search

cellannotation / cell-annotation-schema

General, open-standard schema for cell annotations
9 stars 1 forks source link

Add Author objects #103

Open dosumis opened 3 months ago

dosumis commented 3 months ago

Author objects - draft #102

github-actions[bot] commented 3 months ago

Validation Passes.

dosumis commented 3 months ago

Before we merge this, we need a strategy for compatibility with CAP author fields.

github-actions[bot] commented 1 month ago

Validation Passes.

dosumis commented 1 month ago

TBD - do we still need a separate string field for author?

dosumis commented 1 month ago

Discussed in DOS group call. Still not clear how to proceed if we want bidirectional conversion with CAP. This would be fixed if CAP changed their AnnData specification to support an author table (dataframe) in uns, where each row has various author details - ditching the currently separate fields for this.

@evanbiederstedt - please comment.

evanbiederstedt commented 1 month ago

CC @rm1113

I think this can be closed and disregarded CC @ubyndr

In the end, we decided to not use additional fields for list of authors. So the old logic is fine.

dosumis commented 3 weeks ago

Reopening based on discussion with @evanbiederstedt

github-actions[bot] commented 3 weeks ago

Validation Passes.

github-actions[bot] commented 3 weeks ago

Validation Passes.

github-actions[bot] commented 3 weeks ago

Validation Passes.

dosumis commented 3 weeks ago

Hi @JABelfiore & @ubyndr - did some work on this with @evanbiederstedt - can you please review. Ta

github-actions[bot] commented 3 weeks ago

Validation Passes.

dosumis commented 1 week ago

@hkir-dev @ubyndr I'm happy with this, but there are backwards compatibility issues, so we will need a plan for updating existing taxonomies before releasing.

@hkir-dev - can you plan for this and estimate the work involved?

hkir-dev commented 1 week ago

We need to update:

Additionally we will need a new TDT function that will harmonise existing manual taxonomy curations to this kind of data structure changes. Since we don't have any manual curations in the taxonomies yet, we are recreating TDT tables from scratch now.