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

Melissa M mmorine at gmail.com
Wed Feb 13 05:57:48 PST 2019


Hi John,
For sure. I meant to send this before but had to leave to pick up my son.
I was getting an error when installing the MySQL-python python library, so
I tried the solution indicated here
<https://stackoverflow.com/questions/12218229/my-config-h-file-not-found-when-intall-mysql-python-on-osx-10-8>
and
it worked. From that solution it looks like I needed to first install the
MySQL/C connector before installing MySQL-python.
I'm using macOS version 10.14.
Thanks!
Melissa



On Tue, 12 Feb 2019 at 18:12, John Graybeal <jgraybeal at stanford.edu> wrote:

> Melissa,
>
> you're welcome, and we're very glad to hear it. (if you want to share your
> experience, we could perhaps turn it into advice in the documentation?)
>
> I appreciate the news and your willingness to work with us to find
> solutions. Best of luck!
>
> John
>
> On Feb 12, 2019, at 11:27 AM, Melissa M <mmorine at gmail.com> wrote:
>
> 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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>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>
>>>>
>>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>> ========================
>>> 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
>>
>>
>>
> ========================
> 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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