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监测基因本体论的进化方面以提高可预测性和可用性。

Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability.

作者信息

Park Jong C, Kim Tak-eun, Park Jinah

机构信息

Computer Science Division, KAIST, 373-1 Guseong-dong, Yuseong-gu, Daejeon, 305-701, South Korea.

出版信息

BMC Bioinformatics. 2008 Apr 11;9 Suppl 3(Suppl 3):S7. doi: 10.1186/1471-2105-9-S3-S7.

DOI:10.1186/1471-2105-9-S3-S7
PMID:18426552
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2349298/
Abstract

BACKGROUND

Much effort is currently made to develop the Gene Ontology (GO). Due to the dynamic nature of information it addresses, GO undergoes constant updates whose results are released at regular intervals as separate versions. Although there are a large number of computational tools to aid the development of GO, they are operating on a particular version of GO, making it difficult for GO curators to anticipate the full impact of particular changes along the time axis on a larger scale. We present a method for tapping into such an evolutionary aspect of GO, by making it possible to keep track of important temporal changes to any of the terms and relations of GO and by consequently making it possible to recognize associated trends.

RESULTS

We have developed visualization methods for viewing the changes between two different versions of GO by constructing a colour-coded layered graph. The graph shows both versions of GO with highlights to those GO terms that are added, removed and modified between the two versions. Focusing on a specific GO term or terms of interest over a period, we demonstrate the utility of our system that can be used to make useful hypotheses about the cause of the evolution and to provide new insights into more complex changes.

CONCLUSIONS

GO undergoes fast evolutionary changes. A snapshot of GO, as presented by each version of GO alone, overlooks such evolutionary aspects, and consequently limits the utilities of GO. The method that highlights the differences of consecutive versions or two different versions of an evolving ontology with colour-coding enhances the utility of GO for users as well as for developers. To the best of our knowledge, this is the first proposal to visualize the evolutionary aspect of GO.

摘要

背景

目前人们在基因本体论（Gene Ontology，GO）的开发上投入了大量精力。由于它所涉及信息的动态性质，GO会不断更新，其更新结果会定期作为单独版本发布。尽管有大量计算工具辅助GO的开发，但它们都是基于GO的特定版本运行，这使得GO的注释者难以大规模地预测特定时间轴上特定变化的全面影响。我们提出了一种方法来利用GO的这种进化特性，通过跟踪GO的任何术语和关系的重要时间变化，并因此能够识别相关趋势。

结果

我们开发了可视化方法，通过构建一个颜色编码的分层图来查看GO两个不同版本之间的变化。该图展示了GO的两个版本，并突出显示了两个版本之间添加、删除和修改的那些GO术语。在一段时间内关注一个或多个特定的GO术语，我们展示了我们系统的实用性，它可用于对进化原因做出有用的假设，并为更复杂的变化提供新的见解。

结论

GO经历快速的进化变化。仅由GO的每个版本呈现的GO快照忽略了这种进化特性，因此限制了GO的实用性。用颜色编码突出显示连续版本或一个不断发展的本体的两个不同版本之间差异的方法，增强了GO对用户和开发者的实用性。据我们所知，这是第一个可视化GO进化特性的提议。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/7482d438860b/1471-2105-9-S3-S7-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/6854b157fb0e/1471-2105-9-S3-S7-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/428ed3e03d68/1471-2105-9-S3-S7-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/d59df7d46c97/1471-2105-9-S3-S7-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/d05940099b6d/1471-2105-9-S3-S7-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/ab695fb8f564/1471-2105-9-S3-S7-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/7482d438860b/1471-2105-9-S3-S7-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/6854b157fb0e/1471-2105-9-S3-S7-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/428ed3e03d68/1471-2105-9-S3-S7-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/d59df7d46c97/1471-2105-9-S3-S7-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/d05940099b6d/1471-2105-9-S3-S7-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/ab695fb8f564/1471-2105-9-S3-S7-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/05bc/2349298/7482d438860b/1471-2105-9-S3-S7-6.jpg

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