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

Melissa M mmorine at gmail.com
Tue Feb 12 11:27:03 PST 2019


Hi John,
I wanted to let you know that I just got the last step of the pipeline
working and have generated the SNOMED ttl. I'm now loading it in my VA and
will let you know if I have any issues.
Thanks again for your responsiveness to all of my questions!
Melissa



On Mon, 11 Feb 2019 at 18:09, John Graybeal <jgraybeal at stanford.edu> wrote:

> 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> 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>
> 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> 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> on behalf of Melissa M <
>> mmorine at gmail.com>
>> *Sent:* Thursday, February 7, 2019 09:28
>> *To:* Clement Jonquet
>> *Cc:* 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> 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> 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> 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> 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> 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
>>>>
>>>> <Screen Shot 2019-02-06 at 11.54.52 AM.png>
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>>
>>>>
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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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