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

Melissa M mmorine at gmail.com
Mon Mar 11 02:36:36 PDT 2019


Hi John,
Thanks for your reply.
Basically, starting with the .vmdk that I obtained from your team, I'm
following the instructions here
<https://docs.aws.amazon.com/vm-import/latest/userguide/vmimport-image-import.html>
to
import as an AMI using AWS CLI. Everything goes fine until the step "Import
the VM", where the import passes a number of stages but then gets stuck
indefinitely at 59% at the 'booting' stage. Based on the AWS forums, this
is a problem that a lot of people have but there's no solution.
Thanks in advance for any help,
Melissa





On Sun, 10 Mar 2019 at 21:55, John Graybeal <jgraybeal at stanford.edu> wrote:

> Hi Melissa,
>
> Our VA team reads this support list, but does not support version 2.5 of
> the VA in an AMI. We plan to release an AMI for a newer release of the
> Virtual Appliance as time allows. We will skip version 2.5, however, due to
> lack of resources. (Donations or contracts are always welcome!)
>
> If you would like to share the details of the problem that you have run
> into, we will see if anyone from the team or the support list can
> contribute information directly related to that issue. (I don't know what
> exactly you are referring to.) I know other people in the community are
> working on AWS and similar installations, but so far no one has shared a
> successful strategy or resulting AMI with us or with the community.
>
> John
>
>
>
>
> On Mar 10, 2019, at 11:44 AM, Melissa M <mmorine at gmail.com> wrote:
>
> 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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