1. Facilitating Standardization and
Exchange of Array Design
MAGEML2ADF
17th
June 2004

2. 01/28/15MAGEML2ADF2
ADF Converter Specification
 ADF/MAGE-ML converter
 Standalone application
 Automatic curation
 Error log for correction
 focused on usual application case: G.E., C.G.H and
ChIP.

3. 01/28/15MAGEML2ADF3
ADF Converter Specification
 Application running mode
– One at time
– Batchmode
– ADF Helper
 User modes:
– Command-line
– Graphical user interface (G.U.I.)

4. 01/28/15MAGEML2ADF4

5. 01/28/15MAGEML2ADF5
Main functionalities
 file sanity check
 two levels of checking:
– A relax one: allowing the usual mistakes
If the data are identified, the converting process can be done.
– A strict one: exactly match the specification.
 two execution modes:
– a complete mode, check of all data;
– A step-by-step mode: stop at each error -> correction one by one
 data conversion

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Additional functionalities (GUI)
 Array design data visualisation
 ADF creator helper
– Automatic annotation process (G.O./EnsMart)
– ADF creation steps:
1. Choice of array application (GE | CGH | ChIP) & type of microarray
design
2. Filling of data fields:
 Data pasting or importing from a spotter output file.
 Help for database entry item
 auto-complete mechanism for controlled vocabulary fields
 data sanity check.
3. optional "Automatic annotation“
4. Exporting in ADF or converting to MAGE-ML

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Modules
 Checking module
 Conversion module
– MAGE identifier generator
– Group creation (Species, Chromosome, Chromosome band)
 ADF creator module
 Common tool module
– File reader
– Configuration
– Update
– Logging
– Automatic annotation