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sql/echo_data.sql

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+-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
+DROP TABLE IF EXISTS echo_data; CREATE TABLE echo_data AS 
+-- This code extracts structured data from echocardiographies
+-- You can join it to the text notes using ROW_ID
+-- Just note that ROW_ID will differ across versions of MIMIC-III.
+
+select ROW_ID
+  , subject_id, hadm_id
+  , chartdate
+
+  -- charttime is always null for echoes..
+  -- however, the time is available in the echo text, e.g.:
+  -- , substring(ne.text, 'Date/Time: [\[\]0-9*-]+ at ([0-9:]+)') as TIMESTAMP
+  -- we can therefore impute it and re-create charttime
+  , PARSE_DATETIME
+  (
+      '%Y-%m-%d%H:%M:%S',
+      FORMAT_DATE('%Y-%m-%d', chartdate)
+      || REGEXP_EXTRACT(ne.text, 'Date/Time: .+? at ([0-9]+:[0-9]{2})')
+      || ':00'
+   ) AS charttime
+
+  -- explanation of below substring:
+  --  'Indication: ' - matched verbatim
+  --  (.*?) - match any character
+  --  \n - the end of the line
+  -- substring only returns the item in ()s
+  -- note: the '?' makes it non-greedy. if you exclude it, it matches until it reaches the *last* \n
+
+  , REGEXP_EXTRACT(ne.text, 'Indication: (.*?)\n') as Indication
+
+  -- sometimes numeric values contain de-id text, e.g. [** Numeric Identifier **]
+  -- this removes that text
+  , cast(REGEXP_EXTRACT(ne.text, 'Height: \\x28in\\x29 ([0-9]+)') as numeric) as Height
+  , cast(REGEXP_EXTRACT(ne.text, 'Weight \\x28lb\\x29: ([0-9]+)\n') as numeric) as Weight
+  , cast(REGEXP_EXTRACT(ne.text, 'BSA \\x28m2\\x29: ([0-9]+) m2\n') as numeric) as BSA -- ends in 'm2'
+  , REGEXP_EXTRACT(ne.text, 'BP \\x28mm Hg\\x29: (.+)\n') as BP -- Sys/Dias
+  , cast(REGEXP_EXTRACT(ne.text, 'BP \\x28mm Hg\\x29: ([0-9]+)/[0-9]+?\n') as numeric) as BPSys -- first part of fraction
+  , cast(REGEXP_EXTRACT(ne.text, 'BP \\x28mm Hg\\x29: [0-9]+/([0-9]+?)\n') as numeric) as BPDias -- second part of fraction
+  , cast(REGEXP_EXTRACT(ne.text, 'HR \\x28bpm\\x29: ([0-9]+?)\n') as numeric) as HR
+
+  , REGEXP_EXTRACT(ne.text, 'Status: (.*?)\n') as Status
+  , REGEXP_EXTRACT(ne.text, 'Test: (.*?)\n') as Test
+  , REGEXP_EXTRACT(ne.text, 'Doppler: (.*?)\n') as Doppler
+  , REGEXP_EXTRACT(ne.text, 'Contrast: (.*?)\n') as Contrast
+  , REGEXP_EXTRACT(ne.text, 'Technical Quality: (.*?)\n') as TechnicalQuality
+FROM noteevents ne
+where category = 'Echo';