location_id Data Format in Person Table in final OMOP

USM-CHU-FGuyon / BlendedICU

OMOP standardization pipeline for ICU databases

MIT License

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location_id Data Format in Person Table in final OMOP #13

Closed xinyuejohn closed 10 months ago

xinyuejohn commented 10 months ago

Hi,

I noticed a potential issue in the person table where location_id is mapped to strings:

self.person['location_id'] = self.labels.source_dataset.map(
                                                        {'amsterdam': 'NL',
                                                         'hirid': 'SU',
                                                         'mimic': 'US',
                                                         'eicu': 'US'})

Per the OMOP CDM v5.4 standards (OMOP CDM v5.4), location_id should be an integer, serving as the primary key for the location table. Could you adjust this to meet the OMOP specifications?

Thanks for looking into this!

USM-CHU-FGuyon commented 10 months ago

Hi, Thanks for helping the project ! I will fix this sometime during the week. I will also add :

countries in the LOCATION table
location_id for mimic3 patients Getting back to you soon

USM-CHU-FGuyon commented 10 months ago

It should be fixed now, please tell me if you find other issues especially regarding OMOP standardization !