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Expired Concepts, No Successors, Standard and No invalid Reason


(Rob B) #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

(Rob B) #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?


t