Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development
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DOI：
10.1186/1471-2105-11-530
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发表时间：
2010-10-25
影响因子：
3
通讯作者：
Mungall, Christopher J.
中科院分区：
文献类型：
--
作者：
Deegan (nee Clark), Jennifer I.;Dimmer, Emily C.;Mungall, Christopher J.
背景资料：基因本体论项目支持根据基因产物的作用位置、它们执行的分子功能以及它们参与的过程对基因产物进行分类。虽然本体论是有意开发的分类中立，并涵盖所有物种，但在某些分支中存在固有的分类特异性。例如，“哺乳”过程是哺乳动物特有的，而“哺乳”位置是真核生物特有的。缺乏一个明确的形式化这些约束可能会导致错误和不一致的自动和手动annotation.Results：我们已经正式的分类约束隐含在一些GO类，并指定这些在本体的各个层次。我们还开发了一个推理系统，可用于检查违反这些约束的注释。结合推理系统使用的约束，我们已经检测到并删除注释中的错误，并改进了结构的ontology.Conclusions：检测不一致的分类特异性，使本体，注释和形式化的约束逐步改善。这正在逐步提高我们的数据质量。完整的系统可供下载，新的约束或对约束的建议更改可在线提交，网址为https://sourceforge.net/tracker/? tid =605890&group_id=36855。
Background: The Gene Ontology project supports categorization of gene products according to their location of action, the molecular functions that they carry out, and the processes that they are involved in. Although the ontologies are intentionally developed to be taxon neutral, and to cover all species, there are inherent taxon specificities in some branches. For example, the process 'lactation' is specific to mammals and the location 'mitochondrion' is specific to eukaryotes. The lack of an explicit formalization of these constraints can lead to errors and inconsistencies in automated and manual annotation.Results: We have formalized the taxonomic constraints implicit in some GO classes, and specified these at various levels in the ontology. We have also developed an inference system that can be used to check for violations of these constraints in annotations. Using the constraints in conjunction with the inference system, we have detected and removed errors in annotations and improved the structure of the ontology.Conclusions: Detection of inconsistencies in taxon-specificity enables gradual improvement of the ontologies, the annotations, and the formalized constraints. This is progressively improving the quality of our data. The full system is available for download, and new constraints or proposed changes to constraints can be submitted online at https://sourceforge.net/tracker/?atid=605890&group_id=36855.