MorphoBank: phylophenomics in the "cloud"
MorphoBank: phylophenomics in the "cloud"
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DOI：
10.1111/j.1096-0031.2011.00355.x
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发表时间：
2011-10-01
期刊：
影响因子：
3.6
通讯作者：
Kaufman, Seth
中科院分区：
文献类型：
--
作者：
O'Leary, Maureen A.;Kaufman, Seth
一个高度可互操作的信息学基础设施迅速出现，以处理用于遗传学的基因组数据，并有助于分子系统学的发展。为满足基因组学的特殊需要而开发的软件和数据库的并行增长相对缓慢，而且分散。系统分类学家目前面临的挑战是，地球上可能有数千万物种（活的和化石的）需要描述和分类。这种规模的研究越来越多地导致团队的工作，许多人构建大型表型超矩阵。到目前为止，遗传学家一直在单用户、基于文件的桌面软件中管理数据，完全不适合实时、基于团队的协作工作。此外，表型数据通常与基因组数据不同，因为它们容易将自己借给媒体表示（例如，G. 2D和3D图像、视频、声音）。表型数据是遗传学中不断增长的组成部分，因此团队需要能够使用媒体记录同源性假设并共享和存档这些数据。在这里，我们描述MorphoBank，一个Web应用程序和数据库，利用软件作为一个服务的方法兼容的“云”计算技术的矩阵的表型数据的建设。MorphoBank自成立以来已进入第十个年头，并向广大科学界全面开放，它实现了桌面软件无法实现的交互式协作，允许自组装团队在安全的网络环境中使用链接媒体真实的时间开发矩阵。MorphoBank还为任何用户提供了在矩阵中构建角色和媒体本体（规则集）的工具，并将其显示为有向非循环图。这些规则集记录了字符的系统发育相关性（e。G.如果X不存在，Y不适用，或者X-Z字符共享媒体视图）。MorphoBank已经实现了一个数量级的增加，在基因组学数据收集：最近的合作，超过25名研究人员已经产生了一个数据库的> 4500表型字符支持的> 10000媒体。(C)2011年的Willi Hennig Society。
A highly interoperable informatics infrastructure rapidly emerged to handle genomic data used for phylogenetics and was instrumental in the growth of molecular systematics. Parallel growth in software and databases to address needs peculiar to phylophenomics has been relatively slow and fragmented. Systematists currently face the challenge that Earth may hold tens of millions of species (living and fossil) to be described and classified. Grappling with research on this scale has increasingly resulted in work by teams, many constructing large phenomic supermatrices. Until now, phylogeneticists have managed data in single-user, file-based desktop software wholly unsuitable for real-time, team-based collaborative work. Furthermore, phenomic data often differ from genomic data in readily lending themselves to media representation (e. g. 2D and 3D images, video, sound). Phenomic data are a growing component of phylogenetics, and thus teams require the ability to record homology hypotheses using media and to share and archive these data. Here we describe MorphoBank, a web application and database leveraging software as a service methodology compatible with "cloud" computing technology for the construction of matrices of phenomic data. In its tenth year, and fully available to the scientific community at-large since inception, MorphoBank enables interactive collaboration not possible with desktop software, permitting self-assembling teams to develop matrices, in real time, with linked media in a secure web environment. MorphoBank also provides any user with tools to build character and media ontologies (rule sets) within matrices, and to display these as directed acyclic graphs. These rule sets record the phylogenetic interrelatedness of characters (e. g. if X is absent, Y is inapplicable, or X-Z characters share a media view). MorphoBank has enabled an order of magnitude increase in phylophenomic data collection: a recent collaboration by more than 25 researchers has produced a database of > 4500 phenomic characters supported by > 10 000 media. (C) The Willi Hennig Society 2011.