ADF creator helper

This functionality will help the user to create ADF file - corresponding MAGE-ML file, without having to create file by hand and thus, it will avoid errors and will compose a strict ADF specification compliant file.

Usually, submitter has features, reporters and composite sequences data in files from a spotter robot. So, the user should be able to import data from these specific files or to copy and paste data in relevant fields. Now, a lot of spotter robot output file formats exists. This tool will focus on gal format (Axon)[gal] support, but more file format could be added in the future.

By default, the composite data will not be handled by the user as usual application use case (G.E.), and will be created automatically. But, the user could have the possibility to add them directly, if he has a complex array.

The data could be display as in array design visualisation functionality:

• Header:
  a form with relevant fields and drop-downs list with controlled vocabulary possibility for needed fields; all items (mandatory and optional) will be displayed.
• FeatureReporter:
  a table with active cells and corresponding item names in the table header; Only mandatory items (and so table column) will be displayed, optional items will be added by the user according to a possible added item list added following the microarray use case (ChIP, GE, CGH, ...) and technology (PCR, oligonucleotide,..)..
• CompositeSequence:
  same representation as FeatureReporter. This table will only be displayed if user wishes to manage complex microarray design. But, it will be filled in after the checking process or after the data importation (automatic curation).

Some biosequence annotations could be automatically added by retrieving data from EnsMart[ens] form or Gene Ontology (G.O.)[go] website -specifying the annotation version- .

The mandatory items change from a microarray application use case to another (application dependent), so the application will be asked to the user.

This functionality will not treat all microarray applications; it will focus following application cases: G.E., C.G.H and ChIP.