#1393 closed task (fixed)

Release exporter changes due to Oncoarray data

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

Description

In ticket #1346, we added data from Oncoarray SNP chips to lorry. A new item chain from BloodDNA was created: BloodDNA -> BeadChip -> Scan -> GenotypeCall -> OncoArray500K.

The current release exporter stops at the topmost BloodDNA level. In the database there are typically 3 levels with BloodDNA 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 (8)

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 7007:

References #1393: Release exporter changes due to Oncoarray data

Added OncoarrayWriter implementation. It currently only export name and type of Oncoarray items and link directly to the top-most BloodDNA parent item. No other annotations or files are exported yet.

comment:3 by Nicklas Nordborg, 13 months ago

In 7011:

References #1393: Release exporter changes due to Oncoarray data

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

comment:4 by Nicklas Nordborg, 13 months ago

In 7014:

References #1393: Release exporter changes due to Oncoarray data

Export VCF and GTC files. They are merged to a single directory in the release.

comment:5 by Nicklas Nordborg, 13 months ago

In 7016:

References #1393: Release exporter changes due to Oncoarray data

The GTC file type is linked to DERIVEDBIOSSAY in Reggie, but on relax it need to be linked to the RAWBIOSSAY type. We need to use the item type defined in the factory instead of on the file type itself.

comment:6 by Nicklas Nordborg, 13 months ago

In 7017:

References #1393: Release exporter changes due to Oncoarray data

Added scanner and software information to the export.

comment:7 by Nicklas Nordborg, 13 months ago

In 7018:

References #1393: Release exporter changes due to Oncoarray data

Added more annotation for the oncoarray.

comment:8 by Nicklas Nordborg, 13 months ago

Resolution: fixed
Status: acceptedclosed
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