Facilitating Standardization And Exchange Of Array Design 11 06 2004
Upcoming SlideShare
Loading in...5
×
 

Like this? Share it with your network

Share

Facilitating Standardization And Exchange Of Array Design 11 06 2004

on

  • 1,531 views

 

Statistics

Views

Total Views
1,531
Views on SlideShare
1,528
Embed Views
3

Actions

Likes
0
Downloads
2
Comments
0

1 Embed 3

http://www.slideee.com 3

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

Facilitating Standardization And Exchange Of Array Design 11 06 2004 Presentation Transcript

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