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Predicting the Extension of Biomedical Ontologies

机译:预测生物医学本体论的扩展

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Developing and extending a biomedical ontology is a very demanding task that can never be considered complete given our ever-evolving understanding of the life sciences. Extension in particular can benefit from the automation of some of its steps, thus releasing experts to focus on harder tasks. Here we present a strategy to support the automation of change capturing within ontology extension where the need for new concepts or relations is identified. Our strategy is based on predicting areas of an ontology that will undergo extension in a future version by applying supervised learning over features of previous ontology versions. We used the Gene Ontology as our test bed and obtained encouraging results with average f-measure reaching 0.79 for a subset of biological process terms. Our strategy was also able to outperform state of the art change capturing methods. In addition we have identified several issues concerning prediction of ontology evolution, and have delineated a general framework for ontology extension prediction. Our strategy can be applied to any biomedical ontology with versioning, to help focus either manual or semi-automated extension methods on areas of the ontology that need extension.
机译:开发和扩展生物医学本体是一项非常艰巨的任务,鉴于我们对生命科学的不断发展的理解,它永远不能被认为是完整的。特别是扩展可以从某些步骤的自动化中受益,从而使专家可以将精力集中在更艰巨的任务上。在这里,我们提出了一种策略,以支持在本体扩展中更改捕获的自动化,其中可以识别对新概念或新关系的需求。我们的策略基于通过在先前本体版本的功能上应用监督学习来预测将在将来版本中扩展的本体领域。我们使用基因本体论作为测试平台,并获得了令人鼓舞的结果,其中一部分生物过程项的平均f值达到0.79。我们的策略还能够胜过最新的变更捕获方法。另外,我们已经确定了与本体演化预测有关的几个问题,并勾勒出本体扩展预测的一般框架。我们的策略可以应用于带有版本控制的任何生物医学本体,以帮助将手动或半自动扩展方法集中在需要扩展的本体领域。

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