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OMOP CDM 5.4 missing country

Developers
,
#1

Hello community,

I’m currently building an ETL to map oncology patients in Chile to the OMOP CDM 5.4.
While building it I noticed the country “Chile” is missing from “Geography” domain concepts, therefore I can’t map a patient home address to the LOCATION.country_concept_id column.

I understand the Geography information was fetched from OpenStreetMap, but I don’t understand why a country is missing in the vocabulary database. I used Athena to confirm it (query).

My question is if I should map it to concept 4073752 (query) which is the concept for “Chile” of the Observation domain. Will be any down sight by doing so or I should not worry about it?

Thank you for your time!

#2

To be comply with the ETL specification you should put zero in location.country_concept_id. Which indicates there is no matching concept. (I will add an issue to the Vocabulary git that there is no concept for Chile). But at the same time, I do not see a down side to using concept 4073752 until the vocabulary is corrected.

#3

Hello, @nbravo

Good question. Since all your patients are from Chile I see no problems with using both solutions: either 0 or Observation Chile, as @DTorok stated.

Regarding OSM vocabulary, it hasn’t been refreshed since the very first release, where, obviously, not all available countries were added. The choice was due to known active OMOP users, big CDM instances, and OSM simplicity of chosen countries. And now we should reconsider that decision. Any other countries you see as needed?

I hope we can get in touch on this question.

#4

Hello @zhuk,

Argentina has the same problem (no to confused the “Argentina” results in this query, those are zones of other regions of the planet).

I suppose the vocabulary should have all possible countries of the planet, I noticed there are 246 distinct concepts with the relationship “Is a **** country”. I’m currently using this list to map countries (although I’m using only one country).

Thank you all for your help!

#5

I suggest using either the list of UN member countries or WHO member countries, and every country on the chosen list should be added.

#6

Friends:

This is a conversation that touches a bunch of aspects of that:

  1. Country is not really useful for the vast majority of databases, because they rarely cross country boundaries. So, a database in Chile likely contains only Chileans, which means, every record will contain Chile as the country in the LOCATION. Useless information.
  2. For databases that do, we need country concepts. Which we have in OSM, as @zhuk pointed out. The correct concept is Chille. But nobody is aware of that, because
    • We haven’t de-standardize all the other Chiles
    • Instead of using OSM as a world-wide geographic hierarchy, which it is, we introduced full addresses into the LOCATION table, which is a shame. Instead, we should have a service that takes addresses (or parts thereof) as input and spits out the right OSM concept. We would also need a service that allows for calculating distances between them.
#7

Friends,

I say we should add all LATAM countries :slight_smile: No bias … :wink:

Christian, the concept you mentioned is within France and part of Lons-le-Saunier

We should definitely have that

Sweet!

#8

So I’m using this thread also to discuss the UMI alpha-3 country code which stands for the United States Minor Outlying Islands

There is no corresponding concept in OSM at the moment, we have in SNOMED the concept 45769937, however, this is not adequate for the LOCATION table.

Im working currently on ETL process that originated from US-based Health Insurance
company, however, and there are patients scattered all across the US, Canada, Virgin Islands, Hawaii, UMI, etc.

Would love if a corresponding concept will be added to UMI as well, if possible :slight_smile:

#9

@gil.frenkel:

Couple questions:

  • I thought those islands are uninhabited. What do you know the rest of the world doesn’t?
  • The islands themselves, which do not form a political, administrative or geographical unity, are in OSM. Can you pick, say, Howland Island?
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