COnto-Diff: generation of complex evolution mappings for life science ontologies
COnto-Diff: generation of complex evolution mappings for life science ontologies
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DOI：
10.1016/j.jbi.2012.04.009
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发表时间：
2013-02-01
影响因子：
4.5
通讯作者：
Rahm, Erhard
中科院分区：
文献类型：
--
作者：
Hartung, Michael;Gross, Anika;Rahm, Erhard
生命科学本体经常发展以满足新的要求或更好地反映当前的领域知识。大型且复杂的本体的开发和改编通常由多个策展人协作执行。为了有效管理本体的演化，识别本体版本之间的差异（Diff）至关重要。这样的 Diff 支持协作管理中更改的同步、依赖数据（例如注释）的适应以及本体版本管理。我们提出了一种新颖的方法 COnto-Diff 来确定本体的给定版本之间的表达性和可逆差异演化映射。我们的方法首先匹配本体版本并确定由基本更改操作（插入/更新/删除）组成的初始演化映射。为了在语义上丰富演化映射，我们采用基于规则的方法将基本更改操作转换为较小的一组更复杂的更改操作，例如合并、拆分或整个子图的更改。所提出的算法可以以不同的方式定制，以满足不同本体和应用场景的要求。我们评估了针对大型生命科学本体（包括基因本体和 NCI 同义词库）所提出的方法，并将其与 PromptDiff 进行比较。我们进一步展示了如何将 Diff 结果用于协作管理中的版本管理和注释迁移。 (C) 2012 Elsevier Inc. 保留所有权利。
Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation. (C) 2012 Elsevier Inc. All rights reserved.