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Help Request in MIMIC-IV to OMOP CDM conversion

Hi guys! I’ve been working on the OMOP CDM conversion of MIMIC-IV recently, based on the GitHub repo (https://github.com/OHDSI/MIMIC). I have just finished the conversion and realized that my Measurement table nor some of the Observation table are not mapped. I acknowledge that this is a significant issue as these two tables are very important for a lot of research applications. I have checked that voc_concept table does indeed contain concept_ids for the two tables (Measurement and Observation), but I am not sure why this error is happening.

On another note, it says on the repository that “POC_3 data is loaded and prepared manually (todo: provide both manual scripts)” for waveform_collecting. I don’t have the manual scripts for these. Is this the potential reason why some of my final tables are incorrect? If so, could someone please provide the POC_data scripts?

Thank you so much.

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Hi @jiwoonoh - glad to hear about your MIMIC-IV work. Are you saying that your measurement table comes back empty? That is indeed unexpected. Can you elaborate?

In this repository we made a small “proof of concept” for data derived from waveform recordings (blood pressure, ECG monitor), so that we can show one possible approach for that. However, I would recommend to skip that part, if you try out for yourself. @mkwong has worked (and is working) on that waveform data and could provide you with more background.

Cheers - mik

If you are working with the MIMIC-IV WFDB data, I can provide you some mapping I’ve been using for both the CSV and derived measurements from the waveforms. Regardless of using the clinical vs WFDB data - you should have data that can map into measurements and observations. Please elaborate what data you are trying to convert as well as specific examples if possible.

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Thank you for your reply! I’m assuming that waveform collecting process doesn’t really have any connections with the broken Measurement table.

I should’ve elaborated better – all of the concept_ids for my Measurement table is not populated correctly (nor some of the concept_ids for observation table). I’ve realized that my lk_measurement_mapped table also has concept_ids of 0 (after populating data from lk_measurement_clean tables), so it might be a problem somewhere around there. All the other tables are fine, but it’s just that all my measurement table has concept_id of zero, and it says the concept_ids are ‘unmapped’ as well (although I’m sure I ran all the processes well). Could you please provide any potential reason for this problem and a solution for it? Thank you so much.

I’m just using the full MIMIC-IV data. In that case, do you mean that I won’t need to run the waveform collecting process?

If you are loading the “MIMIC-IV data”, typically that means the ICU patient EHR care data. Odd you are getting measurement.measurement_concept_id = 0. There must be a problem in the load ETL if its populating the other fields. Anyway - you do not then have to concern yourself with the MIMIC-IV WFDB data.

Yes, this is what I get from cdm_measurement table. I’m not sure what problems there could be. I am quite in rush with the data – is it possible for me to obtain the correct full data just for measurement and observation tables?

Sorry for jumping into the discussion. I’m just curious: does it mean we’re able to map our obtained MIMIC-IV dataset into OMOP-CDM? I’m probably interested in mapping my data too.

Yes, it’s definitely possible!

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Hi, guys. I’ve been working on the OMOP CDM conversion of MIMIC-III recently, based on the GitHub repo (GitHub - MIT-LCP/mimic-omop: Mapping the MIMIC-III database to the OMOP schema). At one step, it required me to have NIH licence (which I have no idea how to get sooner) I have applied a forum and all. I am a researcher in Computing Science and would be very helpful to get recommendation on how to fasten up the process of convesion.
Is it possible to covert with some easier way?

Hi Divya. I implemented that MIMIC-III code with some modifications and it worked well. Let me pull out my notes and look at what I did. Was a couple years ago. Will be back in touch, Gigi

That will be really helpful :slight_smile: