COVID-19

Owned by Maryam Abdallah
Last updated: Sept 12, 2022
2 min read

Overview

The COVID-19-specific variables in i2b2 are based on an ontology developed by Visweswaran, Shyam et al1 in an effort to harmonize COVID-19 data in the electronic medical records across several institutions. There are 50,000+ concepts in this ontology that are available for researchers to query in i2b2. The ontology is publicly available at https://github.com/shyamvis/ACT-COVID-Ontology

1Visweswaran, Shyam et al. “Development of a Coronavirus Disease 2019 (COVID-19) Application Ontology for the Accrual to Clinical Trials (ACT) network.” JAMIA open vol. 4,2 ooab036. 19 Apr. 2021, doi:10.1093/jamiaopen/ooab036

Inclusion Criteria for COVID-19 Cohort

Patients are included in the COVID-19 dataset if they meet at least one criterion from any of the following categories:

B97.29 - Other coronavirus as the cause of diseases classified elsewhere (recorded on or after 01/01/2020)

B97.21 - SARS-associated coronavirus as the cause of diseases classified elsewhere (recorded on or after 01/01/2020)

U07.1 - 2019-nCoV acute respiratory disease

87635 – Infectious agent detection by nucleic acid (DNA or RNA); severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Coronavirus disease (COVID-19)), amplified probe technique

U0001 – Coronavirus testing using the Centers for Disease Control and Prevention (CDC) 2019 Novel Coronavirus Real Time RT-PCR Diagnostic Test Panel

U0002 – Validated non-CDC laboratory tests for SARS-CoV-2/2019-nCoV (COVID-19)

94531-1 - SARS coronavirus 2 RNA panel (respiratory specimens)

94306-8 - SARS coronavirus 2 RNA panel (unspecified specimens)

94503-0 - SARS coronavirus 2 Ab.IgG & IgM panel (qualitative results)

94504-8 - SARS coronavirus 2 Ab.IgG & IgM panel (quantitative results)

94500-6 - SARS coronavirus 2 RNA (qualitative) (Respiratory specimen)

94533-7 - SARS coronavirus 2 N gene (qualitative) (Respiratory specimen)

94534-5 - SARS coronavirus 2 RdRp gene (qualitative) (Respiratory specimen)

94532-9 - SARS-related coronavirus + MERS coronavirus RNA (qualitative) (Respiratory specimen)

94502-2 - SARS-related coronavirus RNA (qualitative) (Respiratory specimen)

94309-2 - SARS coronavirus 2 RNA (qualitative) (Unspecified specimen)

94316-7 - SARS coronavirus 2 N gene (qualitative) (Unspecified specimen)

94307-6 - SARS coronavirus 2 N gene (qualitative, CDC primer-probe set N1) (Unspecified specimen)

94308-4 - SARS coronavirus 2 N gene (qualitative, CDC primer-probe set N2) (Unspecified specimen)

94510-5 - SARS coronavirus 2 N gene (quantitative) (Unspecified specimen)

94311-8 - SARS coronavirus 2 N gene (quantitative, CDC primer-probe set N1) (Unspecified specimen)

94312-6 - SARS coronavirus 2 N gene (quantitative, CDC primer-probe set N2) (Unspecified specimen)

94315-9 - SARS coronavirus 2 E gene (qualitative) (Unspecified specimen)

94509-7 - SARS coronavirus 2 E gene (quantitative) (Unspecified specimen)

94314-2 - SARS coronavirus 2 RdRp gene (qualitative) (Unspecified specimen)

94511-3 - SARS coronavirus 2 ORF1ab region (quantitative) (Unspecified specimen)

94310-0 - SARS-like coronavirus N gene (qualitative) (Unspecified specimen)

94313-4 - SARS-like coronavirus N gene (quantitative) (Unspecified specimen)

94507-1 - SARS coronavirus 2 Ab.IgG (qualitative) (Serum or Plasma)

94505-5 - SARS coronavirus 2 Ab.IgG (quantitative) (Serum or Plasma)

94508-9 - SARS coronavirus 2 Ab.IgM (qualitative) (Serum or Plasma)

94506-3 - SARS coronavirus 2 Ab.IgM (quantitative) (Serum or Plasma)

94547-7 - SARS coronavirus 2 Ab.IgG+IgM (qualitative) (Serum or Plasma)

 

Data Available

Click on each category below for more details on the data available

Course of Illness

Diagnosis Data

Diagnostic Lab Tests