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

John Graybeal jgraybeal at stanford.edu
Mon Feb 11 14:09:29 PST 2019


Sorry, I think you're right about that. At least, I can't find anything OWLish on that page. (I just assumed the link ending in /owl was an OWL file. Silly me.)

Back to my licensing studies!

John

On Feb 11, 2019, at 11:45 AM, Melissa M <mmorine at gmail.com<mailto:mmorine at gmail.com>> wrote:

Hi John,
My understanding is that this OWL needs to be generated<https://confluence.ihtsdotools.org/display/DOCTSG/9.2.6+SNOMED+CT+OWL+Distribution+FAQ> using the IHSTDO toolkit that I mentioned before. On that page they indicate a perl script, but that's now been replaced with a command line tool + java API. The command line tool produces the OWL without synonyms that I was mentioning earlier. The java API might do part of what I need but I'm still looking into it. As far as I know, they don't provide a direct download of the OWL file.

As for generating a ttl from the UMLS distribution, I've had no problem with most of the pipeline that you use at NCBO except I'm stuck on the last step. It looks like an issue with the MySQLdb library, but the tips indicated in the umls2rdf repository don't help since I'm using a different OS. I'll keep working on a fix but if it turns out that you're able to provide access to the SNOMED ttl that would be a great help.

Thanks!
Melissa


On Mon, 11 Feb 2019 at 15:24, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Melissa,

Were you aware SNOMEDCT is available as an OWL file at https://confluence.ihtsdotools.org/display/DOCOWL/SNOMED+CT+OWL+Guide ?  (Thank you Clement!) Does this address your need?

We will look into incorporating this version into BioPortal directly, but will not have time to investigate it in the short term.

John

On Feb 7, 2019, at 9:36 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hi Melissa, let me refresh my memory about the .ttl and get back to you directly.

John


________________________________
From: bioontology-support <bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>> on behalf of Melissa M <mmorine at gmail.com<mailto:mmorine at gmail.com>>
Sent: Thursday, February 7, 2019 09:28
To: Clement Jonquet
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Use of SNOMED CT in virtual appliance

Hi Clement,
Thanks very much for your reply.

Regarding the FoodOn issue, I should mention 2 things: 1) I have the same problem both on my VA and on bioportal, and 2) synonyms are properly recognized for some classes and not for others. I've looked at the .owl files to see if I could find any differences in specification of classes whose synonyms are recognized and those whose synonyms aren't recognized, and I couldn't find anything. I'd be happy to provide a few class names as examples if you have time to have a look?

About the SNOMED issue, I contacted IHTSDO and just heard back this morning that the "toolkit is only currently capable of including the Fully Specified Name of concepts" but they're opening my issue as a new feature. In the meantime I'll start working through the pipeline that you use for importing UMLS.

Alternatively, would you be able to provide access to the SNOMED .ttl or are there license restrictions?

Thanks again for your help!
Melissa



On Thu, 7 Feb 2019 at 03:24, Clement Jonquet <jonquet at lirmm.fr<mailto:jonquet at lirmm.fr>> wrote:
Melissa,

A complementary note:

@misha, @john
BioPortal takes SNOMED-CT from UMLS with an export from the UMLS2RDF tool as documented.
But eventually, now that Snomed International (new name for IHTSDO) provide an OWL file directly, it will be interesting one day to drop the import from UMLS and take the OWL directly.
NCBO already does it for NCIt, GO, and a bunch of others that are in UMLS but not imported thru the UMLS export.
MeSH is also concerned as there is now an OWL file produced by NLM.

@melissa
I bet the problem you have with the synonyms in the OWL version of SNOMED-CT is the same that the one for FoodOn. Be sure to specify the right property for synonyms in the « Edit submission information » page.

Bye
Clement
-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  -  PhD in Informatics  -  Assistant Professor
University of Montpellier (LIRMM)
-------------------------------------------------------------------------------------------

Le 7 févr. 2019 à 02:02, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> a écrit :

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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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632



========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632


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