Annotating controls

[seanhatton]

Description

I need guidance on coding diagnoses. In https://neurobagel.org/user_guide/annotation_tool/ "Sex and Diagnosis rows (categorical values)" I want to add a diagnosis column to the participant.tsv, just asking:

Do we code "controls" as "controls", "healthy" etc? Is there a list of diagnoses so I choose the right category (e.g. depression, MMD, bipolar II0)

Relevant documentation pages

No response

Additional details

No response

[alyssadai]

Hi @seanhatton, thanks for the question!

The annotation tool is currently undergoing a major refactor, so the usage instructions and screenshots are a little out of date. We will add a note about this refactor to the docs and the README shortly.

That said, we currently expect labels for healthy controls and specific diagnoses to be in the same column(s) in an input phenotypic TSV. For an example, see the pheno_group column in example_synthetic.tsv and its corresponding annotation in example_synthetic.json from the neurobagel_examples repo.

In the annotation tool, after mapping a column to "Diagnosis", you can annotate individual values in the column as encoding healthy controls by selecting "Healthy Control" in the diagnosis dropdown or using the "Mark as healthy control" button.

Hope this helps!

[alyssadai]

Duplicate of #225

[alyssadai]

@seanhatton, if I answered your questions, mind closing this issue?

[seanhatton]

Thank you for the insight!