Facilitating Standardization And Exchange Of Array Design 11 06 2004

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Facilitating Standardization And Exchange Of Array Design 11 06 2004

  1. 1. Facilitating Standardization and Exchange of Array Design MAGEML2ADF 11 th June 2004
  2. 2. ADF specification – Header(1/2) <ul><ul><li>Audit & Security information: </li></ul></ul><ul><ul><ul><ul><ul><li>o         Person LastName: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Person email: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Person FirstName: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Person office phone : </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>  </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Institution/Company: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Department: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         URL: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Address: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Zip code/PO box: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         City: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         State/Province: </li></ul></ul></ul></ul></ul><ul><ul><ul><ul><ul><li>o         Country:   </li></ul></ul></ul></ul></ul>
  3. 3. ADF specification - Header(2/2) <ul><li>Array Design Description information: </li></ul><ul><li>o         Array Design Name: </li></ul><ul><li>o         Array Version: </li></ul><ul><li>o         Array Design Number of Features : </li></ul><ul><li>o         Application: </li></ul><ul><li>o         Technology Type: </li></ul><ul><li>o         Surface Type: </li></ul><ul><li>o         Substrate Type: </li></ul><ul><li>o         Attachment Type: </li></ul><ul><li>o         Strandedness Type: </li></ul><ul><li>o         Array Description: </li></ul><ul><li>o         Array Protocol: </li></ul><ul><li>Miscellaneous information: </li></ul><ul><li>o         Release Date (date of public release) </li></ul><ul><li>o         User defined value (field used for user defined database) </li></ul><ul><li>o         FeatureReporter filepath (only in case of three plain text files) </li></ul><ul><li>o         CompositeSequence file path (only in case of three plain text file)  </li></ul><ul><li>Items in italic are optional. </li></ul>
  4. 4. ADF specification - Reporter (1/2) <ul><li>Reporter data: </li></ul><ul><li>o         Reporter Name </li></ul><ul><li>o         Reporter ControlType ->mandatory field </li></ul><ul><li>o         Reporter BioSequence Type </li></ul><ul><li>o         Reporter BioSequence Polymer Type </li></ul><ul><li>o         Reporter BioSequence Database Entry [db-tag] </li></ul><ul><li>o         Reporter FailType </li></ul><ul><li>o         Reporter WarningType </li></ul><ul><li>o     Reporter BioSequence [Actual Sequence] </li></ul><ul><li>o     Reporter Group [reportergroup tag ] </li></ul>
  5. 5. ADF specification - Reporter (2/2) <ul><li>ChIP and PCR: another BioSequence object added, call Assigned gene. </li></ul><ul><li>o         Assigned_Gene Name </li></ul><ul><li>o         Assigned_Gene Database Entry [db-tag] </li></ul><ul><li>o         Assigned_Gene Database Entry [db-tag] </li></ul><ul><li>o         Chromosome </li></ul><ul><li>o         Chromosome_band </li></ul><ul><li>The “Reporter Name” item is renamed to “Reporter Name [intergenic]”. </li></ul><ul><li>PCR : </li></ul><ul><li>o         Reporter BioSequence [Fwd Primer] </li></ul><ul><li>o         Reporter BioSequence [Rev Primer] </li></ul><ul><li>CGH use case: </li></ul><ul><li>o         Species </li></ul><ul><li>o         Chromosome: non mandatory but Highly recommended for CGH </li></ul><ul><li>Chromosome_band : recommended field for CGH </li></ul>
  6. 6. ADF specification - CompositeSequence (2/2) <ul><li>Items: </li></ul><ul><li>o          CompositeSequence Name </li></ul><ul><li>o         CompositeSequence BioSequence [Actual Sequence] </li></ul><ul><li>o         CompositeSequence BioSequence Type </li></ul><ul><li>o         CompositeSequence BioSequence Polymer Type </li></ul><ul><li>o         CompositeSequence BioSequence Database Entry [db-tag] </li></ul><ul><li>CompositeSequence Annotation Database Entry [db-tag] </li></ul><ul><li>o         ReporterCompositeMap </li></ul><ul><li>o         Chromosome </li></ul><ul><li>o         Chromosome_band </li></ul><ul><li>  </li></ul><ul><li>Items in italic are optional. All others are mandatory . </li></ul>
  7. 7. <ul><li>One at time </li></ul><ul><li>Batchmode </li></ul><ul><li>ADF Helper </li></ul>
  8. 8. identifier <ul><li>$usr_provided_url :EBI-AE-W2AM -$usr_provided_namespace /ObjectType:A-W2AM-0000=ObjectInitial-number  </li></ul><ul><li>Example : identifier=&quot;ebi.ac.uk:EBI-AE-W2AM-impression/Feature:A-W2AM-0000=F-1&quot; </li></ul>
  9. 9. Database Id checking <ul><li>public_DB_ Accnos . xls </li></ul><ul><li>http://www.ebi.ac.uk/~rayner/curator/public_DB_Accnos.xls </li></ul><ul><li>Format ? </li></ul><ul><li>Location? </li></ul><ul><li>Update? </li></ul>

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