Changes between Initial Version and Version 2 of Ticket #1418


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Timestamp:
Nov 9, 2022, 7:50:43 AM (2 years ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1418 – Description

    initial v2  
    33The starting point is DNA items in BASE. We need to make sure that there are aliquots created that represents the amount taken from the DNA item. Typical name will be something like `1234567.1.l.d.aX` (where X may be missing or a number). The samples sheets that we have only have the `1234567` as identifier so we need to map this first.
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    5 The DNA aliquot should be linked to `PhysicalBioAssay` item representing the actual EPIC chip that was used. It might be possible to re-use the `BeadChip` suptype for this with but with new value for the `BeadChipType` annotation (eg. `Epic850K`). The other alternative is to use a new subtype (eg. `EpicChip`). This item also need the `Barcode` annotation.
     5The DNA aliquot should be linked to `PhysicalBioAssay` item representing the actual EPIC chip that was used. It ~~might~~ is be possible to re-use the `BeadChip` suptype for this with but with new value for the `BeadChipType` annotation (eg. `Epic850K`). ~~The other alternative is to use a new subtype (eg. `EpicChip`).~~ This item also need the `BeadChipID` annotation.
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    7 The `Barcode` allows us to find the data files related to the chip, since they are all contained in a single sub-directory. Each chip has 8 locations which should be linked to the 8 DNA aliquots used on the chip. The DNA aliquots need to have this information as annotations (`R01C01`...`R08C01`).
     7The `BeadChipID` allows us to find the data files related to the chip, since they are all contained in a single sub-directory. Each chip has 8 locations which should be linked to the 8 DNA aliquots used on the chip. The DNA aliquots need to have this information as annotations (`R01C01`...`R08C01`).
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    99Scanning of the chip is represented by a !DerivedBioAssay `Scan` item. Dates, Scanner ID, etc. can be extracted from the data we have and should be imported as annotations or linked Hardware items. The `DataFilesFolder` annotation will point to a folder with the scan data. We will need the *.idat files in the next step.