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[bioontology-support] Populating ontologies on NCBO virtual appliance, and filtering annotator results

Colin Morris colin at sciencescape.org
Mon Mar 25 08:34:31 PDT 2013


Hi Paul,

Yes, that's right. I'm attaching my version of the script, in case you want
to double-check against it.


On Fri, Mar 22, 2013 at 6:56 PM, Paul R Alexander
<palexander at stanford.edu>wrote:

> Colin,
>
> Just to confirm, you are running the script with these settings:
> $FROM = "http://rest.bioontology.org/bioportal"
> $TO = "http://{your domain or ip}:8080/bioportal"
>
> And I assume you are running it directly from the Appliance? I just ran
> the script to import all ontologies from BioPortal and it worked reasonably
> well. There were some initial errors due to running out of disk space, but
> once I resized the VM it seemed to work ok.
>
> Paul
>
>
> On Mar 22, 2013, at 10:35 AM, Colin Morris <colin at sciencescape.org> wrote:
>
> I just tried it and got the same error message.
>
>
> On Thu, Mar 21, 2013 at 8:47 PM, Paul R Alexander <palexander at stanford.edu
> > wrote:
>
>> Colin,
>>
>> I think this was due to some data problems on the NCBO REST services. Can
>> you give it another shot?
>>
>> Thanks,
>> Paul
>>
>>
>> On Mar 20, 2013, at 3:01 PM, Colin Morris <colin at sciencescape.org> wrote:
>>
>> Thanks so much for the fast response. I tried running the import script
>> and got this traceback:
>>
>> ./bioportal/ontology_wrapper.rb:149:in `[]': can't convert String into
>> Integer (TypeError)
>>         from ./bioportal/ontology_wrapper.rb:149:in `initialize'
>>         from ./bioportal/ontology_wrapper.rb:148:in `each'
>>         from ./bioportal/ontology_wrapper.rb:148:in `initialize'
>>         from ./bioportal/BioPortalRestfulCore.rb:1702:in `new'
>>         from ./bioportal/BioPortalRestfulCore.rb:1702:in `generic_parse'
>>         from ./bioportal/BioPortalRestfulCore.rb:1701:in `each'
>>         from ./bioportal/BioPortalRestfulCore.rb:1701:in `generic_parse'
>>         from ./bioportal/BioPortalRestfulCore.rb:487:in `getOntologyList'
>>         from
>> /usr/lib64/ruby/gems/1.8/gems/activesupport-2.3.14/lib/active_support/core_ext/benchmark.rb:17:in
>> `ms'
>>         from /usr/lib/ruby/1.8/benchmark.rb:308:in `realtime'
>>         from
>> /usr/lib64/ruby/gems/1.8/gems/activesupport-2.3.14/lib/active_support/core_ext/benchmark.rb:17:in
>> `ms'
>>         from ./bioportal/BioPortalRestfulCore.rb:487:in `getOntologyList'
>>         from ./import_ontologies.rb:51:in `import_ontologies'
>>         from ./import_ontologies.rb:105
>>
>> I set $API_KEY_TO (using the API key associated with the admin account on
>> my local instance) and $API_KEY_FROM, and left everything else as it was. I
>> ran the script directly (./import_ontologies.rb) rather than the way the
>> FAQ recommended, since that resulted in it being interpreted as a shell
>> script (import_ontologies.rb: line 4: =: command not found, etc.)
>>
>> I'm afraid I've exhausted my limited Ruby debugging capabilities (the
>> error seems to relate to user, which is a global variable defined outside
>> of ontology_wrapper.rb?).
>>
>>
>> On Wed, Mar 20, 2013 at 2:06 PM, Paul R Alexander <
>> palexander at stanford.edu> wrote:
>>
>>> Colin,
>>>
>>> Thanks for your interest. We don't include the ontologies because,
>>> amongst other reasons, many people who use the Appliance are interested in
>>> something other than the biomedical domain. I'm curious if you've already
>>> tried the web services and found them slow?
>>>
>>> There is a script that is included on the Appliance that can facilitate
>>> importing ontologies directly from BioPortal. It won't work for every
>>> ontology for a few reasons:
>>> 1) Some ontologies have licensing restrictions that prevent their
>>> distribution
>>> 2) Some require special processing to work correctly with the system's
>>> back-end
>>>
>>> Here's instructions on using the import script:
>>>
>>> http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_migrate_ontologies_from_BioPortal_or_previous_NCBO_Virtual_Appliance_versions_into_a_new_Appliance.3F
>>>
>>> Each RRF ontology in BioPortal is actually multiple RRF files which are
>>> submitted as a single zip file (make sure there are no subdirectories).
>>> I've CCed Lian, who works with the system that handles RRF ontologies.
>>> Lian, do RRF files from UMLS need any special processing?
>>>
>>> I'll defer to someone more knowledgeable on the Annotator CUI question,
>>> though I believe you would need to use the concept id and do a lookup for
>>> that concept on the BioPortal REST services to see the CUI.
>>>
>>> Let me know if you have further questions or run into problems.
>>>
>>> Paul
>>>
>>>
>>> On Mar 20, 2013, at 9:48 AM, Colin Morris <colin at sciencescape.org>
>>> wrote:
>>>
>>> Hi,
>>>
>>> We're interested in using the NCBO annotator in an application of ours.
>>> Because we have millions of short documents that we'd like to annotate, we
>>> thought we'd run the virtual appliance locally (to speed things up on our
>>> end, and avoid imposing on your servers too much).
>>>
>>> I was (maybe naively) expecting that the image would include the same
>>> ontologies as on bioportal.bioontology.org. Is there an easy way to
>>> reproduce something like that environment locally? That is, easier than
>>> locating each of the ~335 ontologies currently on the site and adding them
>>> through the web interface? (We'd like to cast as broad a net as possible)
>>>
>>> Or, given a copy of the most recent release of the UMLS (which we have),
>>> is there an easy way to plug it into our local NCBO instance? (I see
>>> there's a way to add RRF files as ontologies, but there are 42 associated
>>> with our UMLS install, and I suspect that just dropping them all in won't
>>> have the desired effect.)
>>>
>>>
>>> And a mostly unrelated question: Given the results of a call to the
>>> Annotator web service, is there any way to get the UMLS CUI of each
>>> returned concept? I see that the concept element has an 'id' and a
>>> 'localconceptid', but neither of those seem to correspond to UMLS.
>>>
>>> I see that the annotator has the option to expand its results to infer
>>> new results that have the same CUI as found concepts. What I'd like to do
>>> is the opposite -- get distinct concepts, by CUI.
>>>
>>> Any help very much appreciated!
>>>
>>> Thanks,
>>> Colin
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>>
>>
>>
>
>
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