Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.

Molecular Reproduction and Development
David P HillKimberly M Van Auken

Abstract

Developmental biology, like many other areas of biology, has undergone a dramatic shift in the perspective from which developmental processes are viewed. Instead of focusing on the actions of a handful of genes or functional RNAs, we now consider the interactions of large functional gene networks and study how these complex systems orchestrate the unfolding of an organism, from gametes to adult. Developmental biologists are beginning to realize that understanding ontogeny on this scale requires the utilization of computational methods to capture, store and represent the knowledge we have about the underlying processes. Here we review the use of the Gene Ontology (GO) to study developmental biology. We describe the organization and structure of the GO and illustrate some of the ways we use it to capture the current understanding of many common developmental processes. We also discuss ways in which gene product annotations using the GO have been used to ask and answer developmental questions in a variety of model developmental systems. We provide suggestions as to how the GO might be used in more powerful ways to address questions about development. Our goal is to provide developmental biologists with enough background about the ...Continue Reading

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Citations

Jul 30, 2014·Database : the Journal of Biological Databases and Curation·Kimberly Van AukenZhiyong Lu
Aug 27, 2014·Database : the Journal of Biological Databases and Curation·Yuqing MaoZhiyong Lu
Dec 5, 2014·Molecular Genetics and Genomics : MGG·Jiantao ChenChenbo Ji
Nov 5, 2011·Risk Analysis : an Official Publication of the Society for Risk Analysis·Chiming GuoBo Guo
Jun 17, 2014·Journal of Forensic Sciences·Nickson M Karie, Hein S Venter
Oct 4, 2017·Journal of Biomedical Semantics·Claudia MazoEnrique Alegre
May 26, 2020·Risk Analysis : an Official Publication of the Society for Risk Analysis·Tiancheng CaoLiyu Peng
Dec 12, 2012·Journal of Tissue Engineering and Regenerative Medicine·Noor Hayaty Abu KasimZeti Adura Che Ab Aziz
Feb 4, 2014·The Journal of Heredity·Tomás Morán, Antonio Fontdevila
Sep 23, 2014·Neuroinformatics·Bénédicte BatrancourtGilles Kassel
Oct 9, 2015·Journal of Biomedical Semantics·Yu LinYongqun He
Mar 23, 2011·Developmental Biology·Varsha K KhodiyarRuth C Lovering

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