Real-time PCR Data Markup Language

Transcription

1 Real-time PCR Data Markup Language A new standard for archiving and exchanging real-time PCR data Steve Lefever On behalf of the RDML consortium

2 qpcr = golden standard for nucleic acids quantification Dedicated and precise instruments needed Different software/output format for each instrument/manufacturer Limits possibility to exchange and reanalyse data PubMed citations / year RDML

3 History of RDML Birth on September 1 st 2005 Jan Hellemans : Open discussion about RDML January 1st 2008 : start of the RDML consortium April 1st 2008 : RDML joins MIBBI January 12th 2009 : RDML paper accepted in Nucleic Acid Research

4 RDML consortium Develops and maintains the RDML data exchange format Key developer group, a member community and supporters 41 supporters and members from 20 different countries 22 academic Austria, Switzerland, France Spain, Israel, Canada,... Sweden (2) 19 companies USA (6) UK (2) Belgium (2) Germany (3) UK (3) USA (5) Portugal, Austria Switzerland, Israel, Australia, Korea,...

5 MIBBI Minimum Information for Biological and Biomedical Investigations Published in August 2008 by Nature Biotechnology RDML adopted as standard for qpcr experiments Microarrays MIAME MAGE-ML qpcr MIQE RDML

6 What is RDML? RDML = Real-time PCR Data Markup Language Universal format to store and exchange qpcr data Structured Based on XML Platform independent Easy to extend Small RDML files

7 What is RDML? File size reduction Vermeulen et al. Prognostic gene study in neuroblastoma Excel files ~ 11 Mb samples targets RDML file ~ 300 Kb well plates

8 What is XML? extensible Markup Language Language to store data in a structured manner Defines elements delimited by opening and closing tags Easily extensible <gene> <gene> <symbol>actb</symbol> <symbol>actb</symbol> <function>muscle contraction</function> <function>muscle contraction</function> <location>chromosome 7: </location> </gene> </gene>

9 RDML structure List of Id s List of experimenters List of targets List of samples Experiments Runs Reactions Datapoints List of protocols Documentation annotation qpcr data

10 RDML structure List of Id s List of experimenters qpcr data Experiment List annotation of targets Multiple experiments List of samples per file Standard vocabulary (MIQE) List of protocols - reaction Documentation - Cq Experiments Runs Reactions Datapoints

11 RDML structure List of Id s List of experimenters List of targets List of samples Experiments Accession numbers for online repositories or journals Runs Reactions Datapoints List of protocols Documentation

12 RDML structure List of Id s List of experimenters List of targets List of samples Experiments Contact information of experimenters RunsReactions Datapoints List of protocols Documentation

13 RDML structure List of Id s List of experimenters List of targets List of samples Experiments Target annotation Oligonucleotide sequences RunsReactions Datapoints List of protocols Documentation

14 RDML structure List of Id s List of experimenters List of targets List of samples List of protocols Experiments Sample annotation cdna synthesis RunsReactions Datapoints Documentation

15 RDML structure List of Id s List of experimenters List of targets List of samples List of protocols Experiments Any type of protocol Documentation

16 RDML structure List of Id s List of experimenters List of targets List of samples List of protocols Documentation Experiments Additional information

17 RDML supporting software Under development: - - RDML viewer and editor More to come

18 Website Tool for creating RDML files Tool for converting RDML file to.csv files Libraries in Java, C,.NET and PHP

19 RDML demonstration Online generation of an RDML file Importing the RDML file in qbaseplus for analysis Convert RDML file into.csv files

20 Conclusion Data standard for qpcr data Universal and extensible Easy exchange of data Broad acceptance by community Submit data in RDML format to journals

21 Acknowledgements The RDML consortium Jo Vandesompele Jan Hellemans Filip Pattyn Andreas Untergasser Daniel Przybylski