Works by Osumi-Sutherland, David

Results: 29
    1

    A strategy for building neuroanatomy ontologies.

    Published in:
    2012
    By:
    • Osumi-Sutherland, David;
    • Reeve, Simon;
    • Mungall, Christopher J.;
    • Neuhaus, Fabian;
    • Ruttenberg, Alan;
    • Jefferis, Gregory S. X. E.;
    • Armstrong, J. Douglas
    Publication type:
    Correction Notice
    2

    A strategy for building neuroanatomy ontologies.

    Published in:
    Bioinformatics, 2012, v. 28, n. 9, p. 1262, doi. 10.1093/bioinformatics/bts113
    By:
    • Osumi-Sutherland, David;
    • Reeve, Simon;
    • Mungall, Christopher J.;
    • Neuhaus, Fabian;
    • Ruttenberg, Alan;
    • Jefferis, Gregory S. X. E.;
    • Armstrong, J. Douglas
    Publication type:
    Article
    3

    The Virtual Fly Brain browser and query interface.

    Published in:
    Bioinformatics, 2012, v. 28, n. 3, p. 411, doi. 10.1093/bioinformatics/btr677
    By:
    • Milyaev, Nestor;
    • Osumi-Sutherland, David;
    • Reeve, Simon;
    • Burton, Nicholas;
    • Baldock, Richard A.;
    • Armstrong, J. Douglas
    Publication type:
    Article
    4
    5

    Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

    Published in:
    Systematic Biology, 2023, v. 72, n. 5, p. 1084, doi. 10.1093/sysbio/syad025
    By:
    • Girón, Jennifer C;
    • Tarasov, Sergei;
    • Montaña, Luis Antonio González;
    • Matentzoglu, Nicolas;
    • Smith, Aaron D;
    • Koch, Markus;
    • Boudinot, Brendon E;
    • Bouchard, Patrice;
    • Burks, Roger;
    • Vogt, Lars;
    • Yoder, Matthew;
    • Osumi-Sutherland, David;
    • Friedrich, Frank;
    • Beutel, Rolf G;
    • Mikó, István
    Publication type:
    Article
    6

    Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.

    Published in:
    BMC Bioinformatics, 2025, v. 26, n. 1, p. 1, doi. 10.1186/s12859-025-06105-4
    By:
    • Bridges, Yasemin;
    • Souza, Vinicius de;
    • Cortes, Katherina G.;
    • Haendel, Melissa;
    • Harris, Nomi L.;
    • Korn, Daniel R.;
    • Marinakis, Nikolaos M.;
    • Matentzoglu, Nicolas;
    • McLaughlin, James A.;
    • Mungall, Christopher J.;
    • Odell, Aaron;
    • Osumi-Sutherland, David;
    • Robinson, Peter N.;
    • Smedley, Damian;
    • Jacobsen, Julius O. B.
    Publication type:
    Article
    7
    8

    Dead simple OWL design patterns.

    Published in:
    Journal of Biomedical Semantics, 2017, v. 8, p. 1, doi. 10.1186/s13326-017-0126-0
    By:
    • Osumi-Sutherland, David;
    • Courtot, Melanie;
    • Balhoff, James P.;
    • Mungall, Christopher
    Publication type:
    Article
    9

    PhenoImageShare: an image annotation and query infrastructure.

    Published in:
    Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0072-2
    By:
    • Adebayo, Solomon;
    • McLeod, Kenneth;
    • Tudose, Ilinca;
    • Osumi-Sutherland, David;
    • Burdett, Tony;
    • Baldock, Richard;
    • Burger, Albert;
    • Parkinson, Helen
    Publication type:
    Article
    10

    The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability.

    Published in:
    Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0088-7
    By:
    • Diehl, Alexander D.;
    • Meehan, Terrence F.;
    • Bradford, Yvonne M.;
    • Brush, Matthew H.;
    • Dahdul, Wasila M.;
    • Dougall, David S.;
    • Yongqun He;
    • Osumi-Sutherland, David;
    • Ruttenberg, Alan;
    • Sarntivijai, Sirarat;
    • Van Slyke, Ceri E.;
    • Vasilevsky, Nicole A.;
    • Haendel, Melissa A.;
    • Blake, Judith A.;
    • Mungall, Christopher J.
    Publication type:
    Article
    11
    12

    The Drosophila anatomy ontology.

    Published in:
    Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 1, doi. 10.1186/2041-1480-4-32
    By:
    • Costa, Marta;
    • Reeve, Simon;
    • Grumbling, Gary;
    • Osumi-Sutherland, David
    Publication type:
    Article
    13

    The Drosophila phenotype ontology.

    Published in:
    Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 1, doi. 10.1186/2041-1480-4-30
    By:
    • Osumi-Sutherland, David;
    • Marygold, Steven J.;
    • Millburn, Gillian H.;
    • McQuilton, Peter A.;
    • Ponting, Laura;
    • Stefancsik, Raymund;
    • Falls, Kathleen;
    • Brown, Nicholas H.;
    • Gkoutos, Georgios V.
    Publication type:
    Article
    14

    Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI).

    Published in:
    Journal of Biomedical Semantics, 2024, v. 15, n. 1, p. 1, doi. 10.1186/s13326-024-00320-3
    By:
    • Toro, Sabrina;
    • Anagnostopoulos, Anna V.;
    • Bello, Susan M.;
    • Blumberg, Kai;
    • Cameron, Rhiannon;
    • Carmody, Leigh;
    • Diehl, Alexander D.;
    • Dooley, Damion M.;
    • Duncan, William D.;
    • Fey, Petra;
    • Gaudet, Pascale;
    • Harris, Nomi L.;
    • Joachimiak, Marcin P.;
    • Kiani, Leila;
    • Lubiana, Tiago;
    • Munoz-Torres, Monica C.;
    • O'Neil, Shawn;
    • Osumi-Sutherland, David;
    • Puig-Barbe, Aleix;
    • Reese, Justin T.
    Publication type:
    Article
    15

    OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.

    Published in:
    Database: The Journal of Biological Databases & Curation, 2021, v. 2021, p. 1, doi. 10.1093/database/baab069
    By:
    • Jackson, Rebecca;
    • Matentzoglu, Nicolas;
    • Overton, James A;
    • Vita, Randi;
    • Balhoff, James P;
    • Buttigieg, Pier Luigi;
    • Carbon, Seth;
    • Courtot, Melanie;
    • Diehl, Alexander D;
    • Dooley, Damion M;
    • Duncan, William D;
    • Harris, Nomi L;
    • Haendel, Melissa A;
    • Lewis, Suzanna E;
    • Natale, Darren A;
    • Osumi-Sutherland, David;
    • Ruttenberg, Alan;
    • Schriml, Lynn M;
    • Smith, Barry;
    • Stoeckert Jr., Christian J
    Publication type:
    Article
    16
    17
    18

    Expression Atlas update: insights from sequencing data at both bulk and single cell level.

    Published in:
    Nucleic Acids Research, 2024, v. 52, n. D1, p. D107, doi. 10.1093/nar/gkad1021
    By:
    • George, Nancy;
    • Fexova, Silvie;
    • Fuentes, Alfonso Munoz;
    • Madrigal, Pedro;
    • Bi, Yalan;
    • Iqbal, Haider;
    • Kumbham, Upendra;
    • Nolte, Nadja Francesca;
    • Zhao, Lingyun;
    • Thanki, Anil S;
    • Yu, Iris D;
    • Marugan Calles, Jose C;
    • Erdos, Karoly;
    • Vilmovsky, Liora;
    • Kurri, Sandeep R;
    • Vathrakokoili-Pournara, Anna;
    • Osumi-Sutherland, David;
    • Prakash, Ananth;
    • Wang, Shengbo;
    • Tello-Ruiz, Marcela K
    Publication type:
    Article
    19

    NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource.

    Published in:
    Nucleic Acids Research, 2023, v. 51, n. D1, p. D977, doi. 10.1093/nar/gkac1010
    By:
    • Sollis, Elliot;
    • Mosaku, Abayomi;
    • Abid, Ala;
    • Buniello, Annalisa;
    • Cerezo, Maria;
    • Gil, Laurent;
    • Groza, Tudor;
    • Güneş, Osman;
    • Hall, Peggy;
    • Hayhurst, James;
    • Ibrahim, Arwa;
    • Ji, Yue;
    • John, Sajo;
    • Lewis, Elizabeth;
    • MacArthur, Jacqueline A L;
    • McMahon, Aoife;
    • Osumi-Sutherland, David;
    • Panoutsopoulou, Kalliope;
    • Pendlington, Zoë;
    • Ramachandran, Santhi
    Publication type:
    Article
    20

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

    Published in:
    Nucleic Acids Research, 2019, v. 47, n. D1, p. D1018, doi. 10.1093/nar/gky1105
    By:
    • Köhler, Sebastian;
    • Carmody, Leigh;
    • Vasilevsky, Nicole;
    • Jacobsen, Julius O B;
    • Danis, Daniel;
    • Gourdine, Jean-Philippe;
    • Gargano, Michael;
    • Harris, Nomi L;
    • Matentzoglu, Nicolas;
    • McMurry, Julie A;
    • Osumi-Sutherland, David;
    • Cipriani, Valentina;
    • Balhoff, James P;
    • Conlin, Tom;
    • Blau, Hannah;
    • Baynam, Gareth;
    • Palmer, Richard;
    • Gratian, Dylan;
    • Dawkins, Hugh;
    • Segal, Michael
    Publication type:
    Article
    21

    Bacterial Virus Ontology; Coordinating across Databases.

    Published in:
    Viruses (1999-4915), 2017, v. 9, n. 6, p. 126, doi. 10.3390/v9060126
    By:
    • Hulo, Chantal;
    • Masson, Patrick;
    • Toussaint, Ariane;
    • Osumi-Sutherland, David;
    • de Castro, Edouard;
    • Auchincloss, Andrea H.;
    • Poux, Sylvain;
    • Bougueleret, Lydie;
    • Xenarios, Ioannis;
    • Le Mercier, Philippe
    Publication type:
    Article
    22

    The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.

    Published in:
    BMC Bioinformatics, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s12859-022-04636-8
    By:
    • 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.;
    • Ponferrada, Virgilio;
    • Wang, Dong Zhuo;
    • Kim, Eugene;
    • Agalakov, Sergei;
    • Arshinoff, Bradley I.;
    • Karimi, Kamran;
    • Vize, Peter D.;
    • Zorn, Aaron M.
    Publication type:
    Article
    23
    24

    Virtual Fly Brain--An interactive atlas of the Drosophila nervous system.

    Published in:
    Frontiers in Physiology, 2023, v. 14, p. 1, doi. 10.3389/fphys.2023.1076533
    By:
    • Court, Robert;
    • Costa, Marta;
    • Pilgrim, Clare;
    • Millburn, Gillian;
    • Holmes, Alex;
    • McLachlan, Alex;
    • Larkin, Aoife;
    • Matentzoglu, Nicolas;
    • Kir, Huseyin;
    • Parkinson, Helen;
    • Brown, Nicolas H.;
    • O'Kane, Cahir J.;
    • Armstrong, J. Douglas;
    • Jefferis, Gregory S. X. E.;
    • Osumi-Sutherland, David
    Publication type:
    Article
    25

    A guide to the BRAIN Initiative Cell Census Network data ecosystem.

    Published in:
    PLoS Biology, 2023, v. 21, n. 6, p. 1, doi. 10.1371/journal.pbio.3002133
    By:
    • Hawrylycz, Michael;
    • Martone, Maryann E.;
    • Ascoli, Giorgio A.;
    • Bjaalie, Jan G.;
    • Dong, Hong-Wei;
    • Ghosh, Satrajit S.;
    • Gillis, Jesse;
    • Hertzano, Ronna;
    • Haynor, David R.;
    • Hof, Patrick R.;
    • Kim, Yongsoo;
    • Lein, Ed;
    • Liu, Yufeng;
    • Miller, Jeremy A.;
    • Mitra, Partha P.;
    • Mukamel, Eran;
    • Ng, Lydia;
    • Osumi-Sutherland, David;
    • Peng, Hanchuan;
    • Ray, Patrick L.
    Publication type:
    Article
    26

    Author Correction: Brain Data Standards - A method for building data-driven cell-type ontologies.

    Published in:
    2023
    By:
    • Tan, Shawn Zheng Kai;
    • Kir, Huseyin;
    • Aevermann, Brian D.;
    • Gillespie, Tom;
    • Harris, Nomi;
    • Hawrylycz, Michael J.;
    • Jorstad, Nikolas L.;
    • Lein, Ed S.;
    • Matentzoglu, Nicolas;
    • Miller, Jeremy A.;
    • Mollenkopf, Tyler S.;
    • Mungall, Christopher J.;
    • Ray, Patrick L.;
    • Sanchez, Raymond E. A.;
    • Staats, Brian;
    • Vermillion, Jim;
    • Yadav, Ambika;
    • Zhang, Yun;
    • Scheuermann, Richard H.;
    • Osumi-Sutherland, David
    Publication type:
    Correction Notice
    27
    28

    Brain Data Standards - A method for building data-driven cell-type ontologies.

    Published in:
    Scientific Data, 2023, v. 10, n. 1, p. 1, doi. 10.1038/s41597-022-01886-2
    By:
    • Tan, Shawn Zheng Kai;
    • Kir, Huseyin;
    • Aevermann, Brian D.;
    • Gillespie, Tom;
    • Harris, Nomi;
    • Hawrylycz, Michael J.;
    • Jorstad, Nikolas L.;
    • Lein, Ed S.;
    • Matentzoglu, Nicolas;
    • Miller, Jeremy A.;
    • Mollenkopf, Tyler S.;
    • Mungall, Christopher J.;
    • Ray, Patrick L.;
    • Sanchez, Raymond E. A.;
    • Staats, Brian;
    • Vermillion, Jim;
    • Yadav, Ambika;
    • Zhang, Yun;
    • Scheuermann, Richard H.;
    • Osumi-Sutherland, David
    Publication type:
    Article
    29

    FlyBase: enhancing Drosophila Gene Ontology annotations.

    Published in:
    Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D555
    By:
    • Tweedie, Susan;
    • Ashburner, Michael;
    • Falls, Kathleen;
    • Leyland, Paul;
    • McQuilton, Peter;
    • Marygold, Steven;
    • Millburn, Gillian;
    • Osumi-Sutherland, David;
    • Schroeder, Andrew;
    • Seal, Ruth;
    • Zhang, Haiyan
    Publication type:
    Article