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RxNorm: Ingest / better source #87

Open joeflack4 opened 1 year ago

joeflack4 commented 1 year ago

Overview

Using BioPortal rxnorm.ttl right now, but a better source would be good. Even better to make something like an RxNorm ingest that queries the API and creates FHIR and possibly OWL/SemanticSQL.

Additional info

Native RxNorm source info

This is provided by NLM but it appears to be the most up-to-date resource available. The RxNorm API uses these zip files and is updated after they come out.

RxNorm can be downloaded using stable generic links with the word "current" in it. See below. https://download.nlm.nih.gov/rxnorm/RxNorm_weekly_prescribe_current.zip https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_current.zip

More info from NLM email response:

The most up-to-date RxNorm information will be the monthly release zip files supplemented with the RxNorm weekly zip files. The weekly releases are meant to provide updates in between the RxNorm monthly releases. More information about RxNorm weekly releases can be found here: https://www.nlm.nih.gov/research/umls/rxnorm/docs/techdoc.html#s11_0. You can download the monthly and weekly release files here: https://www.nlm.nih.gov/research/umls/rxnorm/docs/rxnormfiles.html

Below is more information including answers to your questions.

The RxNorm API is updated monthly since it uses the RxNorm monthly release zip files. You can check the RxNorm zip file used in the RxNorm API by clicking on "About" near the top of the RxNav page here: https://mor.nlm.nih.gov/RxNav/#

How many days out of date is the zip from the date that it is released? ***The RxNorm monthly files are typically released a little over a week or so after. RxNorm weekly releases help fill this gap.

Is the script that UMLS uses to build the RxNorm zip open source? That is, if we want updates on a daily basis, can we do the build ourselves? ****The UMLS script does not build the RxNorm zip files; it provides access to the RxNorm zip once it's built internally. The process to build RxNorm is not open source. RxNorm provides monthly and weekly releases, not daily updates. You can download the weekly and monthly releases.

Do you know if the data source that creates the RxNorm zip is the API? ***The API uses the RxNorm zip as its data source.

Do you know of any daily release of RxNorm? ***No, as mentioned earlier, RxNorm is released on a monthly and weekly basis. DailyMed is updated daily with updates from the FDA information. However, the RxNorm content in DailyMed is updated weekly. You can learn more about DailyMed here: https://dailymed.nlm.nih.gov/dailymed/

Alternative sources / ingests

  1. https://fhir-ru.github.io/rxnorm.html

  2. https://build.fhir.org/ig/HL7/UTG/NamingSystem-v3-rxNorm.html

  3. https://terminology.hl7.org/2.1.0/CodeSystem-v3-rxNorm.html

  4. https://github.com/jmandel/fhir-concept-publication-demo/blob/main/scripts/rxnorm-generate.sh Zulip chat: https://chat.fhir.org/#narrow/stream/179202-terminology Josh Mandel wrote:

    My experiment from last year suggest ~6MB gzipped for ~70K concepts. (That's ~100MB expanded as JSON text.) This was generated via https://github.com/jmandel/fhir-concept-publication-demo/blob/main/scripts/rxnorm-generate.sh https://raw.githubusercontent.com/jmandel/fhir-concept-publication-demo/main/CodeSystem-rxnorm-03072022.json.gz zcat CodeSystem-rxnorm-03072022.json | jq '.concepts | length' 71375 Just fixed my link above to the generation script -- I took all designations from ('SY', 'TMSY', 'DF', 'ET', 'DFG', PSY), all attributes defined by RXNORM (but not by third parties), annd all relations defined by RXNORM on concepts (but not by third parties, not on atoms) I intended this as a good reflection of "RxNorm content from RxNormCurrentPrescribableContent"; it could also be worth having a separate file for "RxNorm Full + 3rd party metadata". https://github.com/chb/py-umls/blob/master/databases/rxnorm.sh should get you the initial database

joeflack4 commented 1 year ago

@Sigfried @ShahimEssaid @Leskena2 @putmantime FYI, I found a stable URL where updates to RxNorm will be pushed. This bodes well for an RxNorm ingest. This is something I would consider high up on the priority list, if others agree.

RxNorm can be downloaded using stable generic links with the word "current" in it. See below. https://download.nlm.nih.gov/rxnorm/RxNorm_weekly_prescribe_current.zip https://download.nlm.nih.gov/umls/kss/rxnorm/RxNorm_full_current.zip

Leskena2 commented 1 year ago

@joeflack4 Yes! I agree having RxNorm ingested would be high priority.

joeflack4 commented 1 year ago

Reached on on FHIR Zulip, terminology channel, to see if anyone could point me to if there is an (ideally regularly updated) version of RxNorm and other terminologies: https://chat.fhir.org/#narrow/stream/179202-terminology