Normalizing NAACCR: deduplicating

[mgurley]

Proposal: mapping all duplicate concepts to a new OMOP generated concepts. Ultimately, they should be mapped to a standard concept, but we have not determined them yet. See #9

This process was started in #51. Should be revisited and incorporate prior work.

[mgurley]

Drive this based on use case

[denyskaduk]

Hello! In continue of dedup process, I want to propose dedupping variables which contain stages information:

concept_code	concept_name	standard_code	standard_name
1022	AJCC TNM Post Therapy N	815	Derived EOD 2018 N
2960	Derived AJCC-6 N	815	Derived EOD 2018 N
3410	Derived AJCC-7 N	815	Derived EOD 2018 N
3482	Derived PostRx-7 N	815	Derived EOD 2018 N
3450	Derived PreRx-7 N	815	Derived EOD 2018 N
815	Derived EOD 2018 N	815	Derived EOD 2018 N

But according to this I have a question, if it's good to dedup concept which contain information related to treatment, like 'AJCC TNM Post Therapy N'?

[cgreich]

@denyskaduk:

Why not just "Derived N" or "N"?

And your question: That is a typical problem we have, that a concept contains not just a fact (derived N), but the fact and some longitudinal context. Similar to ICD-10 codes "some condition, first encounter". We usually strip this out. So, the fact there was a therapy is irrelevant to define the N.

[dimshitc]

So, we map it to LOINC: Regional lymph nodes.clinical [Class] Cancer
or Regional lymph nodes.pathology [Class] Cancer
Right?
BTW, @denyskaduk can we know somehow, are the concepts given describe clinical or pathological staging?

[denyskaduk]

@dimshitc, Unfortunately NAACCR didn't give such information for this Items. @cgreich also this vocabulary didn't give us concepts with non-specific names, we can create them, but as from previous discussion I remember, it isn't a good choice or we can create a new Standard concept in this case?

[denyskaduk]

As we already started to talk about mapping to our standard vocabularies, I want to suggest one more mapping case:

concept_code	concept_name	vocabulary_id	standard_code	standard_name	standard_vocabulary
testis@2868	Post-Orchiectomy Human Chorionic Gonadotropin (hCG) Lab Value	NAACCR	67900009	Human chorionic gonadotropin measurement	SNOMED
testis@2862	Pre-Orchiectomy Human Chorionic Gonadotropin (hCG) Lab Value	NAACCR	67900009	Human chorionic gonadotropin measurement	SNOMED
testis@2890	OBSOLETE - Human Chorionic Gonadotropin (hCG)	NAACCR	67900009	Human chorionic gonadotropin measurement	SNOMED
3846	hCG Post-orchiectomy Lab Value	NAACCR	67900009	Human chorionic gonadotropin measurement	SNOMED
3848	hCG Pre-orchiectomy Lab Value	NAACCR	67900009	Human chorionic gonadotropin measurement	SNOMED

[cgreich]

@denyskaduk: I understand the problem. This is not just a matter of picking a useful Standard, we would have to create it. And then we are in the business of vocab production. Urgh. Well, let's take a look how many of these we would need. Do you have an idea?

[sratwani]

Closing. Several other tasks are created and assigned to the label 'De-duplicating NAACCR'