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[bioontology-support] MedDRA Ontology

John Graybeal jgraybeal at stanford.edu
Mon Aug 8 12:17:10 PDT 2022


Manuela,

I will give you what information I can, and my team may be able to clarify a technical point or two, but some of these questions will need to be asked of MedDRA directly, or possibly of the UMLS group. We merely show the information that is made available to us through the UMLS package of MedDRA.

We are looking into using the MedDRA Ontology to code adverse events for one of our projects.

First, I should note that to use MedDRA, you should ensure that the license appropriate to your jurisdiction (Australia) allows such use. The UMLS license has quite detailed specifications about use of some of the resources that come with UMLS, and you are responsible for following those licenses.

Also, I assume you realize we do not provide a download of the ontology itself. You can access information from it only through the BioPortal APIs.

If I understand it correctly, the dictionary is updated twice a year (though seems to be a few version behind)?

The MedDRA dictionary is updated twice a year. The version of the dictionary that is packaged with UMLS, which BioPortal uses, is not updated as frequently (or maybe as currently). You will need to check the MedDRA metadata page in UMLS to see what the MedDRA schedule is.

Then, BioPortal updates its UMLS resources  at some time after they are published, usually within 1 month. You can see the latest version of UMLS that is being served by BioPortal on the history section at the lower left of the BioPortal summary page for MedDRA<https://bioportal.bioontology.org/ontologies/MEDDRA>.

What happens if a code becomes inactive? Eg we select ‘ABC DVB’ but ‘ABC DVB’ becomes inactive in the latest version? Will we be left with a term that is not current anymore?

We can't speak to what MedDRA or UMLS does to indicate a code is inactive. The best practice is to mark the term as deprecated, but some organizations simply delete it.

Of course, how you record a selection like 'ABC DVB' affects the answer as well. Results are unpredictable if all you store is the label. Assuming you are storing the _identifier_ for that label, if the identifier is deprecated but still visible to our processing, we would be able to display the deprecated class for that identifier, but I believe would not show the label in response to a search. (Our MedDRA class display does not show a class tree because of its size.)  One of the team may be able to provide additional information from past experience.

If I understand it correctly, all levels of the dictionary are searched. Is that correct?

It depends on which BioPortal API you use, and what search settings you use. A default search for a class would search through the entire resource, yes. We can't speak to the constitution of the UMLS or MedDRA producsts, though.

Is it possible to get to a specific level eg HLTor SOC?

Assuming the levels are captured in MedDRA—it appears we capture e.g. SMQ TERM LEVEL=5 for 'Depressive disorder'—then you would see them when getting detailed term information from the API. But there is no way to search for a specific level in BioPortal.

John


On Aug 7, 2022, at 11:19 PM, Manuela Armenis <MSchmidt at georgeinstitute.org.au<mailto:MSchmidt at georgeinstitute.org.au>> wrote:

Hello

We are looking into using the MedDRA Ontology to code adverse events for one of our projects.

If I understand it correctly, the dictionary is updated twice a year (though seems to be a few version behind)?

What happens if a code becomes inactive? Eg we select ‘ABC DVB’ but ‘ABC DVB’ becomes inactive in the latest version? Will we be left with a term that is not current anymore?

If I understand it correctly, all levels of the dictionary are searched. Is that correct?

Is it possible to get to a specific level eg HLTor SOC?

Regards
Manuela


Manuela Armenis
Senior Clinical Data Manager, Biostatistics and Data Science Division

The George Institute for Global Health | AUSTRALIA
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
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