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Device_concept_ids invalidated with no 'Maps To' or 'Concept Replaced By'

Vocabulary Users
#1

I’ve got 7 devices that in the previous vocabulary were valid and mapped to itself.

concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
2615860 Dialysis access system (implantable) Device HCPCS HCPCS S C1881 2001-04-01 2099-12-31
4219637 Peripheral intravenous catheter Device SNOMED Physical Object S 82449006 2002-01-31 2099-12-31
4222511 Ileostomy set Device SNOMED Physical Object S 342706005 2002-01-31 2099-12-31
4223561 Urostomy set Device SNOMED Physical Object S 344575009 2002-01-31 2099-12-31
4225474 Colostomy set Device SNOMED Physical Object S 341036005 2002-01-31 2099-12-31
37396766 Ventricular cerebrospinal fluid catheter/external drainage kit Device SNOMED Physical Object S 716690000 2016-07-31 2099-12-31
45761420 Cerebrospinal fluid drainage kit, lumbar Device SNOMED Physical Object S 467541009 2014-07-31 2099-12-31
45762654 Fecal incontinence kit Device SNOMED Physical Object S 469404001 2014-07-31 2099-12-31
45763083 Intraosseous infusion kit Device SNOMED Physical Object S 470066001 2014-07-31 2099-12-31

In the updated vocabulary (May 2023) only 2 have ‘maps to’ and those have wildly incorrect dates:

concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
2615860 Dialysis access system (implantable) Device HCPCS HCPCS S C1881 1970-08-20 1970-08-31
4219637 Peripheral intravenous catheter Device SNOMED Physical Object S 82449006 1970-08-20 1970-08-31
#2

First, dates. I see 1970-01-01 and 2099-12-31 as valid start date and valid end date for relationships respectively. Dates are also correct for concepts: Athena1 and Athena2

SELECT * FROM concept_relationship WHERE concept_id_1 = 4219637 AND relationship_id = 'Maps to';
SELECT * FROM concept_relationship WHERE concept_id_1 = 2615860 AND relationship_id = 'Maps to';

Now, changes of standard_concept status. Again, Snomed is in charge of these changes. They invalided concepts and we followed. You can check these concepts in any available Snomed Browser.
The tricky thing here is the reason for invalidation. Snomed doesn’t offer a replacement, because the Inactivation reason was Nonconformance to editorial policy component (quoting snomed, you can double check in any snomed browser).

For Ileostomy set you can see one Active possibly_equivalent_to inactive (SNOMED) link. But links of this type no longer serve as reasons to construct Maps to, because of their ambiguity.

#3

Forgive me, but the dates from the first set (old vocabulary) are reasonable, but those from the second set, (updarted vocabulary,) are 1970-08-20 and 1970-08-31.

This led me to believe there was an error in the file.

#4

So was there an error in your files? Could you double-check it, please?
I can’t see it. Both dates in Athena in concept_relationship table are fine.

How did you find these erroneous dates?

#5

Roger, we are both on AOU, therefore we should be on the same vocab, did you update again before they asked us to? I am getting the same results as Oleg.

SELECT * FROM dbo.concept c where c.concept_id IN (2615860,4219637);
concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
2615860 Dialysis access system (implantable) Device HCPCS HCPCS S C1881 2001-04-01 2099-12-31
4219637 Peripheral intravenous catheter Device SNOMED Physical Object S 82449006 2002-01-31 2099-12-31
#6 
SELECT 
c1.* ,CR.RELATIONSHIP_ID ,c2.*
    FROM SH_OMOP_DB_PROD.CDM.CONCEPT AS C1
INNER JOIN SH_OMOP_DB_PROD.CDM.CONCEPT_RELATIONSHIP AS  CR
    ON C1.CONCEPT_ID = CR.CONCEPT_ID_1
INNER JOIN SH_OMOP_DB_PROD.CDM.CONCEPT AS  C2
    ON C2.CONCEPT_ID = CR.CONCEPT_ID_2
WHERE C1.concept_id IN (4223561
,4219637
,2615860
,45761420
,45762654
,4225474
,45763083
,37396766
,4222511)

AND UPPER(CR.RELATIONSHIP_ID) IN (‘CONCEPT REPLACED BY’, ‘MAPS TO’)

#7

I’m using the latest vocabulary files from AoU

#8

Very odd, I also am running the latest AOU vocab files, that I downloaded at the first of May, but I am getting different results than you.

concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason RELATIONSHIP_ID concept_id concept_name domain_id vocabulary_id concept_class_id standard_concept concept_code valid_start_date valid_end_date invalid_reason
2615860 Dialysis access system (implantable) Device HCPCS HCPCS S C1881 2001-04-01 2099-12-31 Maps to 2615860 Dialysis access system (implantable) Device HCPCS HCPCS S C1881 2001-04-01 2099-12-31
4219637 Peripheral intravenous catheter Device SNOMED Physical Object S 82449006 2002-01-31 2099-12-31 Maps to 4219637 Peripheral intravenous catheter Device SNOMED Physical Object S 82449006 2002-01-31 2099-12-31
#9

Hi. I am a beginner and a nephrologist of South Korea. I am interested with device vocabulary for peritoneal dialysis(PD). Recently I have a struggle about searching concept Id about PD transfer set. Concept ID 45768371, 45761561 are Deprecated and validity ends 31-Jul-2021. what are new concept IDs mapped these concept IDs? Is tubing set same with transfer set? Hierachy and relationship aren’t there. Another question is what means dialysis access system? Please recommend me some contact points. Thanks a lot!

#10

Hello, @11122. Unfortunately, concepts mentioned by you, do not have active equivalents. Tubing set You can use more general concept from SNOMED vocabulary Athena

#11

@11122 Welcome to OHDSI!

In short, devices are the least standardized Domain in our vocabulary ecosystem. We usually just take what source vocabularies give to us in the Device domain and make them standard if they are valid in the source because it is impossible to standardize devices. Let’s say you have furosemide from Supplier A under Brand A1 and furosemide from Supplier B under Brand B1. It is still the same. But if you take the hemodialysis set from Supplier A, it is so much different from the hemodialysis set from Supplier B (coating, length, connectors, etc.)

Good news for you - most people don’t need to use devices to find peritoneal dialysis patients, because in OHDSI we have a very strong hierarchy of procedures, conditions, and observations.
Peritoneal dialysis, Peritoneal dialysis used, Peritoneal dialysis care, Complication of peritoneal dialysis - there are more, just use what you need.

I highly recommend you begin with the book of OHDSI and pay attention to the work of Phenotype Development and Evaluation Working Group.

t