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Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees
Evolutionary Bioinformatics ( IF 2.6 ) Pub Date : 2020-04-06 , DOI: 10.1177/1176934319899384
Van D Nguyen 1 , Thanh H Nguyen 1 , Abu Saleh Md Tayeen 1 , H Dail Laughinghouse 2, 3 , Luna L Sánchez-Reyes 4 , Jodie Wiggins 4 , Enrico Pontelli 1 , Dmitry Mozzherin 5 , Brian O’Meara 4 , Arlin Stoltzfus 2, 6
Affiliation  

A comprehensive phylogeny of species, i.e., a tree of life, has potential uses in a variety of contexts, including research, education, and public policy. Yet, accessing the tree of life typically requires special knowledge, complex software, or long periods of training. The Phylotastic project aims make it as easy to get a phylogeny of species as it is to get driving directions from mapping software. In prior work, we presented a design for an open system to validate and manage taxon names, find phylogeny resources, extract subtrees matching a user’s taxon list, scale trees to time, and integrate related resources such as species images. Here, we report the implementation of a set of tools that together represent a robust, accessible system for on-the-fly delivery of phylogenetic knowledge. This set of tools includes a web portal to execute several customizable workflows to obtain species phylogenies (scaled by geologic time and decorated with thumbnail images); more than 30 underlying web services (accessible via a common registry); and code toolkits in R and Python (allowing others to develop custom applications using Phylotastic services). The Phylotastic system, accessible via http://www.phylotastic.org, provides a unique resource to access the current state of phylogenetic knowledge, useful for a variety of cases in which a tree extracted quickly from online resources (as distinct from a tree custom-made from character data) is sufficient, as it is for many casual uses of trees identified here.



中文翻译:

Phylotatic:通过灵活,即时的树木交付来改善对生命树知识的获取

物种的全面系统发育,即生命树,在包括研究,教育和公共政策在内的各种环境中都有潜在的用途。然而,访问生命之树通常需要特殊的知识,复杂的软件或长期的培训。Phylotastic项目的目的是使获得物种的系统发育与从制图软件获得行驶指导一样容易。在先前的工作中,我们提出了一个开放系统的设计,该系统可以验证和管理分类单元名称,查找系统发育资源,提取与用户分类单元列表匹配的子树,按时间缩放树并集成相关资源(例如物种图像)。在这里,我们报告了一套工具的实施情况,这些工具一起代表了系统发育知识的动态传递的强大,可访问的系统。这套工具包括一个用于执行多个可自定义工作流的门户网站,以获取物种系统发育(按地质时间缩放并用缩略图装饰);30多种基础Web服务(可通过公共注册表访问);和R和Python中的代码工具包(允许其他人使用Phylotastic服务开发自定义应用程序)。可以通过http://www.phylotastic.org访问的Phylotastic系统提供了一种独特的资源来访问当前的系统发育知识状态,对于在许多情况下从在线资源中快速提取树(不同于树的情况)很有用根据角色数据进行定制)就足够了,因为它可以用于此处标识的树木的许多随意使用。30多种基础Web服务(可通过公共注册表访问);和R和Python中的代码工具包(允许其他人使用Phylotastic服务开发自定义应用程序)。可以通过http://www.phylotastic.org访问的Phylotastic系统提供了一种独特的资源来访问当前的系统发育知识状态,对于在许多情况下从在线资源中快速提取树(不同于树的情况)很有用根据角色数据进行定制)就足够了,因为它可以用于此处标识的树木的许多随意使用。30多种基础Web服务(可通过公共注册表访问);和R和Python中的代码工具包(允许其他人使用Phylotastic服务开发自定义应用程序)。可以通过http://www.phylotastic.org访问的Phylotastic系统提供了一种独特的资源来访问当前的系统发育知识状态,对于在许多情况下从在线资源中快速提取树(不同于树的情况)很有用根据角色数据进行定制)就足够了,因为它可以用于此处标识的树木的许多随意使用。

更新日期:2020-04-06
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