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chanzuckerberg / single-cell-curation

Code and documentation for the curation of cellxgene datasets
MIT License
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Amend assay type for methylation data in "An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types"" #61

Closed pablo-gar closed 3 years ago

pablo-gar commented 3 years ago

The assay type for the methylation datasets (see below) was set as "methylation profiling (EFO:0000751)". However, according to the paper the specific assay is snmC-seq for which there is an appropriate ontology term "snmC-seq (EFO:0008939)"

Solution

When revisions of published collections are available, change assay type to "snmC-seq" with term id "EFO:0008939" for the following datasets:

Which are from this collection:

https://cellxgene.cziscience.com/collections/ae1420fe-6630-46ed-8b3d-cc6056a66467

jahilton commented 3 years ago

Have a ticket with EFO for the more specific snmC-seq2 term https://github.com/EBISPOT/efo/issues/1236

jahilton commented 3 years ago

Updated to snmC-seq during migration (snmC-seq2 is not in the current pinned EFO version)