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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
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Remapping of deprecated codes #489

Closed cukarthik closed 3 years ago

cukarthik commented 3 years ago

How do we handle deprecated codes? I was under the impression there are relationships to point us to a new code to use instead. For example, 40780291 is a LOINC Hierarchy code that is deprecated. Sometimes organizations are mapping to classification codes b/c they do not know what the granular code should be based on their data. @cgreich and @mik-ohdsi interested to get your input.

mik-ohdsi commented 3 years ago

Hi @cukarthik , yes, it should have a "replaced by" relationship if, in the process of updating the vocabulary, we actually have knowledge about a proper replacement. If a code ceases to be valid because the source simply doesn't have it anymore and it is not "replaced", it will become orphaned like this one. I briefly searched LOINC and did not find a proper replacement for this hierarchy component for Total Cholesterol in Serum, Plasma or Blood... Do you know one?

p-talapova commented 3 years ago

Hi @cukarthik, LOINC does not support the replacement of LOINC Hierarchy concepts. Therefore, the vocabulary team has to build the replacement relationships manually that is time-consuming and rarely applicable to Classification concepts. But theoretically, this is possible.

However, in order to obtain all related LOINC descendants, I would propose using the following codes:

  1. A valid Classification LOINC Hierarchy concept with a specified specimen source: 37027885 Cholesterol | Serum or Plasma | Chemistry - non-challenge.
  2. A Standard SNOMED concept with an unspecified specimen source: 4299360 Cholesterol measurement (contains LOINC codes as children as well).
cukarthik commented 3 years ago

Thanks! I'll look into these options. These orphan cases make it hard to keep local mappings up-to-date.