Psytools

We use Psytools questionnaires to collect demographics, clinical and environmental data:

Psytools	Acronym	Instrument name
TS		Testing Situation
SDIM		Socio-demographic Information and Migration questions
EEQ		Environmental Exposures Questionnaire
APQ_CHILD	APQ	Alabama Parenting Questionnaire - Child form
ACEIQ	ACE-IQ	Adverse Childhood Experiences - International Questionnaire
SCQ		School Climate Questionnaire
SFQR		Short Food Questionnaire - Revised
MINI5KID	MINI-KID	Mini International Neuropsychiatric Interview for Children and Adolescents
ASSIST		Alcohol, Smoking, and Substance Involvement Screening Test
FHQ		Family History Questionnaire
MPQ		Medical Problems Questionnaire
PDS		Pubertal Development Scale
DS		Digit Span (PEBL)
CORSI		Corsi block tapping test (PEBL)
KIRBY		Now-or-later test (PEBL)
TMT		Trail Making Test (PEBL)
WCST		Wisconsin Card Sorting Test (PEBL)
SST		Stop Signal Task
BART		Balloon Analogue Risk Task
ERT		Emotion Recognition Task
SOCRATIS		Social Cognition RAting Tools in Indian Setting
ANTHROPOMETRY		Anthropometry
PHIR		Pregnancy History Interview - Revised
IFVCS		Indian Family Violence and Control Scale
CBQ_PARENT		Children's Behavior Questionnaire
APQ_PARENT	APQ	Alabama Parenting Questionnaire - Parent form
SDQ_PARENT	SDQ	Strengths and Difficulties Questionnaire - Parent version
SDQ_CHILD	SDQ	Strengths and Difficulties Questionnaire - Child version
SDQ_ADULT	SDQ	Strengths and Difficulties Questionnaire - Adult version
DEBRIEF		Debrief proforma
AAQ		Adolescent Attachment Questionnaire
SCAMP_SELF	SCAMP	Study of Cognition, Adolescents and Mobile Phones - self report questionnaire
SCAMP_PARENT	SCAMP	Study of Cognition, Adolescents and Mobile Phones - parent questionnaire
EATQr		Early Adolescent Temperament Questionnaire - Revised
PBI		Parental Bonding Instrument
ATQ		Adult Temperament Questionnaire
BIG5		Big-Five Personality Test
MINI5	MINI	Mini International Neuropsychiatric Interview - version 5

Tasks may differ in each age band:

Age band ID	Age range	# Psytools tasks
C1	6-11	29
C2	12-17	33
C3	18-23	33

Details can be found in the Recruitment and Assessment Administration Manual of the c-VEDA project. Here we merely describe how questionnaires are downloaded from the Delosis server as CSV files, then anonymized and further pseudonymized.

Date of birth

We rely on the date of birth (DOB) to further anonymize questionnaires, by changing the date of all events related to a subject (be it a child or a parent) into an age in days at the event. For that we subtract the date of the event to the date of birth. Here is an example of typical Python code:

from datetime import datetime
from cveda_databank import DOB_FROM_PSC1

psc1 = '110001234567'

date_of_birth = DOB_FROM_PSC1[psc1]

timestamp_of_event = datetime.strptime(event, '%Y-%m-%d %H:%M:%S.%f')
date_of_event = timestamp_of_event.date()
age_in_days = date_of_event - date_of_birth

Initially, the authoritative sources for the date of birth used to be Psytools questions ACEIQ_C2 and PHIR_01. Unfortunately there were discrepancies and no way to decide. Additional Excel recruitment files are now provided (recruitment_file_PGIMER_04-06-2018.xlsx for example) that contains results from further investigations. This will probably be the authoritative source for date of birth. Because new discrepancies were in turn detected in the Excel file itself, I have written a script mri/cveda_mri_collect.py to report discrepancies so that acquisition centres can update the Excel file if possible — the Psytools questionnaires will unfortunately not be updated.

De-identification

The goal is to further de-identify Psytools questionnaires using further pseudonymization and anonymization techniques:

1. PSC1 codes are converted to PSC2 codes in field User code.
2. We remove cross-checking questions without scientific purpose from all Psytools questionnaires. Specifically questions id_check_gender, ID_check_gender, id_check_dob, ID_check_dob should only be used for error checking with PSC1 codes and not used with PSC2).
3. We substitute age of subject in days for dates, as described above:
   • in time stamps Completed Timestamp and Processed Timestamp for all questions,
   • in field Trial result of questions ACEIQ_C3, PDS_07a, PHIR_01 and PHIR_02.
4. In the future we may remove or sanitize other questions, if they contain other sensitive information such as names.

Processing

Store identifiers for the Delosis server in the ~/.netrc file of the service account on the c-VEDA server.

Install Ubuntu package moreutils which provides command ts and create a specific directory for log files:

sudo apt-get install moreutils
sudo mkdir /var/log/databank
sudo chown cveda:cveda /var/log/databank

Finally set a crontab on the c-VEDA server to run script /cveda/databank/framework/git/cveda_misc/crontab/cveda_psytools.sh:

sudo crontab -u cveda - <<EOF
10 4 * * * /cveda/databank/framework/git/cveda_misc/crontab/cveda_psytools.sh
EOF

• The Python script cveda_databank/psytools/cveda_psytools_download.py exports Psytools data from the Delosis server into CSV files.
• The R script cveda_r/R/cveda_psytools_derive.R derives Psytools data and converts from long to wide format.
• The Python script cveda_databank/psytools/cveda_psytools_deidentify.py further de-identifies Psytools data.

Codebook, format and units

There is no codebook yet. Field Trial result in CSV files exported from Psytools includes:

• dates (format is dd-mm-yyyy),
• measures of length (formatting rules are currently quite loose and include 12.3 inch, 12.3INCH, 12.3CM, 12.3 cms, 12.3 which would require extensive curation to extract useful information),
• integers,
• floats,
• a choice of F and M for gender
• ...

This needs to be improved as questionnaires mature.