David Osumi-Sutherland

David Osumi-Sutherland

Ontology Developer (Gene Ontology) - Parkinson team: Samples, Phenotypes and Ontologies

David is an Ontology Developer in EMBL-EBI's Samples, Phenotypes and Ontologies team and an expert in semantic modelling of biology. He joined in 2013 as a developer of the Gene Ontology (GO), co-ordinating a successful application for Wellcome Trust funding to support the Virtual Fly Brain (VFB) project. David worked on refactoring the GO ontology through the development of design patterns, and has led collaborative projects with Roche and the Broad Institute. He develops and extends the semantic schema and query system for VFB and maintains its knowledge base of annotated images. Prior to joining EMBL-EBI he worked as an ontology developer and curator for FlyBase, as a science journalist and as a postdoctoral researcher in developmental genetics. David obtained his PhD in developmental biology from the University of Warwick, and holds an MSc in Science Communication from Imperial College London.

ORCID iD: 0000-0002-7073-9172

Tel:+ 44 (0) 1223 494 144 / Fax:+ 44 (0) 1223 494 468

Publications

2016

Guidelines for the functional annotation of microRNAs using the Gene Ontology.
Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.
RNA (New York, N.Y.) Volume 22 (2016) p.667-676

2015

Finding our way through phenotypes.
Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, Balhoff JP, Blackburn DC, Blake JA, Burleigh JG, Chanet B, Cooper LD, Courtot M, Csösz S, Cui H, Dahdul W, Das S, Dececchi TA, Dettai A, Diogo R, Druzinsky RE, Dumontier M, Franz NM, Friedrich F, Gkoutos GV, Haendel M, Harmon LJ, Hayamizu TF, He Y, Hines HM, Ibrahim N, Jackson LM, Jaiswal P, James-Zorn C, Köhler S, Lecointre G, Lapp H, Lawrence CJ, Le Novère N, Lundberg JG, Macklin J, Mast AR, Midford PE, Mikó I, Mungall CJ, Oellrich A, Osumi-Sutherland D, Parkinson H, Ramírez MJ, Richter S, Robinson PN, Ruttenberg A, Schulz KS, Segerdell E, Seltmann KC, Sharkey MJ, Smith AD, Smith B, Specht CD, Squires RB, Thacker RW, Thessen A, Fernandez-Triana J, Vihinen M, Vize PD, Vogt L, Wall CE, Walls RL, Westerfeld M, Wharton RA, Wirkner CS, Woolley JB, Yoder MJ, Zorn AM, Mabee P.
PLoS biology Volume 13 (2015) p.e1002033

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.
Foulger RE, Osumi-Sutherland D, McIntosh BK, Hulo C, Masson P, Poux S, Le Mercier P, Lomax J.
BMC microbiology Volume 15 (2015) p.146

Gene Ontology Consortium: going forward.
Gene Ontology Consortium.
Nucleic acids research Volume 43 (2015) p.D1049-56

2014

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.
Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA.
Journal of biomedical semantics Volume 5 (2014) p.34

TermGenie - a web-application for pattern-based ontology class generation.
Dietze H, Berardini TZ, Foulger RE, Hill DP, Lomax J, Osumi-Sutherland D, Roncaglia P, Mungall CJ.
Journal of biomedical semantics Volume 5 (2014) p.48

2013

FlyBase: improvements to the bibliography.
Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ, FlyBase consortium.
Nucleic acids research Volume 41 (2013) p.D751-7

The Drosophila phenotype ontology.
Osumi-Sutherland D, Marygold SJ, Millburn GH, McQuilton PA, Ponting L, Stefancsik R, Falls K, Brown NH, Gkoutos GV.
Journal of biomedical semantics Volume 4 (2013) p.30

Systematic analysis of experimental phenotype data reveals gene functions.
Hoehndorf R, Hardy NW, Osumi-Sutherland D, Tweedie S, Schofield PN, Gkoutos GV.
PloS one Volume 8 (2013) p.e60847

2012

FlyBase 101--the basics of navigating FlyBase.
McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium.
Nucleic acids research Volume 40 (2012) p.D706-14

Directly e-mailing authors of newly published papers encourages community curation.
Bunt SM, Grumbling GB, Field HI, Marygold SJ, Brown NH, Millburn GH, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas024

A strategy for building neuroanatomy ontologies.
Osumi-Sutherland D, Reeve S, Mungall CJ, Neuhaus F, Ruttenberg A, Jefferis GS, Armstrong JD.
Bioinformatics (Oxford, England) Volume 28 (2012) p.1262-1269

The Virtual Fly Brain browser and query interface.
Milyaev N, Osumi-Sutherland D, Reeve S, Burton N, Baldock RA, Armstrong JD.
Bioinformatics (Oxford, England) Volume 28 (2012) p.411-415

Opportunities for text mining in the FlyBase genetic literature curation workflow.
McQuilton P, FlyBase Consortium.
Database : the journal of biological databases and curation Volume 2012 (2012) p.bas039

2009

FlyBase: enhancing Drosophila Gene Ontology annotations.
Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H, FlyBase Consortium.
Nucleic acids research Volume 37 (2009) p.D555-9

2004

Sick veterans pin hopes on Gulf War inquiry.
Osumi-Sutherland D.
Nature Volume 430 (2004) p.821

Lab chiefs fear European rules will cost postdoc jobs.
Osumi-Sutherland D.
Nature Volume 431 (2004) p.6

Services

GO