mimiciii_derived.pivoted_uo was not found when Calculating Sofa concept
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Description
Prerequisites
- 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/
- Similar ISSUE when calculating Sofa Score (mimic-iii/concepts/pivot/pivoted_sofa.sql) and can't find several data. But it does not apply to my situation
Description
I am trying to write an SQL for a modified version of the SOFA score based on mimic-iii/concepts/pivot/pivoted_sofa.sql. However, when I try to run pivoted_sofa.sql (I haven't made any change yet), it reports "Not found: Table physionet-data:mimiciii_derived.pivoted_uo was not found in location US " Error
Since in README for concepts folder, it mentions
You do not need to generate the concepts if you are using BigQuery! They have already been generated for you. If you have access to MIMIC-III on BigQuery, look under
physionet-data.mimic_derived.
So I checked the file under the direction of physionet-data.mimic_derived in my BigQuery, to see if I could find the result of mimic-iii/concepts/pivot/pivoted_uo.sql. As folder columns show at the left of the image, pivoted_uo is missing. I can see other files (i.e. pivoted_gcs) and am able to access them through SQL.
Any idea why only mimiciii_derived.pivoted_uo is missing?
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- Fork the repository and make your change on a branch.
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Research direction
Start with mimic-iii/concepts/pivot/pivoted_sofa.sql and the concepts README, then compare its pivoted_uo reference with the tables available under physionet-data.mimic_derived in BigQuery. Confirm whether pivoted_uo is absent from the published dataset or whether the query uses a different dataset path. Done means documenting the cause and the correct way to run the SOFA query.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- sql
- Domain
- databases
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100