The Drosophila anatomy ontology.
The Drosophila anatomy ontology.
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DOI：
10.1186/2041-1480-4-32
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发表时间：
2013-10-18
影响因子：
1.9
通讯作者：
Osumi-Sutherland D
中科院分区：
文献类型：
--
作者：
Costa M;Reeve S;Grumbling G;Osumi-Sutherland D
解剖本体是解剖结构的可查询分类。它们提供了一种广泛使用的方法，以人类可读和可编程访问的形式标准化表型和表达的注释。它们还经常用于以生物学上有意义的方式对注释进行分组。准确的注释需要对术语进行清晰的文本定义，最好附有图像。准确的分组和富有成效的程序化使用需要高质量的正式定义，这些定义可用于自动分类和检查错误。果蝇解剖本体（DAO）由8000多个类组成，涵盖了广泛的果蝇解剖。它已被广泛用于各种资源的注释，但直到最近，它的形式化程度很差，并且几乎没有文本定义。我们已经将DAO转换为具有丰富的正式和文本定义的本体，其中大多数分类是自动化的，并且广泛的错误检查确保了质量。在这里，我们概述了DAO的内容、在其形式化中使用的模式以及它的各种用途。作为本文所述工作的结果，DAO为果蝇的野生型解剖结构提供了高质量、可查询的参考资料，并提供了一组术语来注释与该解剖结构相关的数据。广泛的、充分引用的文本定义使其成为可靠和有用的参考，并确保在注释中准确使用。广泛使用形式公理可以使大部分分类自动化，并使用一致性检查来消除错误。这种形式化的增加大大提高了分类的完整性和准确性。正式和非正式定义的广泛使用使得本体的进一步开发具有可持续性和可扩展性。DAO中使用的形式化模式可能对其他解剖本体的开发人员有用。
Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmatically accessible forms. They are also frequently used to group annotations in biologically meaningful ways. Accurate annotation requires clear textual definitions for terms, ideally accompanied by images. Accurate grouping and fruitful programmatic usage requires high-quality formal definitions that can be used to automate classification and check for errors. The Drosophila anatomy ontology (DAO) consists of over 8000 classes with broad coverage of Drosophila anatomy. It has been used extensively for annotation by a range of resources, but until recently it was poorly formalised and had few textual definitions. We have transformed the DAO into an ontology rich in formal and textual definitions in which the majority of classifications are automated and extensive error checking ensures quality. Here we present an overview of the content of the DAO, the patterns used in its formalisation, and the various uses it has been put to. As a result of the work described here, the DAO provides a high-quality, queryable reference for the wild-type anatomy of Drosophila melanogaster and a set of terms to annotate data related to that anatomy. Extensive, well referenced textual definitions make it both a reliable and useful reference and ensure accurate use in annotation. Wide use of formal axioms allows a large proportion of classification to be automated and the use of consistency checking to eliminate errors. This increased formalisation has resulted in significant improvements to the completeness and accuracy of classification. The broad use of both formal and informal definitions make further development of the ontology sustainable and scalable. The patterns of formalisation used in the DAO are likely to be useful to developers of other anatomy ontologies.
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影响因子：
14.9
作者：
Grumbling G;Strelets V
通讯作者：
Strelets V
影响因子：
14.9
作者：
Gallo SM;Gerrard DT;Miner D;Simich M;Des Soye B;Bergman CM;Halfon MS
通讯作者：
Halfon MS
影响因子：
3
作者：
Deegan (nee Clark), Jennifer I.;Dimmer, Emily C.;Mungall, Christopher J.
通讯作者：
Mungall, Christopher J.
影响因子：
9.2
作者：
Chiang, Ann-Shyn;Lin, Chih-Yung;Hwang, Jenn-Kang
通讯作者：
Hwang, Jenn-Kang
影响因子：
3
作者：
Jupp S;Horridge M;Iannone L;Klein J;Owen S;Schanstra J;Wolstencroft K;Stevens R
通讯作者：
Stevens R