Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming
Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming
复制标题
Phylotastic：使用逻辑编程创建、操作和进化系统发生生物学工作流程的实验
DOI：
10.1017/s1471068418000236
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发表时间：
2018
影响因子：
1.4
通讯作者：
Tran Cao Son
中科院分区：
文献类型：
--
作者：
T. Nguyen;Enrico Pontelli;Tran Cao Son
进化生物学家长期以来一直在努力以灵活的方式开发分析工作流程，从而促进系统发育知识的重用。进化生物学工作流可以看作是一个计划，它包含了可以检索、操作和生成系统发生树的web服务。Phylotastic项目于两年前启动，是进化生物学家和计算机科学家的合作项目，其目标是开发一个开放的体系结构，以促进此类分析工作流程的创建。虽然web服务的组合是一个在文献（包括在逻辑编程领域）中被广泛探讨的问题，但在Phylotastic中该问题的体现提供了许多额外的挑战。随着需要在期望的工作流描述中集成偏好和形式化本体，进化生物学家倾向于以增量的方式构建工作流，通过连续地细化工作流，通过指示期望的更改（例如，排除某些服务，修改期望的输出）。这导致需要对增量重新规划进行连续迭代，以开发一个新的工作流，该工作流集成了所请求的更改，同时将对原始工作流的更改最小化。本文阐述了Phylotastic如何利用逻辑编程技术解决创建和改进系统发育分析工作流程的挑战，以及如何在Phylotastic项目的总体框架内使用这些解决方案。
Abstract Evolutionary Biologists have long struggled with the challenge of developing analysis workflows in a flexible manner, thus facilitating the reuse of phylogenetic knowledge. An evolutionary biology workflow can be viewed as a plan which composes web services that can retrieve, manipulate, and produce phylogenetic trees. The Phylotastic project was launched two years ago as a collaboration between evolutionary biologists and computer scientists, with the goal of developing an open architecture to facilitate the creation of such analysis workflows. While composition of web services is a problem that has been extensively explored in the literature, including within the logic programming domain, the incarnation of the problem in Phylotastic provides a number of additional challenges. Along with the need to integrate preferences and formal ontologies in the description of the desired workflow, evolutionary biologists tend to construct workflows in an incremental manner, by successively refining the workflow, by indicating desired changes (e.g., exclusion of certain services, modifications of the desired output). This leads to the need of successive iterations of incremental replanning, to develop a new workflow that integrates the requested changes while minimizing the changes to the original workflow. This paper illustrates how Phylotastic has addressed the challenges of creating and refining phylogenetic analysis workflows using logic programming technology and how such solutions have been used within the general framework of the Phylotastic project.
影响因子：
3.9
作者：
Stephen A. Smith;Jeremy M Beaulieu;A. Stamatakis;M. Donoghue
通讯作者：
Stephen A. Smith;Jeremy M Beaulieu;A. Stamatakis;M. Donoghue
影响因子：
64.8
作者：
Jetz, W.;Thomas, G. H.;Mooers, A. O.
通讯作者：
Mooers, A. O.