The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation
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DOI：
10.1186/2041-1480-5-25
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发表时间：
2014-06-02
影响因子：
1.9
通讯作者：
Stevens, Robert
中科院分区：
文献类型：
--
作者：
Malone, James;Brown, Andy;Stevens, Robert
动机：生物医学本体论的研究主要集中在对生物医学实体的本体论描述，如基因产物及其属性、表型等，近年来，生物医学本体论的研究又转向对生物医学实体的实验室研究。然而，从这些调查产生的数据分析中获得了许多生物学见解，并且缺乏对生物信息学核心的广泛软件的充分描述。我们需要描述如何分析数据的发现，审计跟踪，出处和reproducibility.Results：软件本体（SWO）是用于存储，管理和分析数据的软件的描述。对SWO的投入来自生命科学以外的领域，但其主要重点是生命科学。我们使用敏捷技术为SWO收集信息，并与用户保持互动。其结果是一个本体，通过描述软件，其信息处理任务，数据输入和输出，数据格式版本等，满足了广泛的用户的需求。最近，SWO已纳入埃达姆，用于描述数据和生物信息学相关概念的词汇表。SWO目前被用来描述软件中使用的多个biomedical application.Conclusion：SWO是另一个元素的生物医学本体景观，是必要的生物医学实体的描述，以及它们是如何被发现的。用于分析生命科学研究产生的数据的软件本体可以以这样一种方式制作，即它涵盖了用户所要求和优先考虑的重要功能。因此，SWO适合生物医学本体的景观，并使用旨在使其与用户需求保持一致的技术来产生。可用性：软件本体在Apache 2.0许可下可在http：//theswo.sourceforge.net/获得;软件本体博客可以在http://softwareontology.wordpress.com上阅读。
Motivation: Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility.Results: The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications.Conclusion: The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs.Availability: The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.