AHRQ HCUP conversions

[gowthamrao]

AHRQ HCUP maintains a classification vocabulary at https://www.hcup-us.ahrq.gov/tools_software.jsp . It would be great to have this classification vocabulary as part of OMOP CDM. It will serve the use-cases of 'standard table 1' being discussed here http://forums.ohdsi.org/t/standard-table-1/2797/7 and many others.

AHRQ HCUP has about 15-classification vocabulary systems, that classify concept-id's in ICD-9-CM, ICD-10-CM, CPT, HCPCS, Revenue Code, etc. If we can assign appropriate concept_id's, vocabulary_id, domain_id, concept_class_id to each of the AHRQ HCUP concept's AND maintain the relationships between the AHRQ concept's and OMOP standard-concept-id's - that would help the community perform standardized analytics.

First cut for a plan to do the conversion is at https://goo.gl/0T5MS2 @pbr6cornell @cgreich

[cgreich]

@gowthamrao:

The goo.gl link does not give me permission. Can you open?

[gowthamrao]

@cgreich it opens for me. If the short-url does not work, here is the long one

https://docs.google.com/document/d/1rQYR44x-ziK0PpnqeiCmoMl3Bx-t5TgWGsV_Cpj8liw/edit?usp=sharing

[cgreich]

@gowthamrao:

Now it works. Couple of points:

1. This appears something for the WG, or at least the Forum. Not a Github issue. Or is there a reason you are putting it here?
2. We have considered the CCS before. In fact, it even has a vocabulary_id. But we didn't end up implementing for the following reason: Our classification systems work only for Standard, not for Source Concepts. Reason is simple: You want to use the classification to query the data, but the Source Concepts don't appear in the data (in the main *_concept_id fields that is). So, we would have to re-assign the CCS classifcation to the mapped SNOMED Concepts (which are the Standard Concepts for Conditions), and that proved to be low quality, since the mapping can be "up-hill". Also think of all those odd E and V codes, that really are not conditions to begin with.

But we will take a look at again, maybe the more granular and generally better curated ICD-10-CM work better.

[gowthamrao]

Good points​. And thank you for the background. AHRQ HCUP is more than just ccs categories for ICD diagnosis codes.

The list includes classification for OMOP standard concept codes like procedure codes, CPT codes, revenue code etc. Maybe those are straight forward to include.

[cgreich]

Totally agree. I like them. We'll put them in. Not tomorrow, though. Or are you in a hurry with some of them?

[pbr6cornell]

christian, gowtham has implemented script to implement ccs, we just need go ingest it and then create relations from ccs to snomed via icd, so i advised him to post this here as github issue.

[cgreich]

I see. But we tried it. Comes out ugly. At least the ICD9CM-based ones. We can take another look at ICD10CM. But also: There will be holes. Because the ICDs aren't as comprehensive. CCS covers them all, but not SNOMED Conditions. I am skeptical it would work.

[gowthamrao]

Regarding hurriedness - It would be great to get community assigned concept id's and vocabulary added. Some concept relationship are straight forward and we can add them right away. Others maybe complex and we can solve them over time.

[ericaVoss]

Has progress been made on this item?