabrina Toro, Anna V. Anagnostopoulos, Sue Bello, Kai 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
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). CoRR (2023)
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
Ontology Development Kit: a toolkit for building, maintaining, and standardising biomedical ontologies. CoRR (2022)
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 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
A Simple Standard for Sharing Ontological Mappings (SSSOM). Database J. Biol. Databases Curation 2022 (2022) (2022)
Pablo 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
Expression Atlas update: gene and protein expression in multiple species. Nucleic Acids Res. 50 (D1) (2022)
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
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. BMC Bioinform. 23 (1) (2022)
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
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database J. Biol. Databases Curation 2022 (2022) (2022)
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
A Simple Standard for Sharing Ontological Mappings (SSSOM). CoRR (2021)
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
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. Database J. Biol. Databases Curation 2021 (2021)
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
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 48 (Database-Issue) (2020)
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
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. 47 (Database-Issue) (2019)
Henriette Harmse, Mélanie Courtot, Warren Read, Nicolas Matentzoglu, David Osumi-Sutherland, Simon Jupp
Where Does an Ontology Start? ICBO (2019)
David Osumi-Sutherland, Enrico Ponta, Mélanie Courtot, Helen E. Parkinson, Laura Badi
Using OWL reasoning to support the generation of novel gene sets for enrichment analysis. J. Biomed. Semant. 9 (1) (2018)
Danielle Welter, Simon Jupp, David Osumi-Sutherland
Human Cell Atlas Ontology. ICBO (2018)
Nicolas Matentzoglu, David Osumi-Sutherland
Reconciling Ontology Definitions using the Ontology Pattern Reconciliation Workbench and the DOSDP Framework. ICBO (2018)
David Osumi-Sutherland, Mélanie Courtot, James P. Balhoff, Christopher J. Mungall
Dead simple OWL design patterns. J. Biomed. Semant. 8 (1) (2017)
David Osumi-Sutherland
Cell ontology in an age of data-driven cell classification. BMC Bioinform. 18 (S-17) (2017)
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
Aligning the Human Phenotype and Mammalian Phenotype Ontology using Dead Simple Ontology Design Patterns. ICBO (2017)
Solomon Adebayo, Kenneth McLeod, Ilinca Tudose, David Osumi-Sutherland, Tony Burdett, Richard A. Baldock, Albert Burger, Helen E. Parkinson
PhenoImageShare: an image annotation and query infrastructure. J. Biomed. Semant. 7 (2016)
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
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7 (2016)
James A. Overton, Heiko Dietze, Shahim Essaid, David Osumi-Sutherland, Christopher J. Mungall
ROBOT: A command-line tool for ontology development. ICBO (2015)
Marta Costa, David Osumi-Sutherland, Steven J. Marygold, Nick Brown
Improvements to the Drosophila anatomy ontology. ICBO (2015)
David Osumi-Sutherland, Enrico Ponta, Mélanie Courtot, Helen E. Parkinson, Laura Badi
Cell, Chemical and Anatomical Views of the Gene Ontology: Mapping to a Roche Controlled Vocabulary. SWAT4LS (2015)
Chris Mungall, Heiko Dietze, David Osumi-Sutherland
Use of OWL within the Gene Ontology. OWLED (2014)
David Osumi-Sutherland, Marta Costa, Robert Court, Cahir O'Kane
Virtual Fly Brain - Using OWL to Support the Mapping and Genetic Dissection of the Drosophila Brain. OWLED (2014)
Wasila M. Dahdul, Hong Cui, Paula M. Mabee, Christopher J. Mungall, David Osumi-Sutherland, Ramona L. Walls, Melissa A. Haendel
Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. J. Biomed. Semant. 5 (2014)
Heiko Dietze, Tanya Z. Berardini, Rebecca E. Foulger, David P. Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, Christopher J. Mungall
TermGenie - A web application for pattern-based ontology class generation. J. Biomed. Semant. 5 (2014)
Marta Costa, Simon Reeve, Gary Grumbling, David Osumi-Sutherland
The Drosophila anatomy ontology. J. Biomed. Semant. 4 (2013)
David Osumi-Sutherland, Steven J. Marygold, Gillian H. Millburn, Peter McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H. Brown, Georgios V. Gkoutos
The Drosophila phenotype ontology. J. Biomed. Semant. 4 (2013)
David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
A strategy for building neuroanatomy ontologies. Bioinform. 28 (15) (2012)
David Osumi-Sutherland, Simon Reeve, Christopher J. Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S. X. E. Jefferis, J. Douglas Armstrong
A strategy for building neuroanatomy ontologies. Bioinform. 28 (9) (2012)
Nestor Milyaev, David Osumi-Sutherland, Simon Reeve, Nicholas Burton, Richard A. Baldock, J. Douglas Armstrong
The Virtual Fly Brain browser and query interface. Bioinform. 28 (3) (2012)
Christopher J. Mungall, Melissa A. Haendel, Amelia Ireland, Shahid Manzoor, Terry Meehan, David Osumi-Sutherland, Carlo Torniai, Alexander D. Diehl
Modularization for the Cell Ontology. ICBO (2011)
David Osumi-Sutherland
CARO 2.0. ICBO (2011)
David Osumi-Sutherland
FUNCARO: A Functional Extension to CARO. ICBO (2011)
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
Gene Ontology annotations. Nucleic Acids Res. 37 (Database-Issue) (2009)