Phenotypic files

Record start time

brainflex record semantic_harmonization start

Annotation

Download the following files to your local machine:

  • nipoppy_study/tabular/pheno.tsv

  • nipoppy_study/tabular/pheno.json (if present)

Then, go through the Neurobagel annotation tool workflow using these files. The following columns need to be annotated:

  • Participant ID

  • Session ID

  • Age

  • Sex

Save the annotated data dictionary to nipoppy_study/tabular/pheno_annotated.json.

Harmonization

Harmonize the phenotypic data using Neurobagel’s CLI:

bagel harmonize-pheno \
    --pheno nipoppy_study/tabular/pheno.tsv \
    --dictionary nipoppy_study/tabular/pheno_annotated.json \
    --output nipoppy_study/tabular/harmonized.tsv

The output file at nipoppy_study/tabular/harmonized.tsv should have 4 columns with harmonized column names and values.

head nipoppy_study/tabular/harmonized.tsv
Example output
nb:ParticipantID	nb:SessionID	nb:Sex	nb:Age
sub-1	ses-unnamed	snomed:248153007	20.0
sub-2	ses-unnamed	snomed:248152002	25.0
sub-3	ses-unnamed	snomed:248153007	30.0
sub-4	ses-unnamed	snomed:248152002	35.0
sub-5	ses-unnamed	snomed:248153007	40.0
sub-6	ses-unnamed	snomed:248152002	45.0
sub-7	ses-unnamed	snomed:248153007	50.0
sub-8	ses-unnamed	snomed:248152002	55.0
sub-9	ses-unnamed	snomed:248153007	60.0

Record end time and answer questions

brainflex record semantic_harmonization end