Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Error - Cannot add custom ontology set

Xindi Guo xindi.guo at sagebase.org
Wed May 2 11:24:50 PDT 2018


Hi Jennifer,

Thank you!

As long as the reproducible error can be fixed, we will be able to move
forward with our project. I will follow the progress on Github.

Thanks again.

Best,
Xindi

*--*
*Xindi (Cindy) Guo*
Research Associate, Computational Oncology
Sage Bionetworks
sagebionetworks.org

On Wed, May 2, 2018 at 11:19 AM, Jennifer Leigh Vendetti <
vendetti at stanford.edu> wrote:

> Hi Xindi,
>
>
> On May 1, 2018, at 12:21 PM, Xindi Guo <xindi.guo at sagebase.org> wrote:
>
> I was trying to add the NCIT
> <https://bioportal.bioontology.org/ontologies/NCIT> ontology to my custom
> ontology set. However, it went to the error page (image attached) when I
> clicked on "Save Custom Ontologies". Also, my colleague has tried to add it
> as well in her account.
>
>
>
> As of yet, I haven’t been able to reproduce this error where clicking the
> “Save Custom Ontologies” button results in a 404 error.
>
>
> She saw the same error page when trying to access the NCIT link (
> https://bioportal.bioontology.org/ontologies/NCIT) and she was not even
> able to find NCIT in the list of the custom ontology set.
>
>
>
> I modified my personal account to use a custom ontology set of NCIT, and I
> was able to reproduce this secondary error where trying to view the NCIT
> ontology results in a 500 error. There appears to be a bug in the BioPortal
> software that prevents users with custom ontology sets from accessing
> certain ontologies. I’ve entered an issue in our tracker with more detail:
>
> https://github.com/ncbo/ontologies_api/issues/47
>
> You can follow our progress there in terms of when we’re able to release a
> fix.
>
> Apologies that I’m not aware of any workaround at the moment other than
> removing your custom ontology set. If you navigate to the Account Settings
> page for your account, you should be able to click “clear selection” link
> in the Custom Ontology Set section and click the “Save Custom Ontologies”
> button to clear the set of custom ontologies. This restores your account to
> the previous state in BioPortal where all public ontologies are visible /
> accessible.
>
> Kind regards,
> Jennifer
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180502/9bcb6830/attachment.html>


More information about the bioontology-support mailing list