Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.
Representing ontogeny through ontology: a developmental biologist's guide to the gene ontology.
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DOI：
10.1002/mrd.21130
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发表时间：
2010-04
影响因子：
2.5
通讯作者：
Van Auken, Kimberly M.
中科院分区：
文献类型：
--
作者：
Hill, David P.;Berardini, Tanya Z.;Howe, Douglas G.;Van Auken, Kimberly M.
发育生物学，像许多其他领域的生物学，经历了一个戏剧性的转变，从发展过程的角度来看。我们现在不再关注少数基因或功能性RNA的作用，而是考虑大型功能性基因网络的相互作用，并研究这些复杂的系统如何协调有机体从配子到成年的展开。发育生物学家开始意识到，要理解这种规模的个体发育，需要利用计算方法来捕获、存储和表示我们所拥有的关于潜在过程的知识。本文综述了基因本体论在发育生物学研究中的应用。我们描述了GO的组织和结构，并说明了我们使用它来捕捉当前对许多常见发展过程的理解的一些方法。我们还讨论了如何使用GO的基因产物注释已被用来询问和回答各种模型发展系统中的发展问题。我们提供了建议，如何GO可能会被用于更强大的方式来解决有关发展的问题。我们的目标是为发育生物学家提供足够的关于GO的背景知识，使他们能够开始思考如何有效地以最强大的方式使用本体。
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.
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影响因子：
5.8
作者：
Al-Shahrour, F;Díaz-Uriarte, R;Dopazo, J
通讯作者：
Dopazo, J
DOI：
10.1093/bioinformatics/btn615
发表时间：
2009-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Carbon S;Ireland A;Mungall CJ;Shu S;Marshall B;Lewis S;AmiGO Hub;Web Presence Working Group
通讯作者：
Web Presence Working Group
DOI：
10.1073/pnas.0806007105
发表时间：
2008-12-23
影响因子：
11.1
作者：
Davidson, Eric H.;Levine, Michael S.
通讯作者：
Levine, Michael S.
影响因子：
3.6
作者：
Choi, Youngsok;Qin, Yingying;Rajkovic, Aleksandar
通讯作者：
Rajkovic, Aleksandar
DOI：
10.1152/ajpgi.00454.2004
发表时间：
2005-05-01
影响因子：
4.5
作者：
Agbemafle, BM;Oesterreicher, TJ;Henning, SJ
通讯作者：
Henning, SJ