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[bioontology-support] Updated BioPortal Ontologies

Samad, Bushra Bushra.Samad at ucsf.edu
Mon May 24 11:28:55 PDT 2021


Thanks for the prompt response and the clear explanation Jennifer.
I see the updates on REDcap.
Thanks again
Bushra

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Monday, May 24, 2021 at 11:22 AM
To: "Samad, Bushra" <Bushra.Samad at ucsf.edu>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] Updated BioPortal Ontologies

Hello Bushra, On May 21, 2021, at 4:45 PM, Samad, Bushra <Bushra.Samad at ucsf.edu> wrote: Hi, I am not sure who to contact I wanted to check when the COVID vaccine data (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html ZjQcmQRYFpfptBannerStart
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Hello Bushra,



On May 21, 2021, at 4:45 PM, Samad, Bushra <Bushra.Samad at ucsf.edu<mailto:Bushra.Samad at ucsf.edu>> wrote:

Hi,
I am not sure who to contact I wanted to check when the COVID vaccine data  (https://www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html<https://urldefense.com/v3/__https:/www.nlm.nih.gov/research/umls/rxnorm/covid19vaccines.html__;!!LQC6Cpwp!4hhJSaSQISPFQPnDDWtDnM4UEZMt_cATRLbMTn8OskzIoS5UcUogRAmYeInSShRNNmY$>) will be available in RxNorm in BioPortal. I did not see it in REDcap and the UCSF REDcap administrator said they have no control over the updates of the BioPortal Ontologies available on REDcap.
I contacted NLM support and they directed me to contact you.


We ingest RxNorm from the UMLS Metathesaurus [1]. They do releases twice per year, and we just finished importing the 2021AA release [2]. According to their documentation, the 2021AA release contains RxNorm version 20AA_210301F [3].

I ran a couple of test searches and did find some of the content you asked about has been pulled in, e.g.:

RXCUI 2470234 (Moderna COVID-19 Vaccine):

 https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2470234<https://urldefense.com/v3/__https:/bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http:**Apurl.bioontology.org*ontology*RXNORM*2470234__;Ly8vLy8!!LQC6Cpwp!6JqrYqrQn0vgiPeVQ7kZAJeverkNbEY58YFf2sA3bRDnSJjYs1Dk_ouinGhQrm1Lt9w$>

RXCUI 2468235 (Pfizer-BioNTech COVID-19 Vaccine):

https://bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F2468235<https://urldefense.com/v3/__https:/bioportal.bioontology.org/ontologies/RXNORM?p=classes&conceptid=http:**Apurl.bioontology.org*ontology*RXNORM*2468235__;Ly8vLy8!!LQC6Cpwp!6JqrYqrQn0vgiPeVQ7kZAJeverkNbEY58YFf2sA3bRDnSJjYs1Dk_ouinGhQ0KxxkZg$>

However, there are other RXCUIs that don’t appear to be part of this RxNorm release, e.g., the Janssen vaccine (RXCUI 2479835).

Apologies, but I’m not aware of any plans to ingest a new version of RxNorm until the UMLS Metathesaurus 2021AB release in November of this year.

Kind regards,
Jennifer

[1] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html<https://urldefense.com/v3/__https:/www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html__;!!LQC6Cpwp!6JqrYqrQn0vgiPeVQ7kZAJeverkNbEY58YFf2sA3bRDnSJjYs1Dk_ouinGhQPn5fbSk$>
[2] https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html<https://urldefense.com/v3/__https:/www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/index.html__;!!LQC6Cpwp!6JqrYqrQn0vgiPeVQ7kZAJeverkNbEY58YFf2sA3bRDnSJjYs1Dk_ouinGhQen34t5M$>
[3] https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/metadata.html<https://urldefense.com/v3/__https:/www.nlm.nih.gov/research/umls/sourcereleasedocs/current/RXNORM/metadata.html__;!!LQC6Cpwp!6JqrYqrQn0vgiPeVQ7kZAJeverkNbEY58YFf2sA3bRDnSJjYs1Dk_ouinGhQQWie_qM$>


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