S4. Saving my annotations of AIT99 for others to see

[hkir-dev]

Epic:

Description

User: The same scientists from Use Cases 2 #99 and 3 #100 .   Use Case: We have confirmed that AIT99 is set up properly on our computers and have completed some annotations, and now we want to share these with the other annotators. What we have:

• AIT99 loaded into TDT, with some completed annotations

What we need to know:

• I’ve made a bunch of changes now and want to make sure these get saved locally.  What do I do?  Ideally, I’d also like to update the h5ad file with these annotations. Is this step even necessary, or do all annotations get saved with other folks.
• Once I’m done annotating, how do I share this information back to Scientist 1 and to the other expert annotators? Which action buttons do I push?
• Now I see annotations other folks. How do I know who added each annotation, so I can ask them about it or debate it? More generally, how can we ensure that all of our annotations are stored in AIT99 and that they get properly attributed to the correct person?

Tasks

• [ ] Task1
• [ ] Task2
• [ ] Task3

[dosumis]

Sketch of new action menus here: https://github.com/brain-bican/taxonomy-development-tools/issues/91#issuecomment-1980617177

I’ve made a bunch of changes now and want to make sure these get saved locally. What do I do? Ideally, I’d also like to update the h5ad file with these annotations. Is this step even necessary, or do all annotations get saved with other folks. Once I’m done annotating, how do I share this information back to Scientist 1 and to the other expert annotators? Which action buttons do I push?

Users have 2 options

1. file: save - local. This ensures all changes are saved and committed to the user's computer
2. file: save - sync. This saves and synchronises with changes with any made by other editors. The users's changes are now visible to all other editors who choose to sync their's. Notes: We think it might be best to make save - sync the default, so that people don't forget to share their edits with others

We also have a Publish option. This makes a release with a Permanent URL that includes a version stamp. We would encourage editors to make a release anytime they want others to use the annotated data for analysis. That way the analysis can be tied to a specific version. It is essential to note that PUBLIC visibility is controlled at the level of GitHub permissions. As long as the repo is Private and shared with some agreed set of collaborators, publish - shares only with them. Publishing to a PURL also allows anyone with the URL + access to use our Python libs to merge the data into an AnnData file and inspect that.

Merging into the linked AnnData file is optional and can be run at any time. This gives editors that chance to view and analyse the data + latest annotations in their tool of choice so that they can then make informed decisions about edits to the taxonomy. We currently have no mechanism for updating a shared AnnData file. Supporting this would require infrastructure work that is beyond our group's current capacity.

Now I see annotations [from] other folks. How do I know who added each annotation, so I can ask them about it or debate it? More generally, how can we ensure that all of our annotations are stored in AIT99 and that they get properly attributed to the correct person?

https://github.com/brain-bican/taxonomy-development-tools/issues/110

[dosumis]

Discussion:

• Suggestion:
  • sync always happens with save and on loading. Opting out of this is harder.
• Need Undo
  • currently only undoes the last operation - worth investigating how much work this would be & then assess priority.
• We need a warning through browser if closing a tab without saving.