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Dimitri Papadopoulos Orfanos edited this page Feb 26, 2021 · 64 revisions

We discuss software infrastructure for databank operations of the c-VEDA project.

Recruitment and acquisition centres

The c-VEDA project is an accelerated and planned missing longitudinal study. Participants are organized into 3 age bands which may be administered different instruments:

Age band ID Age band name Age range
C1 Children 6-11
C2 Adolescents 12-17
C3 Adults 18-23

The multiple recruitment and acquisition centres represent the socio-cultural diversity of India:

  • 5 geographical regions
    • Punjab and adjoining states (PGIMER)
    • Eastearn Coalfields (KOLKATA)
    • Northeast India (IMPHAL)
    • Bengaluru & Mysuru (MYSORE, NIMHANS, SJRI)
    • Chittoor (RISHIVALLEY)
  • urban and rural areas
ID CENTRE Site Location MRI
11 PGIMER Postgraduate Institute of Medical Education & Research Chandigarh Siemens Verio
12 IMPHAL Regional Institute of Medical Sciences Imphal, Manipur —
13 KOLKATA Regional Occupational Health Centre (Eastern),
Indian Council of Medical Research 		Kolkata, West Bengal Siemens Trio
14 RISHIVALLEY Rishi Valley Rural Health Centre Rishy Valley, Andhra Pradesh —
15 MYSORE CSI Holdsworth Memorial Hospital Mysuru, Karnataka Philips Ingenia
16 NIMHANS NIMHANS Bengaluru, Karnataka Siemens Skyra /
Philips Ingenia
17 SJRI St. John's Research Institute Bengaluru, Karnataka —

From acquisition centres to databank

Acquisition centres send pseudonymized data to the database team:

  • Acquisition centres collect clinical and environmental data using Psytools. The databank team download CSV files pseudonymized with PSC1 identifiers directly from the Delosis server.
  • Acquisition centres pseudonymize biological samples at the source using PSC1 identifiers. The c-VEDA biobank team collect samples and collate genetic data before sending them to the databank.
  • Acquisition centres anonymize DICOM files before sending them to the databank. Again subjects are identified by their PSC1 identifier only.

The database team, acting as a trusted third party, pseudonymize data a second time, by converting dates to age and PSC1 identifiers to PSC2. We provide a list of valid identifiers to help end-users detect and investigate possible identifier errors.

Databank operations

System software has been installed on the c-VEDA server as described in file /cveda/databank/framework/INSTALL.txt.

Application software has been deployed on the c-VEDA server under /cveda/databank/framework/git:

cd /cveda/databank/framework/git
git clone https://github.com/cveda/cveda_databank.git
git clone https://github.com/cveda/cveda_misc.git
git clone https://github.com/cveda/cveda_r.git

Databank operations, based on the above application software, are described in specific pages:

c-VEDA web site

c-VEDA database

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