chanzuckerberg / single-cell-data-portal

The data portal supporting the submission, exploration, and management of projects and datasets to cellxgene.

MIT License

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Citations in RDS datasets incorrectly reference H5AD dataset versions #6671

Closed brianraymor closed 7 months ago

brianraymor commented 8 months ago

Context

I was examining RDS datasets in RStudio and noted that the citation references the H5AD dataset version and not the RDS dataset version:

cellxgene@misc[["citation"]] [1] "Publication: https://doi.org/10.1126/sciadv.adh1914 Dataset Version: https://datasets.cellxgene.cziscience.com/188dfb70-dd81-44ec-a8fd-648d54cb7b5e.h5ad curated and distributed by CZ CELLxGENE Discover in Collection: https://cellxgene.cziscience.com/collections/8c4bcf0d-b4df-45c7-888c-74fb0013e9e7"

See the requirements and RDS example in citation.

danieljhegeman commented 8 months ago

Brainstorming initial solution idea, which is slightly hacky, but would get the job done: base the rds conversion off of an h5ad file that has the rds-version citation in it.

brianraymor commented 8 months ago

This impacts Embedding "publication/citation" information of queried cells to seurat object.

joyceyan commented 8 months ago

Conversion to RDS is here: https://github.com/chanzuckerberg/single-cell-data-portal/blob/main/backend/layers/processing/make_seurat.R#L16 It uses the sceasy package to do the conversion: https://github.com/cellgeni/sceasy

Note that we will eventually want to remove in 5.1: https://github.com/chanzuckerberg/single-cell-data-portal/issues/6672 so if it's easier to use a different package that could be one potential solution.