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[bioontology-support] labels for Time ontology

Samson Tu swt at
Sun Feb 11 08:43:18 PST 2018

The OWL 2 spec makes a distinction between datatype and class:

"Datatypes are entities that refer to sets of data values. Thus, datatypes are analogous to classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.” [1]

Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.

The OWL API loads the ontology didn’t throw an error. It’s the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.

With best regards,


On Feb 10, 2018, at 10:10 PM, simon.cox at<mailto:simon.cox at> wrote:

I don’t think you are correct.
The RDFS Spec is quite explicit on this [1]: “Each instance of rdfs:Datatype is a subclass of rdfs:Literal.”

The offending lines in the OWL-Time rdf are

  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype
  rdfs:label "dateTimeStamp" ;
  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal

I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause a conforming processor to throw an error.


From: Samson Tu [mailto:swt at]
Sent: Saturday, 10 February, 2018 05:59
To: Cox, Simon (L&W, Clayton) <Simon.Cox at<mailto:Simon.Cox at>>
Cc: Samson Tu <swt at<mailto:swt at>>; John Graybeal <jgraybeal at<mailto:jgraybeal at>>; bioontology-support at<mailto:bioontology-support at>
Subject: Re: [bioontology-support] labels for Time ontology


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

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