PROCEDURE_OCCURRENCE

URL to CommonDataModel

• PROCEDURE_OCCURRENCE

Source Tables

procedures_icd

• procedure_type_concept_id = 38003622 ("Procedure recorded as diagnostic code")
• the ICD9 codes are transformed to match to omop.concept
• mimic.sequence column is lost in the process
• the procedure date is the admission end date

procedureevents_mv

• procedure_type_concept_id = 38000275 ("EHR order list entry")
• code are mapped to SNOMED procedure in procedure_concept_id
• the datetime is the begining of the procedure
• quantity is the duration of the procedure in minutes
• rows cancelled have not been exported from mimic
• visit_detail_id is assigned

cptevents

• procedure_type_concept_id = 257 ("Hospitalization Cost Record")
• the procedure date is the chardate when absent substitued with admission start date

Mapping used

cpt4_to_concept

• it maps CPT4 codes to information in the mimic.cpteevents table
• \copy (SELECT distinct '[' || coalesce(costcenter,'') || '][' || coalesce(sectionheader,'') || '] ' || subsectionheader || ' ' || coalesce(description, '') as procedure_source_value FROM mimic.cptevents order by 1) TO '/tmp/cpt4_to_concept.csv' CSV HEADER QUOTE '"';
• all the relevant information have been collapsed into procedure_source_value field
• the mapping to cpt4 is done manually. When not relevant the field omop_mapping_is_sure is equal to 0

procedure_to_concept

• it maps SNOMED codes to itemid in the mimic.procedureevents_mv table
• No idea how the mapping was made by google

Examples

Explanation of procedure_type_concept_id

SELECT concept_name, concept_id, count(1)
FROM procedure_occurrence
JOIN concept ON concept_id = procedure_type_concept_id
GROUP BY concept_name, concept_id ORDER BY count(1) DESC;

concept_name	concept_id	count
Hospitalization Cost Record	257	573146
EHR order list entry	38000275	250284
Procedure recorded as diagnostic code	38003622	240095

Some interesting record procedures

SELECT procedure_source_value, count(1)
FROM procedure_occurrence
WHERE procedure_type_concept_id = 38000275
GROUP BY procedure_source_value ORDER BY count(1) DESC
LIMIT 10;

procedure_source_value	count
Chest X-Ray	31953
20 Gauge	27631
18 Gauge	20058
EKG	13659
Arterial Line	12374
Invasive Ventilation	10442
Blood Cultured	9873
CT scan	8510
Extubation	7909
Multi Lumen	7664

SELECT concept_name, count(1)
FROM procedure_occurrence
JOIN concept ON concept_id = procedure_source_concept_id
WHERE procedure_type_concept_id = 38003622
GROUP BY concept_name ORDER BY count(1) DESC
LIMIT 10;

concept_name	count
Venous catheterization, not elsewhere classified	14731
Insertion of endotracheal tube	10333
Enteral infusion of concentrated nutritional substances	9300
Continuous invasive mechanical ventilation for less than 96 consecutive hours	9100
Transfusion of packed cells	7244
Extracorporeal circulation auxiliary to open heart surgery	6838
Continuous invasive mechanical ventilation for 96 consecutive hours or more	6048
Prophylactic administration of vaccine against other diseases	5842
Coronary arteriography using two catheters	5337
Arterial catheterization	4737

SELECT procedure_source_value, count(1)
FROM procedure_occurrence
WHERE procedure_type_concept_id = 257
GROUP BY procedure_source_value ORDER BY count(1) DESC
LIMIT 10;

procedure_source_value	count
Hospital inpatient services	268296
Critical care services	106469
Pulmonary	101563
Consultations	25925
Cardiovascular system	21485
Respiratory system	10516
Dialysis	9778
Musculoskeletal system	6275
Digestive system	4979
Nervous system	3662