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Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology

Hill, David P. and Berardini, Tanya Z. and Howe, Douglas G. and Van Auken, Kimberly M. (2010) Representing Ontogeny Through Ontology: A Developmental Biologist’s Guide to The Gene Ontology. Molecular Reproduction and Development, 77 (4). pp. 314-329. ISSN 1040-452X . PMCID PMC2830379. http://resolver.caltech.edu/CaltechAUTHORS:20100412-083317622

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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 GO that they can begin to think about how they might use the ontology efficiently and in the most powerful ways possible.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1002/mrd.21130DOIArticle
http://www3.interscience.wiley.com/journal/122686636/abstractPublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830379/PubMed CentralArticle
ORCID:
AuthorORCID
Van Auken, Kimberly M.0000-0002-1706-4196
Additional Information:© 2009 Wiley-Liss, Inc. Received 7 July 2009; Accepted 2 October 2009. Published online 17 November 2009. The authors wish to thank Monica McAndrews-Hill, Constance Smith and Judith Blake for critically reading the manuscript. DPH, KMVA, and TZB are supported by The GO Consortium grant HG002273 from the National Human Genome Research Institute (NHGRI) at the NIH to M. Ashburner, J. Blake, J.M. Cherry, and S. Lewis. TZB is also supported by grant DBI-0417062 from the NSF. KMVA is supported by grant #P41-HG02223 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health. DGH is supported by grant #P41 HG002659 from the National Human Genome Research Institute (NHGRI) at the United States National Institutes of Health.
Funders:
Funding AgencyGrant Number
NIHHG002273
NSFDBI-0417062
NIHP41-HG02223
NIHP41-HG002659
National Human Genome Research InstituteUNSPECIFIED
PubMed Central ID:PMC2830379
Record Number:CaltechAUTHORS:20100412-083317622
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20100412-083317622
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:17925
Collection:CaltechAUTHORS
Deposited By: Ruth Sustaita
Deposited On:12 Apr 2010 15:58
Last Modified:30 Oct 2017 20:23

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