Dataset creation workflow

What's on this page:

• answer to "how do I add a dataset to a running graph"
• note: this is pre-refactor of the annotator

Create neurobagel metadata

You need:

• a BIDS dataset with a tabular demopgraphics file (participants.tsv)

Demographics

• I load the participants.tsv in the app
• If a data dictionary exists (participants.json) I also load it for added contex
• if I encounter diagnosis I look up the terms as described here
• once I am done, I download a .json format version of the clean / harmonized table to my file system

Diagnosis

• I open the SNOMED-CT terms browser: https://browser.ihtsdotools.org/?
• I pick the international version here
• I look for the term I am annotating, and then filter for "disorder" in the filter tag.
• When I find a matching term, I cope the unique, numerical SNOMED ID from the terms description (e.g. SCTID: 404684003 -> 404684003)
• I enter this numerical value in the annotator in the following format: "snomed:404684003" and then move to the next term

Imaging

To extract the imaging metadata from the BIDS dataset, I use the bagelbids tool.