Facilitating Standardization and Exchange of Array Design MAGEML2ADF   29 th  July 2004
Modules <ul><li>Checking module </li></ul><ul><li>Conversion module </li></ul><ul><ul><li>MAGE identifier generator  </li>...
The Checking module <ul><li>File structure Definition in a XML file </li></ul><ul><ul><li>The item name </li></ul></ul><ul...
Data Structure Header Item Header Item … . … . … Header Item Data Data … … … Data File data Structure
Features Reporters CompositeSequences BioSequences ADF Structure
Feature Reporter +reporter 1..* 1..* Reporters2CompositeSequences Reporter +reporters +compositeSequence CompositeSequence...
Conversion <ul><li>ADF Data -> MAGE object (MAGE-stk) </li></ul><ul><li>MAGE object (MAGE-stk) -> ADF Data  </li></ul><ul>...
Repository <ul><li>MGED sourceforge </li></ul><ul><li>MiamExpress sourceforge </li></ul><ul><li>Separated repository  </li...
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Facilitating Standardization And Exchange Of Array Design 29 07 2004

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Facilitating Standardization And Exchange Of Array Design 29 07 2004

  1. 1. Facilitating Standardization and Exchange of Array Design MAGEML2ADF 29 th July 2004
  2. 2. Modules <ul><li>Checking module </li></ul><ul><li>Conversion module </li></ul><ul><ul><li>MAGE identifier generator </li></ul></ul><ul><ul><li>Group creation (Species, Chromosome, Chromosome band) </li></ul></ul><ul><li>ADF creator module </li></ul><ul><li>Common tool module </li></ul><ul><ul><li>File reader/writer </li></ul></ul><ul><ul><li>Configuration </li></ul></ul><ul><ul><li>Update </li></ul></ul><ul><ul><li>Logging </li></ul></ul>
  3. 3. The Checking module <ul><li>File structure Definition in a XML file </li></ul><ul><ul><li>The item name </li></ul></ul><ul><ul><ul><li>Identifying rule (relax /strict) </li></ul></ul></ul><ul><ul><li>Item cardinality </li></ul></ul><ul><ul><li>field cardinality </li></ul></ul><ul><ul><li>Field value type </li></ul></ul><ul><ul><li>… . </li></ul></ul>
  4. 4. Data Structure Header Item Header Item … . … . … Header Item Data Data … … … Data File data Structure
  5. 5. Features Reporters CompositeSequences BioSequences ADF Structure
  6. 6. Feature Reporter +reporter 1..* 1..* Reporters2CompositeSequences Reporter +reporters +compositeSequence CompositeSequenceMap BioSequence +bioSequences Reporter2BioSequences +bioSequences CompositeSequence2 BioSequences ReporterGroup CompositeSequenceGroup +reporterGroups Reporter2ReporterGroups +compositeSequenceGroups CompositeSequence2 CompositeSequenceGroups ADF data Structure
  7. 7. Conversion <ul><li>ADF Data -> MAGE object (MAGE-stk) </li></ul><ul><li>MAGE object (MAGE-stk) -> ADF Data </li></ul><ul><li>=> ADF tables and MAGE objects parsing? </li></ul>
  8. 8. Repository <ul><li>MGED sourceforge </li></ul><ul><li>MiamExpress sourceforge </li></ul><ul><li>Separated repository </li></ul>

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