@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.
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?
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What’s the proposal? Change Standard Route Concepts to another vocabulary? Don’t want to create bureaucracy, but can you summarize the change?
yes
and also make mappings from all existing a little bit messy routes (SNOMED derived) to these new
And the old ones are mapped to the new ones?
Yes
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.
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
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.
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.
Hello! There are cases in the source data when the drug is administered as an injection and this cannot be reflected in the mapping to the clinical drug form or more detailed classes. It seems to me, this is more suitable for route. Don’t we want to make a super type of different injectable route administrations? @Christian_Reich @Dymshyts
The RxNorm Extension machine (the “boiler”) will figure this out. If you have to map your input information to Drug Concepts the input format allows you to do a fuzzy matching: “Injectable Solution”, “Pen Injector”, “Injection”, “Injectable Foam”, “Injectable Suspension” etc. You can even give an order of preference. The boiler will then find the best match in the existing list of drugs, and if it can’t it will create a new one with the Dose Form you gave the highest priority.
It’s a different story.
You run the “boiler” only against the concepts. You’d not consider the route of administration, only the form of a drug product.
Some sources provide the ingredient only + route of administration. You’d not map them to drug forms since they are more/less specific than forms. And a substantial part won’t end up in any form. That’s why routes are being mapped separately to the route_concept_id where we need a supertype “Injectable” placed above the “Intravascular”, “Intradermal”, “Subcutaneous” and some others.
Also, I’m thinking about the “parenteral” and “systemic” administration being a part of this hierarchy.
Looks like the SNOMED hierarchy of routes of administration is a little lopsided. While there is a rich hierarchy for Digestive tract route, there is nothing for systemic or parenteral routes. IV, intramuscular or subcutaneous are direct desendants of the generic Route of administration value. We may want to talk to SNOMED, and in the meantime put in a manual fix.
Thoughts?
Agree.
I would introduce the following categories:
Systemic
subsumes
Systemic Parenteral , Systemic Enteral , Systemic Topical (Nicotine patches are probably the systemic topical).
Local
Subsumes
Local topical, local intra-organ
And link SNOMED concepts to them
Injection without notion of systemic or local doesn’t make sense for me as, for example, intravenous and intraarticular injections have totally different clinical meaning.
In contrast to what parenteral? Aren’t all alternatives are already in topical?
In contrast to topical enteral? Does it exist?
Sonds like Transdermal route. Want to put it on the top of the hierarchy?
In order to exclude Transdermal route? Is that the point?
How would you know the distribution of the drug? It depends on the drug rather than on the route.
There is no strict connection between the actual route and the drug’s penetration into the bloodstream.
Many sources show the predominance of the “injectable” route. We don’t want to drop it.
It seems we have one option only. Assume they’re all injections to the bloodstream (or close to it - IM, subcutaneous, etc.) since other is not specified. And map them all to the “injectable systemic” leaving the “intraarticular” (and related) outside this hierarchy.
Forum is asking me if I really want to revive this topic, which has been silent for the last 2 years. I do because we didn’t come to any conclusion.
There is no such thing as a systemic or local effect when we are talking about the routes of administration, @Alexdavv mentioned it briefly. The effect is attributable to the drug. Couple of examples:
-
Local anesthetics: injection in the correct dose would not produce any noticeable systemic effect, but increasing the dose would lead to significant systemic side effects (LAST - local anesthetic systemic toxicity)
-
Osmotic diuretics: such as mannitol acts systemically for sure, but the effect is related to the physical properties of the molecule. What happens if we inject mannitol intramuscularly (don’t do that)? The IM route is considered systemic. But it would not be really systemic for the mannitol and other hyperosmolar solutions (KCL 7,5%, NACL 10%, CaCl2 10%, etc.). Therefore I don’t believe, that there are “systemic” and “local” routes of administration.
What we need to do is to support the use case when the source data states, that the drug was given by “Injection”, but not “orally” for example. And the researchers would benefit from distinguishing these routes. They would be able to compare effects in different scenarios. It would make sense to include one OMOP Extension concept to the route domain to unite common injection routes, such as IV, IM, SC, and ID. We can argue whether we need an intraarticular (and other) injection or not. I believe that when anyone in a medical setting says “Injection”, an Intraarticular injection is certainly not the first thing that pops up in the head.
The parenteral route of administration is way too heterogenous and is surprisingly defined differently. I would expect it to be ‘everything except enteral’, but there are people, who think otherwise.
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maybe the people contributing to this topic are also interested in this community contribution to the OHDSI vocabulary on a new route hierarchy which has (coarse but useful) routes based on dose forms (and the newly suggested route will be mapping to current SNOMED routes, which in turn will become non-standard). New routes (and de-standardization of old SNOMED routes) - Vocabulary Users - OHDSI Forums