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[bioontology-support] New ontology submission - file upload error

Jade Hotchkiss giant.plankton at gmail.com
Mon May 15 02:34:56 PDT 2017


I see now I could edit the submission information and set the status to
"Retired". Would I then be able to re-submit the ontology with the same
name?

Thanks,
Jade

On Mon, May 15, 2017 at 11:28 AM, Jade Hotchkiss <giant.plankton at gmail.com>
wrote:

> Great, Thanks for your reply, Jennifer.
>
> I'm still struggling to view the classes tree. If I search for a term in
> the class search I can view it's details and see the classes tree, but I
> still get errors when trying to view the details of other classes if I
> click on them in the tree.
> I'm wondering whether there's a bit of confusion caused by the fact that
> along the way one of the file submissions was done by you?
> Maybe I should delete and resubmit the ontology? Is there a way to do that?
>
> Thanks,
> Jade
>
> On Sat, May 13, 2017 at 1:03 AM, Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hi Jade,
>>
>>
>> On May 12, 2017, at 4:16 AM, Jade Hotchkiss <giant.plankton at gmail.com>
>> wrote:
>>
>> Hi Jennifer
>>
>> I can't figure out what is going on. Sometimes clicking on the "Classes"
>> tab works, other times not.
>> I've found that if I edit the url from http://bioportal.bioontol
>> ogy.org/ontologies/SCDO/?p=classes&conceptid=root to
>> http://bioportal.bioontology.org/ontologies/SCDO/?p=classes it sometimes
>> works, but not always.
>> More often than not, I get this error when trying to view the class tree
>> or navigate to a specific class:
>>
>>  <image.png>
>>
>> Sometimes it works, but not consistently.
>>
>>
>>
>> I’ve examined our monitoring software.  We had an outage yesterday that
>> lasted roughly 35 minutes, beginning at 3:45PM Pacific time.
>>
>> Not sure if that is the time frame that you were trying to browse?
>>
>> I’ve been looking at your ontology today to investigate the issues you
>> reported below, and I’ve not yet been able to reproduce the 500 error.
>>
>>
>>
>> When I have been able to view entities, I have noticed this:
>>
>> - Some object properties are not displayed in the "Properties" tab. E.g.,
>> we have a "modifies" property and a "modified by" property, which aren't in
>> the list.
>>
>>
>>
>> There appears to be an issue on the UI side of the application.  I can
>> retrieve those properties via our REST endpoint, e.g.:
>>
>> http://data.bioontology.org/ontologies/SCDO/properties
>>
>> … returns both “modifies”, and “modified by” in the result set.  However,
>> as you point out, they aren’t displayed in the BioPortal UI.  I’ve entered
>> an issue in our tracker for this, and we’ll take a look:
>>
>> https://github.com/ncbo/bioportal_web_ui/issues/49
>>
>>
>> - The property details provided in the "Properties" tab only give
>> "Labels", "Definitions" (which is a mesh of our "rdfs:comment" and
>> "dc:description" properties) and "ID", what about the other properties we
>> use to describe or properties? (see below examples of annotations we have
>> for our properties)
>>
>>
>>
>> For every ontology in BioPortal, we try to populate and display a set of
>> what we refer to as “standard BioPortal properties”.  For ontology classes,
>> this includes:
>>
>> Class ID
>> Preferred Label
>> Synonyms
>> Definitions
>> Obsolete
>> CUI
>> Semantic Types
>> Parents
>>
>> We refer to all other properties as “user defined”, and display those in
>> addition to the standard BioPortal properties.  *This is only the case
>> for the Classes tab though.*
>>
>> On the Properties tab - as you pointed out - we display the label,
>> definition, and ID only.  I’ve entered an enhancement request in our
>> tracker to augment the display with the complete set of user-defined
>> properties:
>>
>> https://github.com/ncbo/bioportal_web_ui/issues/50
>>
>>
>> - Details of classes do not include links made with object properties.
>> Are those links not usually displayed?
>>
>>
>>
>> No, those links are not displayed.  (If I understood your question
>> correctly - feel free to follow up with a specific example for a particular
>> class).
>>
>> Kind regards,
>> Jennifer
>>
>>
>>
>
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