Facilitating Standardization and
Exchange of Array Design
MAGEML2ADF
17th
June 2004
01/28/15MAGEML2ADF2
ADF Converter Specification
 ADF/MAGE-ML converter
 Standalone application
 Automatic curation
 Er...
01/28/15MAGEML2ADF3
ADF Converter Specification
 Application running mode
– One at time
– Batchmode
– ADF Helper
 User m...
01/28/15MAGEML2ADF4
01/28/15MAGEML2ADF5
Main functionalities
 file sanity check
 two levels of checking:
– A relax one: allowing the usual m...
01/28/15MAGEML2ADF6
Additional functionalities (GUI)
 Array design data visualisation
 ADF creator helper
– Automatic an...
01/28/15MAGEML2ADF7
Modules
 Checking module
 Conversion module
– MAGE identifier generator
– Group creation (Species, C...
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Facilitating Standardization And Exchange Of Array Design 17 06 2004

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Facilitating Standardization And Exchange Of Array Design 17 06 2004

  1. 1. Facilitating Standardization and Exchange of Array Design MAGEML2ADF 17th June 2004
  2. 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. 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. 4. 01/28/15MAGEML2ADF4
  5. 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
  6. 6. 01/28/15MAGEML2ADF6 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
  7. 7. 01/28/15MAGEML2ADF7 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
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