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

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon May 15 11:41:48 PDT 2017


Hi Jade,


On May 15, 2017, at 2:34 AM, Jade Hotchkiss <giant.plankton at gmail.com<mailto:giant.plankton at gmail.com>> wrote:

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?


Ontology acronyms are unique in our system.  You wouldn’t be able to recreate the SCDO ontology without us deleting the existing one in our system first.

Let me know if that’s your desired course of action.

Best,
Jennifer




Thanks,
Jade

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


On May 12, 2017, at 4:16 AM, Jade Hotchkiss <giant.plankton at gmail.com<mailto: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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