Preparing the phenotypic data

Looking for more general guidelines on how to organize your dataset?

We recommend also checking out Nipoppy, a protocol for standardized organization and processing of clinical-neuroimaging datasets that extends BIDS. Neurobagel tools are designed to be compatible with data organized according to the Nipoppy specification, although you do not need to use Nipoppy in order to use Neurobagel.

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

All datasets

A valid dataset for Neurobagel MUST include a TSV file that describes participant attributes.

The TSV MUST contain:

A minimum of two columns
At least one column containing subject IDs

Only one subject ID column can be annotated

Neurobagel currently does not support annotating multiple subject ID columns so you must choose one as the primary ID during annotation
At least one column that describes demographic or other phenotypic information
Unique values in the subject ID column or unique combinations of IDs if both subject and session ID columns are present

The TSV MAY contain:

A column with session IDs, e.g. if the dataset is longitudinal

Only one session ID column can be annotated

Neurobagel currently does not support annotating multiple session ID columns so you must choose one as the primary ID during annotation

The TSV MUST NOT contain:

Missing values in the columns you plan to annotate as containing the primary subject IDs and session IDs (if available)

For all variables currently modeled by Neurobagel, see the data dictionary section.

Datasets with imaging (BIDS) data

If a dataset has imaging data in BIDS format, Neurobagel additionally requires that:

At least one column in the phenotypic TSV contains subject IDs that match the names of BIDS subject subdirectories. If this condition is not met, you will encounter an error when running the Neurobagel CLI on your dataset to generate Neurobagel graph-ready files, indicating that your BIDS directory contains subjects not found in your phenotypic file.

Note

Subject IDs are case-sensitive and must match BIDS subject IDs exactly for Neurobagel to be able to link phenotypic and BIDS information. e.g., a BIDS ID of sub-MNI001 is not the same as subject IDs sub-mni001 or mni001 in a phenotypic TSV and would not be linked by Neurobagel.
All BIDS subjects are included in the phenotypic TSV, even if they only have BIDS imaging information. Neurobagel does not allow for datasets where subjects have BIDS data but are not represented in the phenotypic TSV (however, subjects who have phenotypic data but no BIDS data are allowed).
If the dataset is longitudinal, the session IDs in the phenotypic TSV MAY match the session IDs in the BIDS dataset, but don't have to.

Examples of valid phenotypic TSVs

Depending on your dataset, your tabular data may look like one 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.

Neurobagel currently supports only one subject ID and one session ID

Neurobagel currently does not support annotating multiple subject or session ID columns in the same TSV file. If you have multiple subject or session IDs, you must choose one to use as the primary ID. Additional subject/session ID columns can still be included in the TSV but will be ignored by Neurobagel.

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
...