OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript
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DOI：
10.1186/1471-2105-12-218
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发表时间：
2011-05-29
影响因子：
3
通讯作者：
Swertz, Morris A.
中科院分区：
文献类型：
--
作者：
Adamusiak, Tomasz;Burdett, Tony;Swertz, Morris A.
背景资料：本体已经成为生物信息学工具箱中的重要资产，并且现在可以获得许多本体访问资源，例如，EBI本体检索服务（OLS）和NCBO BioPortal。然而，这些资源在模式、访问的容易程度和本体内容方面有很大的不同。这使得它相对难以单独访问每个本体源，映射其内容的研究数据，这方面的努力正在不同的research groups.Results：OntoCAT提供了一个无缝的编程接口，查询异构本体资源，包括OLS和BioPortal，以及用户指定的本地OWL和OBO文件。每个资源都包含在易于学习的Java，Bioconductor/R和REST Web服务命令中，尽管技术存在差异，但仍然可以重用和集成本体软件。它也可以作为一个独立的MOLGENIS数据库和一个Google App Engine应用程序。结论：OntoCAT提供了一个强大的，可配置的解决方案，用于访问本地和远程服务指定的本体术语，可以作为一个独立的工具，并已在ArrayExpress，MOLGENIS，EFO和Gen 2 Phen表型用例中进行了彻底的测试。可用性：http://www.ontocat.org
Background: Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.Results: OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.Conclusions: OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.Availability: http://www.ontocat.org