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chanzuckerberg / single-cell-explorer

Hosted version of cellxgene
MIT License
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Make plan to remove dataset drawer #483

Open signechambers1 opened 2 years ago

signechambers1 commented 2 years ago

Currently, the info button in explorer expands the dataset drawer. This info is a duplicate of information on the Collections page and we'd like to remove it, however it also contains singleton metadata information (such as organism).

This ticket is a placeholder to come up with a plan for removing it.

brianraymor commented 2 years ago

See related singleton discussion in single-cell-ux.

brianraymor commented 1 year ago

There is also a serious issue with user discoverability of the hidden dataset drawer. Often when the drawer is referenced, users are unaware of its existence. Here's a recent thread from one of the curators that illustrates:

Curator [8:36 AM] Hello, we recently observed that the cell metadata for most of the objects in this collection (Siletti et al, 2022) does not include the cell_type column. This was surprising for us since it’s required to add the cell types according to the schema. We were wondering if there is any specific reason why the cell_type column was not included or if we may have missed something. Additionally, we would appreciate it if you could add the cell type information to the objects or provide the data in another format that includes at least one or two levels of cell annotation, such as cell types and broad cell types/cell compartments. Thanks!

jahilton [8:58 AM] They are there (as you noted, they are required). In the viz, to access the obs metadata that are not variable within the dataset, you need to click on the :information_source: in the upper right. That will open the “dataset drawer” In the downloaded files, it will appear as usual in the obs dataframe The obscurity of the :information_source: has been noted to the devs several times so hopefully we’ll get a solution that makes the information in the drawer more accessible.

Curator [9:01 AM] Oh sorry we haven’t noticed that, thanks for your reply!!