MAGE-TAB Tools - open source applications to support a simple tab-delimited format

Helen Parkinson
Afternoon Session, 2 September (11th MGED Meeting, 1-4 September, 2008)

MAGE-TAB 1.0 was 2006 and 1.1 in 2008. It is a simple, human-readable format (well, as much as spreadsheets are readable by humans ;) ). It scales well. There are 1000s of experiments and 100,000s of assays. There are all sorts of data in ArrayExpress. To submit data, the best way is via MAGETabulator, which is an open-source MAGE-TAB template generation system, and includes syntactic and semantic checking of MAGE-TAB documents. There is also some data validation code. It's available at http://tab2mage.sf.net. There are tutorials avaiable. Database applications include caArray from the NCI and Molgenis (http://www.molgenis.org).

Format conversion tools include GEO SOFT to MAGE-TAB. There is also MAGE-ML <-> MAGE-TAB. There's also a canonical Java parser, and coming soon are converters to ISA-TAB and MIQAS. There is also a MAGE-TAB Bioconductor package.

These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. :)