Literature DB >> 29724079

Virtual Fly Brain - Using OWL to support the mapping and genetic dissection of the Drosophila brain.

David Osumi-Sutherland1, Marta Costa2, Robert Court3, Cahir J O'Kane2.   

Abstract

A massive effort is underway to map the structure of the Drosophila nervous system and to genetically dissect its function. Virtual Fly Brain (VFB; http://www.virtualflybrain.org) is a popular, OWL-based resource providing neuroinformatics support for this work. It provides: curated descriptions of brain regions and neurons; queries for neurons based on their relationship to gross neuroanatomy; and queries for reagents based on their expression patterns. Query results are enriched by OWL axiomatisation allowing basic mereological reasoning. To keep reasoning fast and scalable, VFB confines expressiveness to the EL profile of OWL. As a result, VFB does not provide queries involving negation, despite there being both demand and sufficient information to support them. Recent developments in reasoning technology may make more expressive queries practical. Here we present design patterns to support queries with negation that are compatible with the mereological reasoning used in VFB.

Entities:  

Keywords:  DL reasoning; OWL; closure axioms; negation; neurobiology; neuron; ontology design pattern

Year:  2014        PMID： 29724079      PMCID： PMC5924869     

Source DB:  PubMed          Journal:  CEUR Workshop Proc        ISSN： 1613-0073


  7 in total

1.  The Virtual Fly Brain browser and query interface.

Authors:  Nestor Milyaev; David Osumi-Sutherland; Simon Reeve; Nicholas Burton; Richard A Baldock; J Douglas Armstrong
Journal:  Bioinformatics       Date:  2011-12-16       Impact factor: 6.937

2.  A strategy for building neuroanatomy ontologies.

Authors:  David Osumi-Sutherland; Simon Reeve; Christopher J Mungall; Fabian Neuhaus; Alan Ruttenberg; Gregory S X E Jefferis; J Douglas Armstrong
Journal:  Bioinformatics       Date:  2012-03-07       Impact factor: 6.937

3.  Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution.

Authors:  Ann-Shyn Chiang; Chih-Yung Lin; Chao-Chun Chuang; Hsiu-Ming Chang; Chang-Huain Hsieh; Chang-Wei Yeh; Chi-Tin Shih; Jian-Jheng Wu; Guo-Tzau Wang; Yung-Chang Chen; Cheng-Chi Wu; Guan-Yu Chen; Yu-Tai Ching; Ping-Chang Lee; Chih-Yang Lin; Hui-Hao Lin; Chia-Chou Wu; Hao-Wei Hsu; Yun-Ann Huang; Jing-Yi Chen; Hsin-Jung Chiang; Chun-Fang Lu; Ru-Fen Ni; Chao-Yuan Yeh; Jenn-Kang Hwang
Journal:  Curr Biol       Date:  2010-12-02       Impact factor: 10.834

Review 4.  Power tools for gene expression and clonal analysis in Drosophila.

Authors:  Alberto del Valle Rodríguez; Dominic Didiano; Claude Desplan
Journal:  Nat Methods       Date:  2011-12-28       Impact factor: 28.547

5.  A systematic nomenclature for the insect brain.

Authors:  Kei Ito; Kazunori Shinomiya; Masayoshi Ito; J Douglas Armstrong; George Boyan; Volker Hartenstein; Steffen Harzsch; Martin Heisenberg; Uwe Homberg; Arnim Jenett; Haig Keshishian; Linda L Restifo; Wolfgang Rössler; Julie H Simpson; Nicholas J Strausfeld; Roland Strauss; Leslie B Vosshall
Journal:  Neuron       Date:  2014-02-19       Impact factor: 17.173

6.  A GAL4-driver line resource for Drosophila neurobiology.

Authors:  Arnim Jenett; Gerald M Rubin; Teri-T B Ngo; David Shepherd; Christine Murphy; Heather Dionne; Barret D Pfeiffer; Amanda Cavallaro; Donald Hall; Jennifer Jeter; Nirmala Iyer; Dona Fetter; Joanna H Hausenfluck; Hanchuan Peng; Eric T Trautman; Robert R Svirskas; Eugene W Myers; Zbigniew R Iwinski; Yoshinori Aso; Gina M DePasquale; Adrianne Enos; Phuson Hulamm; Shing Chun Benny Lam; Hsing-Hsi Li; Todd R Laverty; Fuhui Long; Lei Qu; Sean D Murphy; Konrad Rokicki; Todd Safford; Kshiti Shaw; Julie H Simpson; Allison Sowell; Susana Tae; Yang Yu; Christopher T Zugates
Journal:  Cell Rep       Date:  2012-10-11       Impact factor: 9.423

7.  The Drosophila anatomy ontology.

Authors:  Marta Costa; Simon Reeve; Gary Grumbling; David Osumi-Sutherland
Journal:  J Biomed Semantics       Date:  2013-10-18
  7 in total
  3 in total

Review 1.  Cell type ontologies of the Human Cell Atlas.

Authors:  David Osumi-Sutherland; Chuan Xu; Maria Keays; Adam P Levine; Peter V Kharchenko; Aviv Regev; Ed Lein; Sarah A Teichmann
Journal:  Nat Cell Biol       Date:  2021-11-08       Impact factor: 28.824

2.  Two Brain Pathways Initiate Distinct Forward Walking Programs in Drosophila.

Authors:  Salil S Bidaye; Meghan Laturney; Amy K Chang; Yuejiang Liu; Till Bockemühl; Ansgar Büschges; Kristin Scott
Journal:  Neuron       Date:  2020-08-20       Impact factor: 18.688

3.  Octopaminergic neurons have multiple targets in Drosophila larval mushroom body calyx and can modulate behavioral odor discrimination.

Authors:  J Y Hilary Wong; Bo Angela Wan; Tom Bland; Marcella Montagnese; Alex D McLachlan; Cahir J O'Kane; Shuo Wei Zhang; Liria M Masuda-Nakagawa
Journal:  Learn Mem       Date:  2021-01-15       Impact factor: 2.460
  3 in total

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