Read Codes missing from vocabulary?

CDM Builders
1

In comparing UMLS to OMOP, I am finding differences such as this, where

UMLS: MRCONSO.RRF C0036508|ENG|P|L0011612|PF|S0733292|N|A0793400||||RCD|PT|XE1An|Seborrhoeic dermatitis|3|N|256|

OMOP: CONCEPT.csv  45460301,Seborrhoeic dermatitis,Condition,Read,Read,,M101.00,19700101,20991231,

I cannot seem to find an entry in UMLS for Read code = M101.00; but see these entries:

C0036508|ENG|P|L0011612|PF|S0733292|N|A0793400||||RCD|PT|XE1An|Seborrhoeic dermatitis|3|N|256|
C0221244|ENG|S|L0559111|PF|S0733293|Y|A0793401||||RCD|PT|M100.|Seborrhoeic dermatitis of scalp|3|N|256|
C0565892|ENG|P|L1091668|PF|S1311308|Y|A1269809||||RCD|OP|XE1C4|Seborrhoeic dermatitis/eczema NOS|3|O|

I looked through the doco; next step will be the source, but maybe there is a quick explanation.

Thanks,
Don

2

Don:

Not sure what the probelm is. You find seborrheoic dermatitis in UMLS and in OMOP, and you are mentioning a difference, but I can’t see any. What am I missing?

3

The actual Read codes differ for the term: UMLS has XE1An, while OMOP has M101.0.

Is this because OMOP uses Read Codes Version 2, but UMLS uses
Clinical Terms Version 3 (CTV3) for “Read” codes?

4

Maybe. We are not using UMLS as a source for Read. We are using the original distribution file from the NHS. And yes, we are using Version 2.0 because that is the one used in CPRD.

What are you trying to do?

5

Read code Domains are not correct.

Vocabulary; OMOP Vocabulary v4.5 07-OCT-16

We are looking at CPRD which uses Read codes. The following Read codes made up the top 6 conditions. But from the description that these codes should be either measurements or observations.
Code…:Description … Domain Concept Class
137S.00 Ex smoker…Condition Clinical finding
1371.00 Never smoked tobacco …Condition Clinical finding
246…00 O/E - blood pressure reading …Condition Clinical finding
246…11 O/E - BP reading …Condition Clinical finding
137P.00 Cigarette smoker… Condition Clinical finding
138…00 Exercise grading … Condition Clinical finding

select source_code, source_code_description, mapping_type, concept_class
FROM source_to_concept_map
JOIN concept ON concept_id = target_concept_id
WHERE source_vocabulary_id = 17
AND source_code IN
( ‘246…00’,‘246…00’,‘1371.00’,‘137S.00’,‘246…11’,‘138…00’,‘137P.00’ )

6

@DTorok:

Hang on, Don. :slight_smile: You are the one who is working wiht Rimma on the Smoking convention. We need to discuss the proposal and then put it through the system. Is that happening?

Regarding the other ones:
O/E - blood pressure reading …Condition Clinical finding
246…11 O/E - BP reading …Condition Clinical finding
138…00 Exercise grading … Condition Clinical finding

Welcome to the world of Read. They are the ones who submitted these codes to SNOMED and made them “Clinical Finding”. They should really be Measurements or “Observable Entity” in SNOMED lingo.

Let me submit to the SNOMED people. In the mean time, we will overwrite by hand.

7

Putting in the tobacco. Exercise grading - can actually be a clinical finding. The blood pressure is screwed up in SNOMED, intermixed with true findings like orthostatic hypotension.