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[bioontology-support] Use of SNOMED CT in virtual appliance

Melissa M mmorine at
Wed Feb 6 08:28:02 PST 2019

I've recently been discussing with your team regarding use of FoodOn in the
virtual appliance but thought I'd write separately about this question
since it's unrelated to the other.
So far I've been able to import ontologies and perform annotations more or
less successfully, apart from the FoodOn issue that I've already written
about. Now I'm trying to import SNOMED CT but am noticing some issues.
First, I converted the SNOMED RF2 snapshot files to owl using the SNOMED
OWL toolkit jar provided by IHTSDO
<>, then imported the resulting
owl into my virtual appliance using default settings (i.e., selected OWL
format, and no changes to prefLabel/altLabel/etc properties). The resulting
ontology appears to contain all classes in the class browser, and I can
annotate text that contains exact prefLabels of the SNOMED ontology, but
it's missing many of the fields that are present in the SNOMED instance on
the bioportal server (such as synonyms, altLabels, etc.). I therefore can't
annotate any text that contains SNOMED altLabels and synonyms. I've
attached a screenshot of the SNOMED class browser in my virtual appliance
to hopefully show what I mean.
So I'm trying to figure out if I went wrong in my conversion to owl, or
import into the VA.
My question is, was the instance of SNOMED on the bioportal server produced
using the toolkit from IHTSDO? And when importing into bioportal, were
non-default settings used?
Thanks in advance for any info,
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