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

Michael Dorf mdorf at stanford.edu
Wed Feb 6 17:02:06 PST 2019


Hi Melissa,

Yes, that is the script that is being used to import UMLS ontologies into a virtual appliance.  It hasn’t been updated since 2016, but it should still be valid. Let us know if you run into any issues importing.

Thanks,

Michael



On Feb 6, 2019, at 12:10 PM, Melissa M <mmorine at gmail.com<mailto:mmorine at gmail.com>> wrote:

Hi Michael,
Thank you very much for your response. Can you confirm that the pipeline described here<https://www.bioontology.org/wiki/Importing_UMLS_To_Virtual_Appliance> is the one currently used to import UMLS content into bioportal? I'm assuming that NCBO does not provide downloads of the output files from this pipeline (I think in ttl format)?
Thanks again,
Melissa


On Wed, 6 Feb 2019 at 15:42, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:
Hi Melissa,

Thanks for contacting us again. Twice per year we do a bulk import of terminologies distributed by the UMLS [1].  (They have a twice per year release schedule, e.g., for this year it will be 2019AA and 2019AB).  SNOMEDCT is one of the terminologies contained in the UMLS distribution.  So, the version numbers for SNOMEDCT that you see in BioPortal correspond to UMLS releases, e.g., 2018AA, 2018AB, etc. More info on their distributions can be found here:

https://www.nlm.nih.gov/research/umls/sourcereleasedocs/index.html

The page contains an alphabetical list of all the terminologies contained in the UMLS.

Unfortunately, I’m not familiar with the IHTSDO toolkit, but I can only assume that may contain either a different version from the one we have in BioPortal; or a version that may not have all the properties fully populated.

Thanks,

Michael

[1] https://www.nlm.nih.gov/research/umls/




On Feb 6, 2019, at 8:28 AM, Melissa M <mmorine at gmail.com<mailto:mmorine at gmail.com>> wrote:

Hello,
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<https://github.com/IHTSDO/snomed-owl-toolkit>, 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,
Melissa

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