Annotation tool: feature complete

[surchs]

Context

The annotation tool has been sitting at "almost ready" for a long while, and we'd like it to join the rest of the party of "look, it works". Here we're focusing purely on the technical aspect of having the required functionality. But there are other aspects such as ease of use and guidance that we will address soon after.

See for more context: https://docs.google.com/document/d/1jzAWI6dzBCYVPsdczt3U49flOuWRPSOdDQmU9dBRelM/edit?usp=sharing

Why

• Part of Grow the amount and usefulness of data #11
• To enable new node-sites to annotate data on their own
• To make sure users have a good experience for the entire workflow, and they tend to start with annotations
• So that we can use our own tools to add data to nodes we're currently maintaining
• To deliver on our commitments to our friends and collaborators who want to reuse this tool

Outcomes

• Tool creates a valid bagel.json, i.e.: I can give the file to the CLI and it'll be happy with it
• I can classify "healthy control" as part of the diagnosis annotation workflow
• The discrete value mapping dropdowns give me all valid options to choose from (e.g. diagnosis -> SNOMED-CT)
• I can annotate assessment tools

What

• Make sure assessment tool annotations make it to the output .json annotation_tool#585
• [ENH] Adding 'Subject ID'/'Participant ID' to 'Annotations' section of data dictionary annotation_tool#477
• Add ability to annotate assessment tools annotation_tool#285
• Make sure we create valid .json annotation_tool#597
• Provide all valid options for dropdowns of discrete categories annotation_tool#589
  • Lets get the task names from Cognitive Atlas annotation_tool#238
  • Provide all valid diagnosis options annotation_tool#591
• Allow annotation of healthy controls annotation_tool#553
• Ensure there's no MissingValues key for a column when it has no missing values
  • e.g. "MissingValues": [] --> this should not happen ?
  • CLI doesn't mind empty missingValues
• Filter SNOMED-CT terms to children of "disorders of central nervous system" #52

[surchs]

@alyssadai / @rmanaem, can you take a look to

• see if we're missing any implementation things ("What")
• if there are existing issues that cover the non-issueified steps
• have any other notes

[alyssadai]

Added a couple related issues under What. This list otherwise looks good to me!

[rmanaem]

@alyssadai When you get a chance could you see if CLI is happy with the output of the annotation tool with the new changes?
We can then check the last item on the outcomes Tool creates a valid bagel.json, i.e.: I can give the file to the CLI and it'll be happy with it and close this.