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[bioontology-support] Rxnorm

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Mar 14 18:49:57 PDT 2022


Hi Steve,


On Mar 10, 2022, at 1:19 PM, Steve Hart <steve at curai.com<mailto:steve at curai.com>> wrote:

Funny, I did email the listed contact at NLM customer service first!  They directed me to your support system.  The response suggested they disavow any ownership of the content published in BioPortal.   It's not clear to me who is adding it to Bioportal at the moment!

I do not believe the bioportal graph contains the full set.  Based on your link, I suspect you're publishing the UMLS Metathesaurus version which until now I didn't realize was yet another release type.


The UMLS Metathesaurus has two big releases per year - one in May and one in November. The releases are generally labeled as AA and AB, i.e., the releases this year will be 2022AA and 2022AB. Shorty after they do a release, we download the data and import a subset of the terminologies into our system. They publish data in a MySQL database. BioPortal is backed by an RDF store, so we developed an (open source) Python program that translates their relational data into RDF, such that we can ingest the terminologies using a format that BioPortal understands. The Python program is here:

https://github.com/ncbo/umls2rdf

The complete list of terminologies that we import can be seen here:

https://github.com/ncbo/umls2rdf/blob/master/umls.conf

As far as I understand it, the Python script imports all the terms from each of these terminologies. In other words, if you can search for and find a term from RxNorm in the UMLS Metathesaurus Browser (https://uts.nlm.nih.gov/uts/umls/home), you should be able to find the same term in BioPortal.



As to your question about filters:

The "full" version of RxNorm includes a lot of not-normalized drug concepts and other information from their various sources (such as SNOMED CT or DrugBank).  It also includes a number of concept types that aren't officially supported in RxNorm, too.  Supplies come to mind.  I do not believe this is what your site hosts based on some sampling - the full version includes much more data than what I see in the bioportal graph.

The SAB=RxNORM set only includes RxNorm normalized data - their overview page<https://www.nlm.nih.gov/research/umls/rxnorm/overview.html> describes it in more depth (within 2nd and 3rd bullets).   It excludes descriptions from outside sources, un-normalized drugs and other content.   In my experience, this is what most entities use.


They provide detailed information about their source representation here:

https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/sourcerepresentation.html

In particular, I noticed this sentence: "Note: Selected portions of MSH and SNOMEDCT are included in the RxNorm release files, however, they are not processed as part of RxNorm for the Metathesaurus except in assigning RXCUI and RXAUI attributes.”

I don’t understand why someone at NLM couldn’t explain the differences between the “full” version, the “prescribable” version you mention below, and the Metathesaurus version. Did you use this contact address: rxnorminfo at nlm.nih.gov<mailto:rxnorminfo at nlm.nih.gov>? This is the contact listed on their metadata page:

https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/metadata.html


I'm fairly sure it includes RXCUI TTY data and other data that is missing from the bioportal graph, though.  So I'm not sure this is what was used either.  Maybe some data types are not included in the transformation, though?
They also have a "prescribable<https://www.nlm.nih.gov/research/umls/rxnorm/docs/prescribe.html#:~:text=The%20RxNorm%20Current%20Prescribable%20Content,over%2Dthe%2Dcounter%20drugs.>" version that only includes US human prescribable products only.   They do this with additional filtering.

It would be useful to know what subset of RxNorm was used prior to transformation to better understand what to expect from the graph's content.



I’m seeing RXCUI data in BioPortal, e.g.:

[cid:18DFD176-BC32-4983-8413-3B0AEEBFC0F4]



Is there somewhere you’re expecting it and it’s absent?

Kind regards,
Jennifer


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