Transcript
MI-compliant ISA configurations
Philippe Rocca-SerraOxford University, Oxford, UK
MIBBI workshop, December,1st-3rd 2010, Germany**(...and Heathrow airport)
proccaserra@gmail.com
mage-tab | pride-ml | sra-xml | others
ISA infrastructure overview
IISAcreator: a tool for reporting studies
structured reports...declaring variables
Making sense: ontology term tagging
Not just microarray data....
Telling more about experimental design
A focus on standards...
comply to common standards
ISAcreator Configurator provides configurations to ISAcreator...
These configurations tell ISAcreator what is the minimum amount of information needed to describe experiments.
ISAcreator is packaged with a default set of configurations, however you can create your own...
MIAPEXML
MIAMEXML
MIMSXML
MIENSXML
MIGSXML
From MIENS checklist...http://precedings.nature.com/documents/5252/version/2
ISA configurator tool
....to MIENS compliant ISA configuration
Using the Configuration in ISA creator
Using the Configuration in ISA creator
enforcing next gen sequencing requirements
MISFISHIE configuration• Emage project at MRC,in Edimborough
creating an ISA- MISFIHIE configuration
Using ISA-MISFIHIE configuration
Using ISA-MISFIHIE configuration
Conclusions and future work
• From requirements to data collection
• Coherent framework helping implementing annotation guidelines
• Outreach to existing efforts to help and assist designing configurations (Chip-Seq, RNA structure mapping....)
• Further integration with MIBBI checkout
• Creation of a repository for those resources
MIBBI project / ISA configurations
AcknowledgementsDawn Field, NEBC,Eamonn Maguire, Un. of OxfordSusanna Sansone, Un. of OxfordAnnapaola Santarsiero, Un. of OxfordPeter Sterk, NEBC, WTSCChris Taylor, NEBC, MIBBI
All MIBBI collaborators
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