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[bioontology-support] labels for Time ontology

Simon.Cox at csiro.au Simon.Cox at csiro.au
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.

Simon

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Saturday, 10 February, 2018 06:23
To: bioontology-support at lists.stanford.edu
Cc: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au>; John Graybeal <jgraybeal at stanford.edu>; Samson Tu <swt at stanford.edu>
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,
Jennifer




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

Hi,

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,
Samson


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

John – there are rdfs:label annotations on every class and property … https://www.w3.org/2006/time ... So I’m not sure what the issue is? – Simon

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

Simon,

(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.)

John


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

Hello Simon,




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

Name: Simon Cox
Email: simon.cox at csiro.au<mailto:simon.cox at csiro.au>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTIME

Feedback:
I tried to register the W3C OWL-Time ontology last year.
Its listed here http://bioportal.bioontology.org/ontologies/TIME
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:

https://github.com/ncbo/bioportal-project/issues/66

… so that we can spend some time debugging.

Kind regards,
Jennifer

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632

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