Expired Concepts, No Successors, Standard and No invalid Reason

Vocabulary Users
1

Hello. We are successfully mapping records to valid standard codes, but found that there are some with valid_end_dates in the past and no successor concept. I ran the query below and found just over 8,700 concepts that have this issue. This seems to violate the Standard Vocabulary Life Cycle from The Book Of OHDSI. Can I safely use these expired values or is there something I’m missing? We’re using Vocab v5.0 from Sept 2020. I searched for this topic but didn’t find a good match. Apologies if it’s already been asked.

SELECT count(*)
  FROM omop_dev.concept
 WHERE concept.valid_end_date < '2099-12-31'
   AND standard_concept = 'S'
   AND invalid_reason IS NULL; --9,088
   
SELECT count(*)
  FROM concept c1
  JOIN (
        SELECT concept_code
          FROM omop_dev.concept
         WHERE concept.valid_end_date < '2099-12-31'
           AND standard_concept = 'S'
           AND invalid_reason IS NULL
        ) c2
    ON c2.concept_code = c1.concept_code
   AND c1.valid_end_date = '2099-12-31'; --350
2

After browsing for a while I think I did find the answer in icd10pcs bringing back deprecated codes in response to deprecated codes.

Christian_Reich
Jul 30
We have that. We set the valid_end_date to something in the past, but leave the invalid_reason and standard_concept intact.

Is there a better source than The Book of OHDSI to find up-to-date rules for this?

1 Like
3

This seems to still be an issue. The quality assurance checks listed in the Vocabulary wiki say:

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But we’re seeing a lot of concepts that violate this rule. In terms of ETL, should these concepts be used to map our data?
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4

Hi @KSimon,
There are cases when obsolete concepts that cannot be consistently mapped to Standard equivalents still widely persist in the clinical data tables. Since users may need to query them in their studies, there’s a workaround approach applied in OMOP vocabulary system: the concepts turned into Standard and valid, but with the validity end date defined in the past.
Please read the forum discussion and find more information here.

In short, if you cannot find a standard, valid concept with a 12/31/2099 valid_end_date, you may use such concepts in your study.

5

Thank you!