MyOPMD - a Laboratory Information Management System (LIMS) for Microarray Data

DNA microarrays for two of the oral pathogens – Porphyromonas gingivalis and Streptococcus mutans, have been made available to the research community through the collaborative effort between NIDCR and NIAID. The policy for using these arrays is that the data should be released timely to a public database. Objective: To design and provide an online laboratory information management system (LIMS) that also serves as a centralized public data repository for the oral pathogen microarray data. Methods: The database was constructed using MySQL system running on a dedicated Linux server. The user management system was implemented based on the content management system POSTNUKE and the web interface to the databases was designed using the PHP programming language. The latest version of SAOPMD uses the LIMMA microarray analysis package for advance statistic inference of array data. Results: MyOPMD is a web-based LIMS system designed especially, but not exclusively for the oral pathogen microarray data. It integrates with the statistics analysis tool SAOPMD and allows investigators to streamline their microarray data analysis and management tasks ranging from uploading the microarray experiment data, performing statistics analyses such as normalization and significance assessment, to storing, sharing and publicizing the results all at one place. The data can be shared among designated collaborators or made publicly accessible for publication purposes. A unique web access identification code is generated for each of the public data entity in the format of: http://www.brop.org/idn:0123456789, which can be used in the citation. Conclusion: MyOPMD is an ideal solution for analyzing, managing, and storing microarray data and related information. MyOPMD can be accessed at http://www.brop.org/myOPMD. Supported by NIH grant NIDCR K22 DE14742.