PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data
PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data
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DOI：
10.1186/1471-2105-12-109
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发表时间：
2011-04-20
影响因子：
3
通讯作者：
Sozhamannan, Shanmuga
中科院分区：
文献类型：
--
作者：
Chang, Wenling E.;Sarver, Keri;Sozhamannan, Shanmuga
背景资料：OmniLog T表型微阵列（PM）能够测量和比较生物样品在暴露于数百种生长条件（如不同代谢物和抗生素）后数小时至数天的生长反应。为了管理OmniLog T仪器产生的大量数据，设计了PheMaDB（表型微阵列数据库），一个基于Web的关系数据库。PheMaDB支持OmniLog T PM数据的高效存储、检索和快速分析。描述：PheMaDB允许用户通过项目、菌株、表型、重复和温度的层次排序过滤，快速识别数据分析所需的记录。然后，PheMaDB提供各种统计分析选项以识别实验菌株的特定生长模式特征，例如：离群值分析、阴性对照分析（信号/背景校准）、条形图、皮尔逊相关矩阵、生长曲线轮廓搜索、k均值聚类和热图图。这个基于网络的数据库管理系统允许多个用户之间的数据共享和强大的工具表型organisms of interests.Conclusions：PheMaDB是一个开源系统标准化的OmniLog T PM数据。PheMaDB可以促进表型数据的存储和共享。源代码可从http://phemadb.sourceforge.net下载。
Background: OmniLog T phenotype microarrays (PMs) have the capability to measure and compare the growth responses of biological samples upon exposure to hundreds of growth conditions such as different metabolites and antibiotics over a time course of hours to days. In order to manage the large amount of data produced from the OmniLog T instrument, PheMaDB (Phenotype Microarray DataBase), a web-based relational database, was designed. PheMaDB enables efficient storage, retrieval and rapid analysis of the OmniLog T PM data.Description: PheMaDB allows the user to quickly identify records of interest for data analysis by filtering with a hierarchical ordering of Project, Strain, Phenotype, Replicate, and Temperature. PheMaDB then provides various statistical analysis options to identify specific growth pattern characteristics of the experimental strains, such as: outlier analysis, negative controls analysis (signal/background calibration), bar plots, pearson's correlation matrix, growth curve profile search, k-means clustering, and a heat map plot. This web-based database management system allows for both easy data sharing among multiple users and robust tools to phenotype organisms of interest.Conclusions: PheMaDB is an open source system standardized for OmniLog T PM data. PheMaDB could facilitate the banking and sharing of phenotype data. The source code is available for download at http://phemadb.sourceforge.net.