Changes between Version 1 and Version 5 of Ticket #868

Feb 5, 2008, 2:49:25 PM (16 years ago)
Nicklas Nordborg


  • Ticket #868

    • Property Priority criticalmajor
    • Property Owner changed from everyone to Nicklas Nordborg
    • Property Status newassigned
  • Ticket #868 – Description

    v1 v5  
    55If we could do this from scratch without having to worry about backwards compatibility it would probably be easy. I think the hard part is to maintain the backwards compatibility.
     8'''Implementation idea'''
     10This was a really hard thing. After some discussion we think we have found a way forward:
     12 1. The ArrayDesign and Hybridization gets an additional field: numArrays.
     14 2. When selecting Labeled extracts for a Hyb, the user can also specify which array(s) the labeled extract should go on. On the Illumina platform there can only be one labeled extract per array, but BASE should support the multi-channel case also. A single labeled extract (for example the reference) may go into more than one array.
     16 3. The RawBioassay gets a many-to-many link to LabeledExtract. This link should also contain the channel number. 0 = not known
     18 4. When creating a Raw bioassay the user can also select Labeled extracts and specify channels for them. With some smart coding it may be possible to make intelligent default guesses about which Labeled extracts to select. Note! The Scan->Hybridization link chain is optional, but it should still be possible to select Labeled extracts.
     20 5. Inheriting annotations: The RBA->LE links are considered the primary path, and it is always possible to inherit from this path if it is present. If a Hyb has numArrays > 1, it should not be possible to inherit from the Hyb -> LE links.
     22 6. Update from 2.5: We create the RBA->LE links by just copying the RBA->Scan->Hyb->LE links. If we copy the links, the channel number must be set to 0 = unknown.
     24 7. Experiment overview/validator: If the RBA -> LE links exists they are used as the primary links to biomaterials, otherwise the old route is used. If the links exists it is checked that they are a subset of the Hyb -> LE links, but the Hyb->LE route is not followed any further. A RBA which is connected with a Hyb with numArrays > 1 should have RBA -> LE links. Channel numbers in the RBA -> LE links should be validated.
     26 8. Migration: In BASE1 there is channel information in the Hyb->LE connection. This information should be copied to the new RBA -> LE links.
     28 9. Backwards compatibility: Older tools/plug-ins may have a hard time with the old route since the number of Hyb->LE link can provide more Labeled extracts than expected by the number of channels from the raw data type. Tools/plug-ins should be upgraded to use the new route.