Edinburgh Research Explorer

A strategy for building neuroanatomy ontologies.

Research output: Contribution to journalArticle

  • David Osumi-Sutherland
  • Simon Reeve
  • Christopher J. Mungall
  • Fabian Neuhaus
  • Alan Ruttenberg
  • Gregory S. X. E. Jefferis
  • J. Douglas Armstrong

Related Edinburgh Organisations

Open Access permissions

Open

Documents

  • Download as Adobe PDF

    Final published version, 305 KB, PDF document

    Licence: Creative Commons: Attribution Non-Commercial (CC-BY-NC)

Original languageEnglish
Pages (from-to)1262-1269
Number of pages8
JournalBioinformatics
Volume28
Issue number9
DOIs
Publication statusPublished - 2012

Abstract

Motivation: Advancing our understanding of how nervous systems work will require the ability to store and annotate 3D anatomical datasets, recording morphology, partonomy and connectivity at multiple levels of granularity from subcellular to gross anatomy. It will also require the ability to integrate this data with other datatypes including functional, genetic and electrophysiological data. The web ontology language OWL2 provides the means to solve many of these problems. Using it, one can rigorously define and relate classes of anatomical structure using multiple criteria. The resulting classes can be used to annotate datasets recording, for example, gene expression or electrophysiology. Reasoning software can be used to automate classification and error checking and to construct and answer sophisticated combinatorial queries. But for such queries to give consistent and biologically meaningful results, it is important
that both classes and the terms (relations) used to relate them are carefully defined.

Results: We formally define a set of relations for recording the spatial and connectivity relationships of neuron classes and brain regions in a broad range of species, from vertebrates to arthropods. We illustrate the utility of our approach via its application in the ontology that drives the Virtual Fly Brain web resource.

Availability and implementation: The relations we define are available from http://purl.obolibrary.org/obo/ro.owl. They are used in the Drosophila anatomy ontology (http://purl.obolibrary.org/obo/ fbbt/2011-09-06/), which drives the web resource http://www.virtualflybrain.org

    Research areas

  • dblp

Download statistics

No data available

ID: 22256387