#1451 closed task (fixed)

Release exporter changes due to Methylation data

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.44
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

In tickets #1418 and #1419, we added data from Methylation EPIC chips to lorry. A new item chain from DNA was created: DNA -> DNA aliquot -> BeadChip -> Scan -> Methylation. The BeadChip and Scan items are shared with the Oncoarray genotyping pipeline (#1393).

The current release exporter stops at the topmost DNA level. In the database there is typically a single intermediate DNA aliquot before the BeadChip level.

We need to decide which data that should be included in releases and how to represent the item chain in a more condensed way.

Change History (7)

comment:1 by Nicklas Nordborg, 13 months ago

Milestone: Reggie v4.xReggie v4.44
Status: newaccepted

comment:2 by Nicklas Nordborg, 13 months ago

In 7006:

References #1451: Release exporter changes due to Methylation data

Added MethylationWriter implementation. It currently only export name and type of Methylation items and link directly to the DNA parent item. No other annotations or files are exported yet.

comment:3 by Nicklas Nordborg, 13 months ago

In 7009:

References #1451: Release exporter changes due to Methylation data

A safer implementation for getting the top-most DNA that should be linked with the methylation item.

comment:4 by Nicklas Nordborg, 13 months ago

In 7010:

References #1451: Release exporter changes due to Methylation data

Added information about the bead array chip used, including id, type and position.

comment:5 by Nicklas Nordborg, 13 months ago

In 7019:

References #1451: Release exporter changes due to Methylation data

Added scanner and software information to the export.

comment:6 by Nicklas Nordborg, 13 months ago

In 7020:

References #1451: Release exporter changes due to Methylation data

Added more annotation for the methylation data.

comment:7 by Nicklas Nordborg, 13 months ago

Resolution: fixed
Status: acceptedclosed
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