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

Colin Morris colin at sciencescape.org
Fri Mar 22 10:35:13 PDT 2013


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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