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

Colin Morris colin at
Wed Mar 20 15:01:16 PDT 2013

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/lib/ruby/1.8/benchmark.rb:308:in `realtime'
        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

On Wed, Mar 20, 2013 at 2:06 PM, Paul R Alexander
<palexander at>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:
> 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> 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 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
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