mimic Chartevents / Labevents -> omop Measurement / Observation

[parisni]

hi

OMOP

[CLINICAL] The MEASUREMENT table contains records of Measurement, i.e. structured values (numerical or categorical) obtained through systematic and standardized examination or testing of a Person or Person's sample. The MEASUREMENT table contains both orders and results of such Measurements as laboratory tests, vital signs, quantitative findings from pathology reports, etc.

[CLINICAL] The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.

MIMIC

CHARTEVENTS contains all the charted data available for a patient. During their ICU stay, the primary repository of a patient’s information is their electronic chart. The electronic chart displays patients’ routine vital signs and any additional information relevant to their care: ventilator settings, laboratory values, code status, mental status, and so on. As a result, the bulk of information about a patient’s stay is contained in CHARTEVENTS. Furthermore, even though laboratory values are captured elsewhere (LABEVENTS), they are frequently repeated within CHARTEVENTS. This occurs because it is desirable to display the laboratory values on the patient’s electronic chart, and so the values are copied from the database storing laboratory values to the database storing the CHARTEVENTS. WARNING: Some items are duplicated between the labevents and chartevents tables. In cases where there is disagreement between measurements, labevents should be taken as the ground truth.

The LABEVENTS data contains information regarding laboratory based measurements. The process for acquiring a lab measurement is as follows: first, a member of the clinical staff acquires a fluid from a site in the patient’s body (e.g. blood from an arterial line, urine from a catheter, etc). Next, the fluid is bar coded to associate it with the patient and timestamped to record the time of the fluid acquisition. The lab analyses the data and returns a result within 4-12 hours

Based on that descriptions, I d'say the way to direct the data could be: -> all labevents -> measurements -> chartevents[duplicates related with labs] -> trash -> chartevents[vital signs, with numerical values] -> measurements -> chartevents[vital signs, with categorical values] -> measurements -> chartevents[vital signs, with free text values] -> observations

What about you @alistairewj & @tompollard ?

[alistairewj]

That sounds sensible.