GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.
GOMMA: a component-based infrastructure for managing and analyzing life science ontologies and their evolution.
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DOI：
10.1186/2041-1480-2-6
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发表时间：
2011-09-13
影响因子：
1.9
通讯作者：
Rahm E
中科院分区：
文献类型：
--
作者：
Kirsten T;Gross A;Hartung M;Rahm E
本体论越来越多地用于结构和语义描述领域的实体，如生命科学中的基因和蛋白质。它们不断增长的规模和高频率的更新导致了大量的本体版本集，因此需要对这些数据进行有效的管理和分析。我们提出了GOMMA，一个用于管理和分析生命科学本体及其演变的通用基础设施。GOMMA利用通用存储库统一有效地管理本体版本和不同类型的映射。此外，它还提供了本体匹配和确定演化本体变化的组件。这些组件用于分析工具，如本体进化浏览器（OnEX）和检测不稳定的本体区域。我们介绍了基于组件的基础架构，并展示了选定组件和生命科学应用的分析结果。GOMMA网站：http://dbs.uni-leipzig.de/GOMMA。GOMMA提供了一个全面的、可扩展的基础设施来管理大型生命科学本体并分析它们的演变。关键功能包括本体版本和映射的通用存储，支持本体匹配和确定本体更改。用于分析本体更改的支持特性有助于评估它们对依赖于本体的应用程序（如术语充实）的影响。GOMMA通过提供管理两个本体之间的各种版本映射的功能来补充OnEX，并允许组合不同的匹配方法。
Ontologies are increasingly used to structure and semantically describe entities of domains, such as genes and proteins in life sciences. Their increasing size and the high frequency of updates resulting in a large set of ontology versions necessitates efficient management and analysis of this data. We present GOMMA, a generic infrastructure for managing and analyzing life science ontologies and their evolution. GOMMA utilizes a generic repository to uniformly and efficiently manage ontology versions and different kinds of mappings. Furthermore, it provides components for ontology matching, and determining evolutionary ontology changes. These components are used by analysis tools, such as the Ontology Evolution Explorer (OnEX) and the detection of unstable ontology regions. We introduce the component-based infrastructure and show analysis results for selected components and life science applications. GOMMA is available at http://dbs.uni-leipzig.de/GOMMA. GOMMA provides a comprehensive and scalable infrastructure to manage large life science ontologies and analyze their evolution. Key functions include a generic storage of ontology versions and mappings, support for ontology matching and determining ontology changes. The supported features for analyzing ontology changes are helpful to assess their impact on ontology-dependent applications such as for term enrichment. GOMMA complements OnEX by providing functionalities to manage various versions of mappings between two ontologies and allows combining different match approaches.
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影响因子：
5.8
作者：
Beissbarth, T;Speed, TP
通讯作者：
Speed, TP
影响因子：
14.9
作者：
Barrell D;Dimmer E;Huntley RP;Binns D;O'Donovan C;Apweiler R
通讯作者：
Apweiler R
影响因子：
9.5
作者：
Bairoch, A;Boeckmann, B;Gasteiger, E
通讯作者：
Gasteiger, E
影响因子：
5.8
作者：
Aitken, Stuart;Chen, Yin;Bard, Jonathan
通讯作者：
Bard, Jonathan