Closed PozhidayevaDarya closed 1 year ago
Sorry, just noticed something that I didn't catch in my first round of testing...
The GeoMx DSP ROI Segment Annotation Metadata
template is essentially meant to be the machine-output Segment Summary file (example from OHSU attached), with minimal adjustments, right? We informed centers that it is just the file as is, but with HTAN Parent Biospecimen ID
added. However, currently many Segment Summary file column names would need to be modified to match the template values and pass validation.
e.g. ROI X Coordinate
--> GeoMx DSP ROI X Coordinate
@PozhidayevaDarya if this is expected behavior, please feel free to ignore- happy to leave as is :)
Otherwise, maybe a possible suggestion could be to only include fields in our validation template that match exactly to the Segment Summary file fields, and allow all others to be 'custom' additions?
@clarisse-lau Thanks for highlighting this! Yeah this was expected on my end. I kind of wanted to prioritize things being clear in the data model and I feel like it wouldn't be big deal for them to just rename the column before submitting. I'm happy to change it though if folks disagree!
Ok! Happy to leave however you think best
My only concern is that it is not too clear how the template should be used and which column names should be changed (and to what) e.g. is template attribute Segment Tag
equivalent to Segment Name
or Tags
in the summary file?
There are also a number of non-required fields in the template that don't exactly align (name or case-wise) with the summary file. If they're not required, then the center isn't obligated to change names to align with the template. So the source fields may ultimately just be entered 'as is' as custom fields, bypassing validation and use of these attributes in the data model. | HTAN Template | Segment Summary file |
---|---|---|
ROI QC Passed | QC Status | |
GeoMx DSP Slide Scan Height | Scan Height | |
GeoMx DSP Slide Scan Width | Scan Width | |
GeoMx DSP RCC or DCC Filename | RCC File Name | |
Positive Norm Factor | Positive norm factor |
We should also clarify the instructions that were provided to OHSU (submission of this template will in fact require more than just addition of the biospecimen column) - though maybe this can wait until the PR has been merged and the template is actually in DCA :)
That all makes sense and honestly I will adjust it to match exactly to prevent issues. Thanks @clarisse-lau :)
Information
Changes based on suggestions from Vesteinn & Clarisse following testing:
Additional modifications: Split "NanoString GeoMx DSP ROI Segment Annotation Metadata" into DCC/RCC-specific templates
PR: https://github.com/ncihtan/data-models/pull/283