From 934c2e77325f6a47f6617471addc22a461b02d7b Mon Sep 17 00:00:00 2001 From: Brian Raymor Date: Tue, 5 Nov 2024 11:20:19 -0800 Subject: [PATCH] updated assay_ontology_term_id (#1085) --- schema/drafts/5.3.0.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/schema/drafts/5.3.0.md b/schema/drafts/5.3.0.md index e5a62639..425c6f8a 100644 --- a/schema/drafts/5.3.0.md +++ b/schema/drafts/5.3.0.md @@ -410,7 +410,7 @@ Curators MUST annotate the following columns in the `obs` dataframe:
  • the most accurate descendant of "EFO:0010183" for single cell library construction
    • - If assay_ontology_term_id is either "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2 then all observations MUST contain the same value.

    + If assay_ontology_term_id is either a descendant of "EFO:0010961" for Visium Spatial Gene Expression or "EFO:0030062" for Slide-seqV2 then all observations MUST contain the same value.

    An assay based on 10X Genomics products SHOULD either be "EFO:0008995" for 10x technology or preferably its most accurate descendant. An assay based on SMART (Switching Mechanism at the 5' end of the RNA Template) or SMARTer technology SHOULD either be "EFO:0010184" for Smart-like or preferably its most accurate descendant.


    Recommended values for specific assays:

    @@ -443,8 +443,16 @@ Curators MUST annotate the following columns in the `obs` dataframe: "EFO:0008931" - Visium Spatial Gene Expression - "EFO:0010961" + Visium Spatial Gene Expression V1 + "EFO:0022857" + + + Visium CytAssist Spatial Gene Expression, 6.5mm + "EFO:0022859" + + + Visium CytAssist Spatial Gene Expression, 11mm + "EFO:0022860"