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

Jade Hotchkiss giant.plankton at gmail.com
Mon May 15 02:28:50 PDT 2017


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.
> bioontology.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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