Facilitating%20Standardization%20and%20Exchange%20of%20Array%20Design%20MAGEML2ADF

1
Facilitating Standardization and Exchange of
Array DesignMAGEML2ADF

• 29th July 2004

2
Modules

• Checking module
• Conversion module
• MAGE identifier generator
• Group creation (Species, Chromosome, Chromosome
  band)
• ADF creator module
• Common tool module
• File reader/writer
• Configuration
• Update
• Logging

3
The Checking module

• File structure Definition in a XML file
• The item name
• Identifying rule (relax /strict)
• Item cardinality
• field cardinality
• Field value type
• .

4
Data Structure
File data Structure
Header Item
Header Item
Header Item
.
.

Data
Data



Data
5
Reporters
CompositeSequences
Features
BioSequences
ADF Structure
6
ReporterGroup
CompositeSequenceGroup
reporterGroups
compositeSequenceGroups
CompositeSequence2 CompositeSequenceGroups
Reporter2ReporterGroups
Feature
Reporters2CompositeSequences
Reporter
Reporter
1..
1..
reporter
reporters
compositeSequence
CompositeSequence2 BioSequences
Reporter2BioSequences
CompositeSequenceMap
bioSequences
bioSequences
BioSequence
ADF data Structure
7
Conversion

• ADF Data -gt MAGE object (MAGE-stk)
• MAGE object (MAGE-stk) -gt ADF Data
• gt ADF tables and MAGE objects parsing?

8
Repository

• MGED sourceforge
• MiamExpress sourceforge
• Separated repository