Representing Ontogeny Through Ontology: A Developmental Biologist's Guide to The Gene Ontology
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.
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.Attached Files
Accepted Version - nihms-163751.pdf
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Additional details
- PMCID
- PMC2830379
- Eprint ID
- 17925
- Resolver ID
- CaltechAUTHORS:20100412-083317622
- HG002273
- NIH
- DBI-0417062
- NSF
- P41-HG02223
- NIH
- P41-HG002659
- NIH
- National Human Genome Research Institute
- Created
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2010-04-12Created from EPrint's datestamp field
- Updated
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2021-11-08Created from EPrint's last_modified field