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gf-dcc / data-model

Gray Foundation data model
https://gf-dcc.github.io/data-model/
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Patch/clin data updates concept 2 #89

Closed anngvu closed 7 months ago

anngvu commented 7 months ago

Alternative to #87 (likely merge this one and close the other).

@cconrad8 So we could do a separate template for ovarian cohort or we could use the current core one. But since there is a lot of overlap, I agree keeping in it in the same template to keep it simple. Click on the preview below, then in the template choose the right Cohort to highlight the more specific attributes. image

github-actions[bot] commented 7 months ago

Test Suite Report

Template Generation

template result link
BulkMethylation-seqLevel1 :smile: template link
BulkMethylation-seqLevel2 :smile: template link
BulkMethylation-seqLevel3 :smile: template link
CohortCoreTemplate :smile: template link
ImagingLevel2 :smile: template link
ImagingLevel2Channels :smile: template link
ScRNA-seqLevel1 :smile: template link
ScRNA-seqLevel2 :smile: template link
ScRNA-seqLevel3 :smile: template link
ScRNA-seqLevel4 :smile: template link

Manifest Validation

TODO

cconrad8 commented 7 months ago

@anngvu yes this is very nice! I like the one template

cconrad8 commented 7 months ago

@anngvu not related to this PR, but it's not clear to me where "Class BRCA1 and class BRCA2" originated from and what the expected fields are - do you have info on that?

anngvu commented 7 months ago

@cconrad8 Glad you asked! It stands for "classification of the BRCA mutation pathogenicity". Here's an early example of what classBRCA1/2 was going to be used for: https://github.com/gf-dcc/data-model/blob/main/drafts/core_sample.json#L8. This was supposed to address https://github.com/gf-dcc/data-model/issues/9. You can add the description and make sure they're linked to the right enum definitions, which would help finally close #9 and #88 😃 !