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Columbia Open Health Data for COVID-19 Research

About

Columbia Open Health Data (COHD) for COVID-19 Research provides access to counts and visit prevalence (i.e., prevalence from electronic health records) of conditions, procedures, drug exposures, and the co-occurrence frequencies between them. Count and frequency data were derived from the Columbia University Irving Medical Center's OHDSI database including inpatient data. Counts are the number of visits with the concept, e.g., diagnosed with a condition, exposed to a drug, or a procedure was performed. Frequencies are the number of visits with the concept divided by the total number of visits in the dataset. Clinical concepts (e.g., conditions, procedures, drugs) are coded by their standard concept ID in the OMOP Common Data Model. To protect patient privacy, all concepts and pairs of concepts where the count ≤ 10 were excluded, and counts were randomized by the Poisson distribution.

Datasets from three primary cohorts are available:

  1. COVID-19: Hospitalized patients aged 18 or older with a COVID-19 related condition diagnosis and/or a confirmed positive COVID-19 test during their hospitalization period or within the prior 21 days. Date range: March 1, 2020 to September 1, 2020. This cohort is also further stratified by sex (male and female) and age (adult: 18-64, senior: 65+).
  2. General inpatient: All hospitalized patients aged 18 or older. Date range: January 1, 2014 to December 31, 2019.
  3. Influenza: Hospitalized patients aged 18 or older who had at least one occurrence of influenza conditions or pre-coordinated positive measurements or positive influenza testing in the prior 21 days or during their hospitalization period. Date range: January 1, 2014 to December 31, 2019.

Both hierarchical and non-hierarchical datasets are available for each cohort. In the hierarchical datasets, the counts for each concept include the visits from all descendant concepts. For example, the count for ibuprofen (ID 1177480) includes visits with Ibuprofen 600 MG Oral Tablet (ID 19019073), Ibuprofen 400 MG Oral Tablet (ID 19019072), Ibuprofen 20 MG/ML Oral Suspension (ID 19019050), etc.

COHD-COVID was developed at the Columbia University Department of Biomedical Informatics as a collaboration between the Weng Lab, Tatonetti Lab, and the NCATS Biomedical Data Translator program (Red Team). This work was supported in part by grants: NCATS 1OT2TR003434, NLM R01LM012895, NCATS OT3TR002027, NLM R01LM009886-08A1, and NIGMS R01GM107145.

Instructions

Retrieve data for a single concept

  1. Choose a data set to retrieve data from
  2. Choose Concept 1 by either:
    1. entering the OMOP concept ID (e.g., "313217" (without the quotation marks) for "Atrial fibrillation"
    2. searching for a concept by typing the name and selecting the concept ID from the drop down list
  3. Press the "Get single concept" button

Retrieve association data for pair(s) of concepts

  1. Choose a data set to retrieve data from
  2. Choose an association method
  3. Choose Concept 1 by either:
    1. entering the OMOP concept ID (e.g., "313217" (without the quotation marks) for "Atrial fibrillation"
    2. searching for a concept by typing the name and selecting the concept ID from the drop down list
  4. Choose Concept 2 by either:
    1. leaving the field blank to retrieve associations with all concepts
    2. entering an OMOP domain to retrieve associations with all concepts in the given domain (hint: press the "down" keyboard key when this field is blank to show the list of OMOP domains present in the selected data set)
    3. entering the OMOP concept ID (e.g., "313217" (without the quotation marks) for "Atrial fibrillation"
    4. searching for a concept by typing the name and selecting the concept ID from the drop down list
  5. Press the "Get concept pairs" button
  6. For results between multiple pairs, links to download the data as JSON or CSV are presented below the results table

Examples

Example 1: Atrial fibrillation

COHD can be used to retrieve the patient prevalence of individual concepts. In this example, information for the condition "Atrial fibrillation" (OMOP concept ID 313217) is retrieved from the 5-year non-hierarchical data set. The results show the concept definition (concept ID, concept name, concept domain, concept class, source vocabulary for the OMOP concept, and concept code in the source vocabulary) and the occurrence data (patient count and patient prevalence).

Example 2: Drugs associated with atrial fibrillation

COHD can be used to retrieve association data calculated from the co-occurrences of pairs of concepts. In this example, the relative frequency of drugs associated with the condition "Atrial fibrillation" (OMOP concept ID 313217) is retrieved from the 5-year non-hierarchical data set. The relative frequency informs investigators that among patients who have taken the drug identified in each row, this proportion of patients experienced atrial fibrillation at some time within the 5-year inclusion period of the data set. Note that the relative frequency can exceed the upper limit of 100% due to the Poisson randomization.

Example 3: Conditions associated with albuterol

Similar to Example 2, in this example, the relative frequency of conditions associated with the drug "Albuterol 0.83 MG/ML Inhalant Solution" (OMOP concept ID 19123989) is retrieved from the 5-year non-hierarchical data set. The relative frequency informs investigators that among patients who have had the condition identified in each row, this proportion of patients have taken "Albuterol 0.83 MG/ML Inhalant Solution" at some time within the 5-year inclusion period of the data set. Note that the relative frequency can exceed the upper limit of 100% due to the Poisson randomization.

API

The COHD RESTful SmartAPI provides a more powerful method to interact with the COHD data. The web user interface provides access to a few of the most frequently used endpoints in the COHD API. The COHD API additionally provides access to metadata, methods to explore the OMOP concept hierarchy, and cross-referencing between OMOP and external ontologies.

Useful Links