Clinical Data in the ODM

Support
, ,
1

A user requested support with integrating COVID-19 case counts and hospitalization data into the larger wastewater/environmental surveillance database that is in ODM format. They were wanting to integrate the data in a wide format.

As a reminder, the wide names for measures follow the structure: compartment_specimen_fraction_measure_unit_aggregation_index_attribute

So the pieces for this clinical data would be:

  • Compartment = hum (for human)
  • Specimen = po (for population)
  • Fraction = NA (not relevant for clinical data)
  • Measure = cov (for covid-19 infection)
  • Unit = confEp (if we’re talking about confirmed cases by episode date) OR
  • Unit = confRep (if we’re talking about confirmed cases by report date) OR
  • Unit = acti (if we’re talking about active cases) OR
  • Unit = hosa (if we’re talking about Hospital admissions) OR
  • Unit = vax1plus, vax2plus, vax3plus, vax4plus, or vax1, vax2, vax3, vax4 (if we’re talking about vaccination levels, depending on how many doses and one weather you want “at least x doses” or “exactly x doses”)
  • Aggregation = 7dma (if we’re talking about a 7-day moving average) OR
  • Aggregation = sum14 (if we’re talking about a rolling sum of previous 14 days -? I’d also recommend checking out the parts for daily count (daiCo) and cumulative count (cuCo)) OR
  • Aggregation = total (if it’s just a count).
  • index = NA (not relevant)
  • Attribute = value (given that we are reporting/integrating the counts/numbers).

So:

  • COVID-19 confirmed cases by episode date by sewershed → hum_po_NA_cov_confEp_total_NA_value
  • 7-day moving average of sewershed’s COVID-19 confirmed cases by episode date → hum_po_NA_cov_confEp_7dma_NA_value
  • COVID-19 active cases by episode date (rolling sum of previous 14 days) by sewershed → hum_po_NA_cov_acti_sum14_NA_value
  • COVID-19 cases by reported date (date case was reported to public health) by sewershed → hum_po_NA_cov_confRep_total_NA_value
  • 7-day moving average of sewershed’s COVID-19 cases by reported date → hum_po_NA_cov_confRep_7dma_NA_value
  • COVID-19 hospital admissions by sewershed → hum_po_NA_cov_hosa_total_NA_value
  • 7-day moving average of sewershed’s COVID-19 hospital admissions → hum_po_NA_cov_hosa_7dma_NA_value
  • COVID-19 vaccine coverage by sewershed - All ages with at least two doses → hum_po_NA_cov_ vax2plus_total_NA_value
  • COVID-19 vaccine coverage by sewershed - All ages with at least three doses → hum_po_NA_cov_ vax3plus_total_NA_value
  • COVID-19 vaccine coverage by sewershed - All ages with at least four doses → hum_po_NA_cov_ vax4plus_total_NA_value

@asmabahamyirou

1 Like
2

Thank you @matthomson. is that make sense to use

  • actiEp - as active cases by episode date
3

For sure! If your active cases are organized/recorded by episode date, then that part makes sense. I’ll double check we don’t already have it, but you should see it in the development dictionary shortly.

1 Like