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

Paul R Alexander palexander at stanford.edu
Wed Mar 20 11:06:38 PDT 2013


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
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> bioontology-support at lists.stanford.edu
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