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

Melissa M mmorine at gmail.com
Sun Mar 10 11:44:59 PDT 2019


Hi John,
I was recently in contact about the NCBO BioPortal appliance and the
pipeline to convert UMLS to RDF. Now that I have a working ttl of SNOMED
I'm setting up our cloud infrastructure using AWS.
I was hoping you could put me in touch with whoever at NCBO produced the
Amazon Machine Image of the BioPortal appliance (the one here
<https://aws.amazon.com/marketplace/pp/B00MX5YKVU?qid=1552243336935&sr=0-1&ref_=srh_res_product_title>).
I've tried it and it does work for me, but seems to have a problem that the
never version (2.5) of the appliance does not have. So I've tried
converting the VA of version 2.5 to AMI but have run into a problem in the
conversion that many others seem to have, but for which there's no solution
from AWS.
Thanks in advance for any help,
Melissa



On Fri, 15 Feb 2019 at 23:39, John Graybeal <jgraybeal at stanford.edu> wrote:

> Thanks, I did add that to our documentation.
>
> john
>
> On Feb 13, 2019, at 5:57 AM, Melissa M <mmorine at gmail.com> wrote:
>
> 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
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> bioontology-support mailing list
>>>>> 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
>>
>>
>>
> ========================
> 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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