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[bioontology-support] Ontology Help

Doug Wendel douginator2000 at
Fri Jan 27 14:00:51 PST 2012

Fantastic thank you Paul. The ontologies I tried with the tree widget
were 1069 (ENVO), 2092 (a view of the ENVO ontology), and I think I
tried a couple of other IDs to try and get it to display something as
the default ontology. Maybe I'm missing some configuration options as
well - I followed the instructions on the website but that doesn't
mean I'm doing everything right :D


On Fri, Jan 27, 2012 at 2:50 PM, Paul R Alexander
<palexander at> wrote:
> Doug,
> Thanks for contacting us and sorry about the issues you are having. I've
> fixed the problem with the ontology not being found at the URL, which was a
> bug on our side. However, it looks like there is a problem displaying terms
> for the ontology and we're looking into that.
> Now that the ontology page is viewable, you can edit the information and
> submit new versions using the "Administer" menu that should show up when you
> are at the ontology page and logged in with the account you used to submit
> the ontology. The "Administer" menu should appear next to the ontology name
> on this page:
> For the tree widget, can you provide the ids for the ontologies you are
> trying to view?
> Thanks,
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
> On 1/27/12 11:53 AM, Doug Wendel wrote:
>> Hello,
>> I'm trying to upload a new ontology to the site. I uploaded a test
>> version to see if it was possible for the site to host it like the
>> other ontologies. I got an email back stating that the ontology was
>> successfully parsed but there's nothing that shows up on the URL that
>> was provided
>> It's been about 24 hours since I submitted it so maybe something went
>> wrong?
>> A second question: Is it possible to easily manage the ontology once
>> it's been uploaded? I.e. I see how to submit a new ontology, but how
>> can I upload a new ontology file for an ontology I already submitted?
>> Finally, we're attempting to use the tree widget however it doesn't
>> seem to load ontologies supplied in the parameter field. You can
>> browse for ontologies once the tree object loads but it seems to throw
>> an "Ontology Not Found" error when supplied as a parameter. The URL it
>> appears to be generating looks incorrect - the REST service returns
>> the not found value to the tree control so maybe the interface has
>> changed but the widget has not?
>> Thanks in advance!
>> Doug Wendel
>> University of Colorado at Boulder
>> Department of Chemistry and BioChemistry
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at

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