Abstract
BackgroundThe universal qPCR data exchange file format RDML is today well accepted by the scientific community, part of the MIQE guidelines and implemented in many qPCR instruments. With the increased use of RDML new challenges emerge. The flexibility of the RDML format resulted in some implementations that did not meet the expectations of the consortium in the level of support or the use of elements.ResultsIn the current RDML version 1.2 the description of the elements was sharpened. The open source editor RDML-Ninja was released (http://sourceforge.net/projects/qpcr-ninja/). RDML-Ninja allows to visualize, edit and validate RDML files and thus clarifies the use of RDML elements. Furthermore RDML-Ninja serves as reference implementation for RDML and enables migration between RDML versions independent of the instrument software. The database RDMLdb will serve as an online repository for RDML files and facilitate the exchange of RDML data (http://www.rdmldb.org). Authors can upload their RDML files and reference them in publications by the unique identifier provided by RDMLdb. The MIQE guidelines propose a rich set of information required to document each qPCR run. RDML provides the vehicle to store and maintain this information and current development aims at further integration of MIQE requirements into the RDML format.ConclusionsThe editor RDML-Ninja and the database RDMLdb enable scientists to evaluate and exchange qPCR data in the instrument-independent RDML format. We are confident that this infrastructure will build the foundation for standardized qPCR data exchange among scientists, research groups, and during publication.
Highlights
The universal quantitative PCR (qPCR) data exchange file format Real-time PCR Data Markup Language (RDML) is today well accepted by the scientific community, part of the MIQE guidelines and implemented in many qPCR instruments
The RDML consortium aims to overcome these issues by clarification of the RDML elements that led to misinterpretation and by supporting the software developers with tools to create, analyze and validate RDML files
In this paper we describe the evolution of RDML up to version 1.2, present the data file editor RDML-Ninja and the database RDMLdb, a database dedicated to the storage and exchange of RDML files
Summary
The universal qPCR data exchange file format RDML is today well accepted by the scientific community, part of the MIQE guidelines and implemented in many qPCR instruments. The flexibility of the RDML format resulted in some implementations that did not meet the expectations of the consortium in the level of support or the use of elements. Many elements in the RDML data tree are optional and documentation fields are present in several places. This choice allows the flexible use of RDML even in non-qPCR applications. Some qPCR instrument software export only a small set of the collected data and ignore available RDML elements, or the data are stored in different elements or in different formats than intended. The RDML consortium aims to overcome these issues by clarification of the RDML elements that led to misinterpretation and by supporting the software developers with tools to create, analyze and validate RDML files
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