title: PheMaDB: a solution for storage, retrieval, and analysis of high throughput phenotype data.
abstract: BACKGROUND
  OmniLog™ 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™ instrument, PheMaDB (Phenotype Microarray DataBase), a web-based relational database, was designed. PheMaDB enables efficient storage, retrieval and rapid analysis of the OmniLog™ PM data.
  
  
  METHODS
  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™ PM data. PheMaDB could facilitate the banking and sharing of phenotype data. The source code is available for download at http://phemadb.sourceforge.net.
authors.affiliation: Biotechnology, The MITRE Corporation, McLean, VA, USA. wchang@mitre.org
authors.forename: Wenling E
authors.initials: WE
authors.lastname: Chang
authors.forename: Keri
authors.initials: K
authors.lastname: Sarver
authors.forename: Brandon W
authors.initials: BW
authors.lastname: Higgs
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Read
authors.forename: Nichole Me
authors.initials: NM
authors.lastname: Nolan
authors.forename: Carol E
authors.initials: CE
authors.lastname: Chapman
authors.forename: Kimberly A
authors.initials: KA
authors.lastname: Bishop-Lilly
authors.forename: Shanmuga
authors.initials: S
authors.lastname: Sozhamannan
mesh_terms: D001408:Bacillus anthracis / Q000145:classification / Q000254:growth & development / Q000378:metabolism; D016208:Databases, Factual; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D046228:Microarray Analysis; D010641:Phenotype; D012984:Software