RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape.The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis.Reverse Phase Protein Arrays (RPPA) provide an analytical platform with the potential to characterize proteomic pathways similarly to the use of microarrays for gene expression studies. RPPAs are a high throughput tool for probing cell or tissue lysates that quantifies levels of selected proteins for which high quality antibody exist [1]. Consequently, RPPA analysis has the potential to be a major tool in the high throughput screening of biopsies for markers of prognosis and therapy response in cancer and other complex diseases.Protein microarrays can be classified into two groups: forward phase protein arrays (FPPA), and reverse phase protein arrays (RPPA). Forward phase protein arrays, also known as antibody arrays, employ high affinity bait molecules such as antibodies immobilize