Resource Reference

The CALM-Brain resource consists of data collected from at-risk families along multiple modalities - Magnetic Resonance Imaging, Electroencephalography, Functional near-infrared spectroscopy, Eye tracking, Cognition, Genomics, and Clinical assessments. This document describes how these modalities are stored. For information on how these were acquired, please refer to the resource publication. For information on how these can be accessed, please refer to Almirah documentation.

Data in the resource can be divided into two based on their content: tabular records and data files. Tabular records are stored as tables in a Relational Database Management System. Data files are stored in various repositories in an in-house G-node Infrastructure instance (GIN).

Clinical assessments

Participants undergo a series of clinical assessments that aid in understanding their background, experiences, and aid in the diagnosis. Each assessment is stored as a table in the database cbm of the Relational Database Management system. In cases where a questionnaire has multiple modules, each module is stored as a table to reduce redundancy. In this setup, each record typically corresponds to a row in the tables. In case of repetitive questions, there might be more than one row for each record as the tables are normalized. The recommended way to identify a record is using a combination of D-number and Session ID.

The list of tables and the questionnaires they map to are below:

Table name	Questionnaire or Table details
subjects	List of all subjects recruited
assessments	List of assessments performed
physical_examination	General Physical examination of subject
recent_life_events	Interview for Recent Life Events (IRLE)
mental_status_assessment	General comments on mental status.
adult_adhd_self_report_scale	Adult ADHD self-report scale (version 1.1)
adult_temperament	Adult temperament questionnaire
adverse_childhood_experiences	Adverse Childhood Experiences International Questionnaire (ACE-IQ)
clinical_global_impression	Clinical Global Impression Scale
global_assessment_of_functioning	Global Assessment of Functioning
hamilton_anxiety_rating	Hamilton Anxiety Rating Scale (HARS)
hamilton_depression_rating	Hamilton Depression Rating Scale (HDRS)
hindi_mental_state_examination	Hindi Mental State Examination (HMSE)
mini_ipip_scale	20 Item mini-IPIP
modified_kuppuswamy_socioeconomic_scale	Socioeconomic Status Scale
negative_symptoms_assessment	Schedule for Assessment of Negative Symptoms (SANS)
positive_symptoms_assessment	Schedule for Assessment of Positive Symptoms (SANS)
agoraphobia	M.I.N.I International Neuropsychiatric Interview (Agoraphobia module)
alcohol_abuse	M.I.N.I International Neuropsychiatric Interview (Alcohol Abuse module)
alcohol_dependence	M.I.N.I International Neuropsychiatric Interview (Alcohol Dependence module)
antisocial_personality_disorder	M.I.N.I International Neuropsychiatric Interview (Antisocial Personality Disorder module)
anorexia_nervosa	M.I.N.I International Neuropsychiatric Interview (Anorexia Nervosa module)
bulimia_nervosa	M.I.N.I International Neuropsychiatric Interview (Bulimia Nervosa module)
obsessive_compulsive_disorder	M.I.N.I International Neuropsychiatric Interview (Obsessive-Compulsive Disorder module)
panic_disorder	M.I.N.I International Neuropsychiatric Interview (Panic Disorder module)
post_traumatic_stress_disorder	M.I.N.I International Neuropsychiatric Interview (Posttraumatic Stress Disorder module)
socialphobia	M.I.N.I International Neuropsychiatric Interview (Social Phobia module)
suicidality	M.I.N.I International Neuropsychiatric Interview (Suicidality module)
severity_of_alcohol_dependence
work_and_social_adjustment_scale	Work and Social Adjustment Scale (WSAS)
yale_brown_obsessive_compulsive_scale	Yale-Brown Obsessive Compulsive Scale (Rating module)
yale_brown_obsessive_compulsive_symptoms	Yale-Brown Obsessive Compulsive Scale (Symptoms module)
young_mania_rating_scale	Young's Mania Rating Scale (YMRS)

Endophenotype data files

Data acquired via neuroimaging (MRI), electroencephalography (EEG), functional near-infrared spectroscopy (NIRS), and eye tracking (eyetrack) are called endophenotype data files. The raw data for each of these modalities is encrypted and stored in the cbm/{modality} GIN repository. The {modality} name used for each is mentioned in brackets. The organized (anonymized and format converted) version of the endophenotype data files is stored in the cbm/data repository collectively.

Both the raw data and the organized data are stored according to the BIDS specification.

Genetic data files

Genome sequence reads are stored in the cbm/genetics GIN repository in a BIDS-like specification. This has been separated from the endophenotype data files based on standard practice.