JERM Templates Update Transcriptomics by yurtgc548


									JERM Templates Update
         Tools to Help
                                     Tools Update

Auto generation of templates
 ISA Creator and ISA configurator (beta)

 MAGE-TAB Generator

Help with annotating experiments
 Ontology annotator
     Orcha (it needs a new name!)
                                     ISA Creator

   Generates ISA-TAB compliant templates to help
    with submission of ISA format data
   Stand-alone java tool available for download
                             Testing Orcha Out

   Auto-generate a new MIAME compliant file from
   Use Orcha to set particular cells to particular
    ontology terms
                                 MIAME Compliance

   Data
       Raw data, processed data
   Metadata
       sample annotations (experimental factors),
        experiment design (including sample-data
        relationships), array design, experiment and data
        processing protocols
                                     MIAME Files

   IDF: Investigation Description Format
   SDRF: Sample and Data Relationship Format
   ADF: Array Design Format
   Raw and processed data files, including "data
    matrix" files
Taken from the ArrayExpress Website
                  Orcha Ontology Annotator

   Helps keep templates consistent
   Makes filling in the metadata easier
   Keeps data MIAME (or other MIBBI) compliant
   Go to
   Download the Orcha file: orcha-0.9.0(2).zip
   Unzip it and click run
   Auto generate a MIAME file from

   Or download one I made earlier from

   Load this file into Orcha by selecting File -> Open
   Load the Microarray Experimental Conditions
    ontology from the BioPortal (File -> Open from

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