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jaygee-on-github / The-APHRC-LSHTM-MUBAS-IDSR-Project

During the pandemic countries in the African region used data systems they built on top of the WHO Integrated Disease Surveillance and Response (IDSR) framework to track COVID-19 and formulate public health responses. Our IDSR project wrangles these data systems into instances of a common data model and conducts network research on top of them.
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Mapping the "admission" #1

Open jaygee-on-github opened 1 year ago

jaygee-on-github commented 1 year ago

The admission is mapped to one or more CONDITION_OCCURRENCEs, depending on whether presenting symptoms were captured or not.

The CONDITION_OCCURRENCE corresponding to the suspected disease (COVID-19) has a condition_concept_id corresponding to "Suspected COVID-19" in ATHENA (37311060). This is a concept from the SNOMED vocabulary. This CONDITION_OCCURRENCE has a condition_status_concept_id corresponding to "Admission diagnosis" in ATHENA (32890). This concept comes from the Condition Status vocabulary. This same CONDITION_OCCURRENCE takes a condition_type_concept_id in line with its "provenance" (32809). This is the concept for a "Case Report Form" in the Type Concept vocabulary.

Alternatively, the condition_concept_id can be "At an increased risk to exposure by Severe acute respiratory system corona virus 2".

jaygee-on-github commented 1 year ago

Tathagata reported that it wasn't feasible to create a CONDITION_OCCURRENCE with a condition_concept_id of "Suspected COVID-19" because this concept_id doesn't belong to the Condition domain in ATHENA. Instead it being to the Observation domain.

In future ETLs (including the one that Amelia and Moses are building, I propose that we create two CONDITION_OCCURRENCEs -- one with an "Admission Diagnosis" -- 32890 -- and the other with a "Confirmed Diagnosis" -- 32893). Both would have the same condition_concept_id 37311061 and different dates. The Admission Diagnosis CONDITION_OCCURRENCE has a date corresponding to when the person was first seen (Line 7 of the WHO CRF) or the date of onset of the first symptoms (Line 18). The Confirmed Diagnosis CONDITION_OCCURRENCE has a date corresponding to if and when the district was notified of the lab results (Lines 27/28).

jaygee-on-github commented 1 year ago

In the absence of an Admission Diagnosis in the synthetic data, we constructed a target cohort of "COVID Suspected from Symptoms" based on a set symptoms Malawi and other MoHs have recorded as additional CONDITION_OCCURRENCEs. See here.