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Route 'standard' concepts not standard anymore?


(Patrick Ryan) #21

i am not understanding the problem with the rxnorm dose form concepts.
they are very specific, and sometimes you want to group them, but they
seem to cover the space we need and are already contained in the
vocabulary. are we talking about adding a set of classification concepts
(from hl7) that map to the rxnorm dose form concepts?


(Dmytry Dymshyts) #22

I suppose we need the “Route” concepts to fill route_concept_id in DRUG_EXPOSURE table.
And RxNorm Dose Form isn’t good for that, because that represent actual drug form, like Lotion, Cream, Oil, etc.
But we need only “Oral” as a Route. This way we aren’t satisfied with RxNorm Dose Form concepts only.
And then, @Patrick_Ryan, you are right, it would be nice to introduce these HL7 Routes and build relationships to existing Dose Forms


(Mark Danese) #23

You might take a look at RxTerms if you have not done so. It rolls up dose forms. I used it to derive “oral”. It is also an NLM product. Apologies if this has already been investigated.


(Patrick Ryan) #24

We should not be inferring the value for ‘route_concept_id’ in the
DRUG_EXPOSURE table, that should only be used if a source has verbatim data
to indicate the route. If its derived from the RxNorm concept, then
there’s no reason to store it there, because it’d be a direct look-up in
the vocabulary. Also, while sometimes you may want to aggregate to
‘Oral’, other times, you may want to specificity of the type of
administration, so it would seem reasonable to offer a classification atop
RxNorm Dose Forms, but not as a replacement.


(Dmytry Dymshyts) #25

Ok, let’s take a look on the use case.
@rtmill, can you please provide us with the use case you need Route concepts for?


(Robert Miller) #26

@Dymshyts
I ran into the problem while trying to map HL7 Immunization records and found no standard concept for intramuscular. An example from HL7 can be found here.

In @Patrick_Ryan’s words, the source has verbatim data to indicate the route.


(Irina Yabbarova) #27

@Dymshyts,
I had the same problem with non-standard routes (that were discussed in this topic) while making route custom mappings, so I think that we need more reliable standard concept set.


(Dmytry Dymshyts) #28

I reviewed different approaches for Route definition, and I like this:
https://phinvads.cdc.gov/vads/ViewValueSet.action?id=73D34BBC-617F-DD11-B38D-00188B398520
@rtmill gave us as example, but it can be used as a separate vocabulary for Routes.
Then we will map existing routes to this list, and in the future there will be no problems.
@IYabbarova, please take a look on this list. Does it satisfy your needs?


(Irina Yabbarova) #29

@Dymshyts,
yes, it looks good)


(Dmytry Dymshyts) #30

@Christian_Reich, need your approval for a new vocabulary implementation


(Christian Reich) #31

What’s the proposal? Change Standard Route Concepts to another vocabulary? Don’t want to create bureaucracy, but can you summarize the change?


(Dmytry Dymshyts) #32

yes
and also make mappings from all existing a little bit messy routes (SNOMED derived) to these new


(Christian Reich) #33

And the old ones are mapped to the new ones?


(Dmytry Dymshyts) #34

Yes


(Dmytry Dymshyts) #35

Hi all!
I made some analysis and discovered that SNOMED, actually gives us pretty nice Routes list.
Here it is
snomed_routes.xlsx (17.2 KB)

Please, review and tell me if it satisfies your needs.


(Dmytry Dymshyts) #36

Standard Route concepts from SNOMED added, looks that they cover every existing Route.
Note, some concepts that were the standard Route changed their domain now, so you need use the new concepts:

Old concept_id concept_name -> new concept_id concept_name
45956873 Obsolete-Oromucosal other -> 4186839 Oromucosal
45956876 Obsolete-Intraventricular -> 4222259 Intraventricular cardiac
4112421 Intravenous -> 4171047 Intravenous
4115462 Rectal -> 4290759 Rectal
4120036 Inhaling -> 45956874 Inhalation
4128792 Nasal -> 4262914 Nasal
4128794 Oral -> 4132161 Oral
4136280 Intravaginal -> 4057765 Vaginal
4139962 Subcutaneous -> 4142048 Subcutaneous
4231622 Topical -> 4263689 Topical route


(Karthik) #37

This is really helpful. I somehow missed this discussion. @Dymshyts is there a mapping from RxNorm Dose Forms to these standard routes? I like how SNOMED has the routes, but our data is mainly in RxNorm.


(Christian Reich) #38

@karthik:

You cannot really do that. The relationship between form and route is fuzzy. So, Oral Tablet is Oral, but Solution for injection? Could be subcutaneous or intravenous or intraperitoneal.

@aostropolets probably has a pragmatic many to many (few to few really) crosswalk for her drug mapping. Just go down the hallway and ask her.


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