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首页> 外文期刊>Journal of Biomedical Semantics >Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL
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Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL

机译：逻辑基因本体注释（GOAL）：使用OWL探索基因本体注释

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Motivation Ontologies such as the Gene Ontology (GO) and their use in annotations make cross species comparisons of genes possible, along with a wide range of other analytical activities. The bio-ontologies community, in particular the Open Biomedical Ontologies (OBO) community, have provided many other ontologies and an increasingly large volume of annotations of gene products that can be exploited in query and analysis. As many annotations with different ontologies centre upon gene products, there is a possibility to explore gene products through multiple ontological perspectives at the same time. Questions could be asked that link a gene product’s function, process, cellular location, phenotype and disease. Current tools, such as AmiGO, allow exploration of genes based on their GO annotations, but not through multiple ontological perspectives. In addition, the semantics of these ontology’s representations should be able to, through automated reasoning, afford richer query opportunities of the gene product annotations than is currently possible. Results To do this multi-perspective, richer querying of gene product annotations, we have created the Logical Gene Ontology , or GOAL ontology, in OWL that combines the Gene Ontology , Human Disease Ontology and the Mammalian Phenotype Ontology, together with classes that represent the annotations with these ontologies for mouse gene products. Each mouse gene product is represented as a class, with the appropriate relationships to the GO aspects, phenotype and disease with which it has been annotated. We then use defined classes to query these protein classes through automated reasoning, and to build a complex hierarchy of gene products. We have presented this through a Web interface that allows arbitrary queries to be constructed and the results displayed. Conclusion This standard use of OWL affords a rich interaction with Gene Ontology , Human Disease Ontology and Mammalian Phenotype Ontology annotations for the mouse, to give a fine partitioning of the gene products in the GOAL ontology. OWL in combination with automated reasoning can be effectively used to query across ontologies to ask biologically rich questions. We have demonstrated that automated reasoning can be used to deliver practical on-line querying support for the ontology annotations available for the mouse. Availability The GOAL Web page is to be found at http://owl.cs.manchester.ac.uk/goal .
机译：诸如基因本体论（GO）之类的动机本体论及其在注释中的使用使基因的跨物种比较以及广泛的其他分析活动成为可能。生物本体论社区，特别是开放式生物医学本体论（OBO）社区，提供了许多其他本体论以及越来越多的基因产品注释，可用于查询和分析。由于许多具有不同本体论的注释都集中在基因产物上，因此有可能同时从多个本体论角度探索基因产物。可能会提出将基因产物的功能，过程，细胞位置，表型和疾病联系起来的问题。当前的工具，例如AmiGO，允许基于其GO注释探索基因，但不能通过多个本体论视角进行探索。此外，这些本体表示形式的语义应该能够通过自动推理提供比当前可能更多的基因产物注释查询机会。结果为了对基因产物注释进行这种多角度，更丰富的查询，我们在OWL中创建了逻辑基因本体论（即GOAL本体论），该本体论将基因本体论，人类疾病本体论和哺乳动物表型本体论结合在一起，并代表了这些本体论的注释用于小鼠基因产品。每个小鼠基因产物都被表示为一类，并与GO方面，表型和所注释的疾病具有适当的关系。然后，我们使用定义的类通过自动推理查询这些蛋白质类，并构建复杂的基因产物层次。我们已经通过一个Web界面展示了这一点，该界面允许构造任意查询并显示结果。结论OWL的这种标准用法可与小鼠的基因本体论，人类疾病本体论和哺乳动物表型本体论注释进行丰富的交互，从而在GOAL本体论中对基因产物进行精细划分。 OWL与自动推理相结合可以有效地用于跨本体查询，以提出生物学上丰富的问题​​。我们已经证明自动推理可以用于为鼠标可用的本体注释提供实用的在线查询支持。可用性GOAL网页位于http://owl.cs.manchester.ac.uk/goal。

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