Created
July 23, 2021 16:20
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Demonstrate the richness of the data that are available in OMOP at UCLH for patients with a stroke phenotype
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-- example script to extract stroke diagnoses | |
-- concept_id pulled from https://athena.ohdsi.org/search-terms/start by searching for ICD or OPCS codes | |
-- e.g. OPCS U54.3 --> https://athena.ohdsi.org/search-terms/terms/44514242 | |
SELECT | |
c.* | |
FROM dsf_omop.condition_occurrence c | |
LEFT JOIN dsf_omop.concept co ON c.condition_concept_id = co.concept_id | |
WHERE | |
-- see https://github.com/spiros/chronological-map-phenotypes/blob/master/secondary_care/ICD_Isch_stroke.csv | |
-- ischaemic stroke | |
co.concept_id IN (443454, 45591475, 45562366, 45605808, 45586592, 45596216, 45605810) | |
OR | |
-- sequaele of ischaemic stroke | |
co.concept_id IN (45533476) | |
OR | |
-- haemorrhagic stroke | |
co.concept_id IN (45576882, 45591473, 45562361, 45557547, 45567186, 45605803, 45562360, 45557546, 45576881, 376713, 40475099) | |
OR | |
-- sequaele of haemorrhagic stroke | |
co.concept_id IN (45538404) | |
--LIMIT 3 | |
; | |
-- I think the nice thing would then be to show the richness of the data here | |
-- so if we joined against visit occurrence onto a CTE then we could report how many | |
-- different measuresments we have for these patients | |
-- and then repeat for obs, procedures, drugs, etc. | |
WITH q AS ( | |
SELECT | |
M.measurement_concept_id | |
,COUNT(*) N | |
FROM dsf_omop.measurement M | |
GROUP BY M.measurement_concept_id | |
ORDER BY n DESC | |
LIMIT 1000 | |
) | |
SELECT | |
q.measurement_concept_id | |
,C.concept_name | |
,q.n | |
FROM q | |
LEFT JOIN dsf_omop.concept C | |
ON q.measurement_concept_id = C.concept_id | |
; | |
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