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Wide MAPPING table (in vocabulary) (problems with relationship)

#21

Let me add some thought here:

  1. A wide mapping table should serve both OMOP vocabularies and custom project-related mappings.
    That’s why there are 2 options for linkage:
  • in addition to source_concept_id add source_vocabulary_id / source_code combination, but they’re not unique for some vocabularies and 2 approaches at once doesn’t seem consistent.
  • handle custom mappings using 2B+ source concepts and forget source_to_concept_map table, what creates some difficulties in implementation.

  1. Text string, being a type of the source_code_description and information that sometimes lands on the value_as_string field, is probably required to be added. But wouldn’t it be better to have the source_code_description by itself? Seems no, since it’s a duplication of the concept_name from the concept table.
    But once we introduce the source_string field, the custom mappings are not being processed using the 2B+ concepts. This conflicts with item 1.

  2. Unit of measure. May be reflected in the source in different ways:

  • being a part of the question or answer. It works well since we have target_unit field.
  • being a separate entity coming from another field. Isn’t the concept of the wide mapping table is to provide ETL with a comprehensive way of mapping (without using any additional custom vocabularies and logic, i.e. for unit)? But if we add the source_unit field, it gets us to a сombinatorial explosion for most of the real-world data sources, even thought it might be useful (affecting the target concept) for clean vocabularies/sources.

BTW, the concept of the wide mapping table will be presented tomorrow March 19 at 10 am Eastern Time during the EHR WG call.

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#22

Is there a recording of this meeting or was a table standard agreed upon? If so, will the ddl be released to create soon?

#23

Not anymore. MSTeams stores it for 2 weeks only. But you can find very detailed notes in the EHR WG team.

Methodology for Converting Source-To-Concept-Map to Concept/Concept_Relationship (2 billionaires)
#24

I found your reply while looking for a clue regarding “Maps to value” for which we do not fully understand the purpose. Can you briefly clarify? Thank you.

#25

It’s a relationship if you need to split up a precoordinated code into a variable concept and a (postcoordinated) value concept. E.g.: take a code “Positive Covid-19 test”. This would have to be split into “Covid-19 Test”, which is a measurement concept, and “Positive”, which is the resulting value concept. The former is linked through “Maps to”, and the latter through “Maps to value”.

It’s all in the Book of OHDSI.

#26

The poster on the topic we end up with at the OHDSI Symposium: link.

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