Channel Metadata Antibody Role Valid Value

PozhidayevaDarya commented 3 months ago

Information

In the submission of GeoMx Channel Metadata, the submitter reached out with a request:

Antibody Role (col G): “secondary antibody” is inaccurate: Syto13 is not an antibody at all. It is a cell-permeant dye/stain that exhibits enhanced green fluorescence when bound to nucleic acid. Not sure how to fix col G; neither option given is valid:

Possible to leave it blank (ie. make it not required) Or better add “N/A” as an option Out or reach I know, ideally this header would be more useful if more flexible and it was called “Molecular Probe Type” (then options could be primary antibody, secondary antibody, dye/stain..).

RRID Identifier (col J): Syto13 is not an antibody and the RRID ID doesn’t seem to include non-antibody molecular probes. ”AB _0000000” – would be fine in combination with I and K edits as noted.

Proposed change:

Add an additional valid value to the Antibody Role Attribute - "Neither - Dye/Stain" Add "Not Applicable" as valid value to RRID Identifier Attribute

Additional context

PR is linked here: https://github.com/ncihtan/data-models/pull/432

Implementation checklist

[x] Branch created
[x] HTAN.model.csv editied and pushed
[x] HTAN.model.jsonld validated and created by Github action
[x] PR opened
[ ] PR approved
[ ] PR merged into main
[ ] New Component added to ncihtan/HTAN-data-curator (if required)
[ ] DCA update requested
[ ] DCA updated

aclayton555 commented 3 months ago

I see this was added mid-sprint. If possible, let's try to wrap this up as part of our 24-6 sprint, which ends 2024.06.28

PozhidayevaDarya commented 3 months ago

@aclayton555 Thank you!

ncihtan / data-models