CONP Portal | Dataset


Integrated Biological Markers for the Prediction of Treatment Response in Depression: Data Release from the foundational study of the Canadian Biomarker Integration Network in Depression (CAN-BIND-01)
Creators: Ontario Brain Institute
Contact: Brain-CODE, datarelease@braincode.ca
Licenses: Refer to Brain-CODE Governance Policy
Version: 1.0
Size: 52.0 GB
No of Files: 77
No of Subjects: 323
Primary Publication: Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort. Raymond W. Lam et al. BMC Psychiatry. https://doi.org/10.1186/s12888-016-0785-x
Metadata file: DATS.json
Is About: Homo sapiens
Acknowledges: Ontario Brain Institute, Canadian Institute of Health Research, Government of Ontario
Spatial Coverage: Canada
Other Dates: Start Date: 2013-06-03 00:00:00 -- End Date: 2018-12-31 00:00:00
Description:
The Canadian Biomarker Integration Network in Depression (CAN-BIND) is a national program of research and learning. From 2013 to 2017, data were collected from 211 participants with major depressive disorder and 112 healthy individuals. The objective of this data-set is to integrate detailed clinical, imaging, and molecular data to predict outcome for patients experiencing a Major Depressive Episode (MDE) and receiving pharmacotherapy reflective of standard practice. The clinical characterization consists of symptom assessment, behavioural dimensions, and environmental factors. The neuroimaging data consist of structural, resting and task-based functional, and diffusion-weighted MRI images, as well as scalp-recorded EEG data. The molecular data currently consist of DNA methylation, inflammatory markers and urine metabolites. This data release includes baseline data for 309 participants.

Dataset README information

README.md

Integrated Biological Markers for the Prediction of Treatment Response in Depression

Dr. Sidney Kennedy, Dr. Pierre Blier, Dr. Faranak Farzan, Dr. Benicio Frey, Dr. Jane Foster, Dr. Raymond Lam, Dr. Glenda MacQueen, Dr. Roumen Milev, Dr. Daniel Mueller, Dr. Sagar Parikh, Dr. Susan Rotzinger, Dr. Stephen Strother, Dr. Claudio Soares, Dr. Valerie Taylor, Dr. Gustavo Turecki, Dr. Rudolf Uher, and the CAN-BIND Study Team

Overview

The Canadian Biomarker Integration Network in Depression (CAN-BIND) is a national program of research and learning. From 2013 to 2017, data were collected from 211 participants with major depressive disorder and 112 healthy individuals. The objective of this data-set is to integrate detailed clinical, imaging, and molecular data to predict outcome for patients experiencing a Major Depressive Episode (MDE) and receiving pharmacotherapy reflective of standard practice. The clinical characterization consists of symptom assessment, behavioural dimensions, and environmental factors. The neuroimaging data consist of structural, resting and task-based functional, and diffusion-weighted MRI images, as well as scalp-recorded EEG data. The molecular data consist of DNA methylation, inflammatory markers and urine metabolites.

Data organization

Data is organized into packages by Treatment Group (Control vs Major Depressive Disorder), Imaging Scan Type, Genomic Data Type, and Clinical Data Collection Domain.

Access information

To gain access to Brain-CODE Controlled Data Release data, Study Investigators will submit requests via Data Release Portals at www.braincode.ca. These requests will be reviewed by the Brain-CODE Data Access Committee and the Brain-CODE Steering Committee. Learn more about these Committees in the Brain-CODE Governance Policy (https://braininstitute.ca/docs/Brain-CODE-Governance-Policy-version-FINAL.pdf).

Visit outhe Brain-CODE Knowledge Base to learn more about our data releases.

Citation

Lam, R.W., Milev, R., Rotzinger, S. et al. Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort. BMC Psychiatry 16, 105 (2016). https://doi.org/10.1186/s12888-016-0785-x

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. Future portal functionality may include downloads directly from the web browser. Dataset download is currently enabled through DataLad.

Note: The conp-dataset requires version >=0.12.5 of DataLad and version >=8.20200309 of git-annex.

To install DataLad on your system, please refer to the install section of the DataLad Handbook (installation via miniconda is recommended in order to obtain the latest version of DataLad).

1) Initiate the CONP dataset

To initiate the CONP dataset (conp-dataset), run the following command in the directory where you want CONP datasets to be installed:

datalad install https://github.com/CONP-PCNO/conp-dataset.git

2) Install the braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release dataset

To install the dataset, go into the created conp-dataset directory and run datalad install on the dataset braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release:

cd conp-dataset
datalad install projects/braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release

3) Download the braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release dataset

Now that the DataLad dataset has been installed, go into the dataset directory under projects/braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release.

cd projects/braincode_CAN-BIND_Biomarkers_for_Depression_Baseline_Data_Release

Note that files visible in the dataset are symlinks and will need to be downloaded manually using the datalad get command in the dataset directory:

datalad get <filepath>

Note, if you run datalad get * command, all the files present in the dataset directory will be downloaded.

For more information on how DataLad works, please visit the DataLad Handbook documentation .