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[bioontology-support] [BioPortal] Feedback from Fred Trotter

fred trotter fred.trotter at
Wed Jun 5 17:31:38 PDT 2019

On Tue, Jun 4, 2019 at 5:50 PM Jennifer Leigh Vendetti
<vendetti at> wrote:
> Hi Fred,
> I’m not sure I understand what you’re asking. I navigated to the CMT release page to read about these release files: In particular, I downloaded the Vascular Procedures List, which is described as a “collection of concepts” from Kaiser Permanente’s electronic medical record system. The concepts are stored in Excel format. BioPortal is able to handle ontology submissions in OWL, OBO, and/or SKOS. Were you asking us to convert the spread sheet content to one of these formats?

That would be best for me, as apparently someone has to do it.
Kaiser Permenente supplies the updates to the CMT file to the NIH as a
donated ontology, and perhaps they have the data available in a better
I think I might be able to arrange an introduction, but you are
physically closer to them than me and I suspect you might have better
connections with them than I do.
If you don't have the bandwitdth and we cannot get it by asking KP
nicely, I am willing to (evventually) take this on and write and
release a conversion tool that you might be able to use.

> I also looked at the vocabulary documentation for the latest UMLS Metathesaurus release: It doesn’t appear that they offer CMT as a distinct vocabulary.

Because its job is to link an existing vocabulary to natural language.
I believe that the right way to think about it is that your Snomed CT
work is incomplete because it is not properly decorated with CMT. (75%
sure of this)

> Wondering if you might be able to offer a little more detail on what you’d like to see in BioPortal?

There are two killer features here. The first is to see natural
language descriptions of all of the conditions on snomed through
bioportal (I am 95% sure that CMT links to snomed)

The second is to enable your general search functionality to "find"
snomed  codes (and by proxy the other resources that you have embedded
into bioportal) by searching for natural language terms, like "heart
attack" rather than "cardio something blah blah"

Thank you for giving this such careful consideration. No matter what
you decide to do, I very much appreciate the attention.


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