Smoking status in MIMICIII_Derived dataset

[hakim89]

Prerequisites

• [X ] Put an X between the brackets on this line if you have done all of the following:
  • Checked the online documentation: https://mimic.mit.edu/
  • Checked that your issue isn't already addressed: https://github.com/MIT-LCP/mimic-code/issues?utf8=%E2%9C%93&q=

Description

Description of the issue, including:

• what you have tried
• references to similar issues
• queries demonstrating your question (if applicable)

I am trying to look for the smoking status in the MIMIC3 dataset. Can't find any columns when I search the information schema DB.

 SELECT
  *
 FROM
  `physionet-data.mimiciii_derived.INFORMATION_SCHEMA.COLUMN_FIELD_PATHS`
 WHERE
  column_name like "%smok%"

referring to the mechanical power repository here. https://github.com/alistairewj/mechanical-power/blob/master/sql/mpwr-smoker.sql look like it can be done in MSFT sql but the same functionality can't be done in google Bigquery.

If you can point me to where the smoking hx field is located, I would greatly appreciate it. If one is not available, I will try to rewrite the above smoking hx query to use Lucene/Bigquery syntax.

Thank you.

[alistairewj]

You should be able to adapt that query pretty easily to BigQuery. It is looking in the discharge summaries to find mentions of smoking history, as usually the smoking history is described in the social history section. You'll need to use the mimiciii_notes dataset instead of mimiciii_clinical on BigQuery though - that's where the noteevents table is.

[hakim89]

Thank you. I was able to convert the regex to BigQuery syntax like below. WHEN REGEXP_CONTAINS(ne.text, r'(never|not|not a|none|non|no|no history of|no h\/o of|denies|denies any|negative)[\s-]?(smoke|smoking|tabacco|tobacco|cigar|cigs)') Thank you for your reply.