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] labels for Time ontology

Simon.Cox at Simon.Cox at
Sat Feb 10 22:34:44 PST 2018

As I just commented in response to Samson, I think we’ve probably hot one of those places where OWL processors have made some assumptions inconsistent with the original RDFS definitions. The RDFS Spec is quite explicit on this [1]: “Each instance of rdfs:Datatype is a subclass of rdfs:Literal.” so while the subclass axiom is arguably redundant, there should not be an error thrown.

However, I can suggest that it is removed from the official ontology.


From: Jennifer Leigh Vendetti [mailto:vendetti at]
Sent: Saturday, 10 February, 2018 06:23
To: bioontology-support at
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at>; John Graybeal <jgraybeal at>; Samson Tu <swt at>
Subject: Re: [bioontology-support] labels for Time ontology

Hello All,

It was my suspicion as well that this particular axiom might be causing the issue. Here’s a screenshot in the Protege ontology editor that shows rdfs:Literal appearing in the class tree:

[cid:image001.png at 01D3A35B.E5890530]

I removed this axiom and uploaded the modified version of the ontology to our private staging environment. Without that axiom, the ontology is processed without errors in BioPortal:

[cid:image002.png at 01D3A35B.E5890530]

Simon - any chance an updated version of the ontology could be provided to us?

Kind regards,

On Feb 9, 2018, at 10:59 AM, Samson Tu <swt at<mailto:swt at>> wrote:


I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.

With best regards,

On Feb 8, 2018, at 9:49 PM, simon.cox at<mailto:simon.cox at> wrote:

John – there are rdfs:label annotations on every class and property … ... So I’m not sure what the issue is? – Simon

From: John Graybeal [mailto:jgraybeal at]
Sent: Friday, 9 February, 2018 16:35
To: bioontology-support at<mailto:bioontology-support at>
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at<mailto:Simon.Cox at>>
Subject: labels for Time ontology


(not sure if you got copied on that first response, which is below)

Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)


On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hello Simon,

On Feb 8, 2018, at 4:18 PM, support at<mailto:support at> wrote:

Name: Simon Cox
Email: simon.cox at<mailto:simon.cox at>

I tried to register the W3C OWL-Time ontology last year.
Its listed here
Something went wrong, but I do not understand the error message.
In particular the class tree does not render properly.
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.
Any comments?

I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes don’t have labels declared. After generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasn’t immediately obvious to me what the problem is. I’ve entered an issue in our tracker:

… so that we can spend some time debugging.

Kind regards,

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 100066 bytes
Desc: image001.png
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 131969 bytes
Desc: image002.png
URL: <>

More information about the bioontology-support mailing list