|
|
The Real-time PCR
Data Markup Language (RDML) is a structured and universal data standard
for exchanging quantitative PCR (qPCR) data. Together with the
accompanying guidelines for Minimal Information (MIQPCR), the data
standard should contain sufficient information to understand the
experimental setup, re-analyse the data and interpret the results. The
data standard is a flat text file in Extensible Markup
Language (XML) and enables transparent exchange of annotated
qPCR data between instrument software and third-party data analysis
packages, between colleagues and collaborators, and between authors,
peer reviewers, journals and readers. To support the public acceptance
of this standard, both an on-line RDML file generator is available for
end users, as well as RDML software libraries to be used by software
developers, enabling import and export of RDML data files.
|
RDML:
structured
language and reporting guidelines for real-time quantitative PCR data.
Lefever S, Hellemans J, Pattyn F, Przybylski DR,
Taylor C, Geurts R, Untergasser A, Vandesompele J; on
behalf of the RDML consortium.
Center for Medical Genetics, Ghent University
Hospital, Ghent, Belgium.
Nucleic Acids
Res. 2009 Apr;37(7): 2065-2069
The
XML-based Real-Time PCR Data Markup Language (RDML) has been developed
by the RDML consortium (http://www.rdml.org) to enable
straightforward exchange of qPCR data and related
information between qPCR instruments and third party data analysis
software, between colleagues and collaborators and between
experimenters and journals or public repositories. We
here also propose data related guidelines as a subset
of the Minimum Information for Publication of Quantitative Real-Time PCR
Experiments (MIQE) to guarantee inclusion of key data information when reporting
experimental results.
|
|
The
RDML-consortium was founded to develop a universal
data format for real-time PCR data, named RDML (Real-time PCR Data
Markup Language). The intention to design an universal data
format is
based on the experience that it is difficult to share qPCR data between
different laboratories and users, or exchange data between different
software packages or analysis tools.
The
problem is founded in the data collection software
packages that, depending on the company that provides these with their
instrument(s), save data in a proprietary format and allow to export
information in various file formats (.CSV, .TXT, .XLS), with different
layout and data field terminology.
A
common universal format would allow easy exchange of
raw annotated data between different laboratories. It would make it
possible to include qPCR data in scientific papers, allowing both
reviewers and readers to re-analyse the data, similar to the MIAME
guidelines propose for microarray experiments (Brazma et al., Nat
Genet., 2001; see publication below).
In
principle, the universal data format should contain
sufficient information to understand the experimental setup, re-analyse
the data and interpret the results. The data format is a flat text file
in Extensible Markup Language (XML), termed RDML, an acronym for "Real-time
PCR Data Markup Language". The file extension is *.rdml or
*.rdm. The format is independent of computer hardware, operating system
or available software package, and can be extended in the future to
include additional information if required.
You
can find the RDML schema here.
Contact
information here
Minimum
information about a microarray experiment (MIAME)-toward standards for
microarray data.
Brazma
A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach
J, Ansorge
W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim
IF, Markowitz
V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R,
Vilo J, Vingron M.
Nat Genet. 2001
29(4): 365-3671
Comment in: Nat Genet. 2001
Dec;29(4):373. Nat Genet. 2006 38(10):1089.
European
Bioinformatics Institute, EMBL outstation, Wellcome Trust Genome
Campus, Hinxton,
Cambridge CB10 1SD, UK.
Microarray analysis
has become a widely used tool for the generation of gene expression data on a
genomic scale. Although many significant results have been derived from
microarray studies, one limitation has been the lack of standards for presenting and
exchanging such data. Here we present a proposal, the Minimum Information About a
Microarray Experiment (MIAME), that describes the minimum information required
to ensure that microarray data can be easily interpreted and that results derived
from its analysis can be independently verified. The ultimate goal of this
work is to establish a standard for recording and reporting microarray-based gene
expression data, which will in turn facilitate the establishment of
databases and public repositories and enable the development of data analysis tools.
With respect to MIAME, we concentrate on defining the content and structure
of the necessary information rather than the technical format for
capturing it.
|
|
