Preparing the phenotypic data

To use the Neurobagel annotation tool, please prepare the tabular data for your dataset as a single, tab-separated file (.tsv).

Note

In the Neurobagel context, tabular or phenotypic data for a dataset refers to any demographic, clinical/behavioural, cognitive, or other non-imaging-derived data of participants which are typically stored in a tabular file format.

General requirements for the phenotypic TSV

The TSV must contain a minimum of two columns: at least one column must contain subject IDs, and at least one column must describe demographic or other phenotypic information (for variables currently modeled by Neurobagel, see the data dictionary section).
If the dataset has a corresponding BIDS directory (i.e., imaging data), at least one column in the TSV must contain subject IDs that match the names of BIDS subject subdirectories. Further, the IDs in this column must be the same or a superset of the subject labels in the BIDS directory. That is, Neurobagel does not currently allow for datasets where subjects have BIDS data but are not represented in the phenotypic TSV.

Accepted forms of tabular data

Depending on your dataset, your tabular data may represent one or more of the following:

A BIDS `participants.tsv` file

If you have a BIDS compliant participants.tsv that contains all the demographic and clinical/behavioural information for participants, you can annotate this file with Neurobagel's annotation tool to create a data dictionary for the file.

Example TSV:

participant_id	age	sex	tools
sub-01	22	female	WASI-2
sub-02	28	male	Stroop
...

A longitudinal data file

If you have longitudinal tabular data (e.g. age collected at multiple sessions/visits), then the information for all sessions should be combined into a single TSV. Each row must describe a unique combination of subject and session.

Example TSV:

participant_id	session_id	age	tools
sub-01	ses-01	22	WASI-2
sub-01	ses-02	23
sub-02	ses-01	28	Stroop
...

Tip

A participants.tsv file with multiple sessions is not BIDS compliant. If you want to store multi-session phenotypic data in a BIDS dataset, you could do so in the phenotype/ subdirectory (see also the BIDS specification section on Longitudinal and multi-site studies).

Multiple participant or session identifier columns

In some cases, there may be a need for more than one set of IDs for participants and/or sessions.

For example, if a participant was first enrolled in a behavioural study with one type of ID, and then later joined an imaging study under a different ID. In this case, both types of participant IDs should be recorded in the tabular file.

The only requirement is that the combination of all ID values for a row is unique.

Example invalid TSV:

participant_id	alternative_participant_id	...
sub-01	SID-1234
sub-01	SID-2222
sub-02	SID-1234

The same rules apply when multiple session IDs are present.

Example valid TSV:

participant_id	alt_participant_id	session_id	alt_session_id	age
sub-01	SID-1234	ses-01	visit-1	22
sub-01	SID-1234	ses-02	visit-2	23
sub-02	SID-2222	ses-01	visit-1	28
...