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 | |
| ... |