Using a suite of ontologies for preserving workflow-centric research objects
Using a suite of ontologies for preserving workflow-centric research objects
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DOI：
10.1016/j.websem.2015.01.003
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发表时间：
2015-05-01
影响因子：
2.5
通讯作者：
Goble, Carole
中科院分区：
文献类型：
--
作者：
Belhajjame, Khalid;Zhao, Jun;Goble, Carole
科学工作流是一种流行的机制，用于在计算机实验中指定和自动化数据驱动。它们的价值的一个重要方面在于它们被重复使用的潜力。共享后，工作流将成为有用的构建块，可以组合或修改以开发新的实验。然而，以前的研究表明，仅存储工作流规范并不足以确保它们可以被成功地重用，而不能理解工作流的目标是什么或重新制定它们。为了了解工作流，以及如何根据他们的需求对其进行使用和重新调整用途，科学家需要访问其他资源，例如描述工作流的注释、工作流使用和产生的数据集以及记录工作流执行情况的来源跟踪。在本文中，我们提出了一种通过应用研究对象来保存科学工作流的新方法--数据和元数据的聚合丰富了工作流规范。我们的方法实现为一套支持创建以工作流为中心的研究对象的本体。它们的设计是由先前对工作流衰败和修复的经验分析得出的要求指导的。开发的本体利用并扩展了现有的众所周知的本体，即对象重用和交换(ORE)词汇、注释本体(AO)和W3CProv本体(PROVO)。我们通过与莱顿大学医学中心(HG-LUMC)的一个团队合作进行的亨廷顿病调查案例研究，说明了本体论在构建工作流研究对象方面的应用。最后，我们介绍了一些为创建和管理以工作流为中心的研究对象而开发的工具。(C)2015年提交人。爱思唯尔出版公司(Elsevier B.V.)
Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies in their potential to be reused. Once shared, workflows become useful building blocks that can be combined or modified for developing new experiments. However, previous studies have shown that storing workflow specifications alone is not sufficient to ensure that they can be successfully reused, without being able to understand what the workflows aim to achieve or to re-enact them. To gain an understanding of the workflow, and how it may be used and repurposed for their needs, scientists require access to additional resources such as annotations describing the workflow, datasets used and produced by the workflow, and provenance traces recording workflow executions.In this article, we present a novel approach to the preservation of scientific workflows through the application of research objects-aggregations of data and metadata that enrich the workflow specifications. Our approach is realised as a suite of ontologies that support the creation of workflow-centric research objects. Their design was guided by requirements elicited from previous empirical analyses of workflow decay and repair. The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate the application of the ontologies for building Workflow Research Objects with a case-study that investigates Huntington's disease, performed in collaboration with a team from the Leiden University Medial Centre (HG-LUMC). Finally we present a number of tools developed for creating and managing workflow-centric research objects. (C) 2015 The Authors. Published by Elsevier B.V.