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[bioontology-support] labels for Time ontology

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Feb 14 15:05:21 PST 2018


Hi Simon,

Thanks! BioPortal picked up the new version overnight. Initially it failed to parse in our production environment due to a subtlety that I didn’t account for the other day when I was doing some testing in our staging environment. It looks like when the ontology was originally submitted to us, there were some property overrides specified in the add/edit submission form:

Preferred Name Property: local:OWL-Time
Synonym Property: local:Time ontology in OWL

BioPortal doesn’t recognize the “local:” syntax for property overrides - instead, a full URL is required. Apologies that this isn’t evident from the placeholder text on the form. We have an open issue in our tracker to add better validation for these fields.

I looked at the ontology content and it seems that it already adheres to standard practices for specifying preferred names (rdfs:label). BioPortal checks this property for preferred names, so the override doesn’t seem necessary. Also, it wasn’t clear to me what the override was meant to be for the synonym property. At any rate, I removed these overrides and reprocessed the ontology, which is now fully available in BioPortal, and via the REST API (http://data.bioontology.org/ontologies/TIME). The appearance of the class tree mimics what I see when I load the OWL file in the Protege ontology editing application. Let me know if you see anything awry.

Kind regards,
Jennifer



On Feb 13, 2018, at 2:24 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

The RDF representation of the OWL-Time ontology has been updated, removing the declaration of xsd:DateTimeStamp.
See https://www.w3.org/2006/time

From: John Graybeal [mailto:jgraybeal at stanford.edu]
Sent: Monday, 12 February, 2018 08:41
To: Cox, Simon (L&W, Clayton) <Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au>>
Cc: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

perhaps we should do a quick test with that change in BioPortal, to see if it behaves better.

john

On Feb 11, 2018, at 1:09 PM, Simon.Cox at csiro.au<mailto:Simon.Cox at csiro.au> wrote:

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

Yes. And that's also partly why owl:Class != rdfs:Class.
But I don't think that's the issue here.
It's about how a datatype is formally defined.

RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
Else this is where Bioportal might be too fierce.

Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.

Simon
________________________________
From: Samson Tu <swt at stanford.edu<mailto:swt at stanford.edu>>
Sent: Sunday, 11 February 2018 4:43:18 PM
To: Cox, Simon (L&W, Clayton)
Cc: Samson Tu; John Graybeal; bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
Subject: Re: [bioontology-support] labels for Time ontology

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,
Samson

[1] https://www.w3.org/TR/owl2-syntax/#Datatypes


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

xsd:dateTimeStamp
  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.

[1] https://www.w3.org/TR/rdf-schema/#ch_datatype

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

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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bioontology-support mailing list
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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

_______________________________________________
bioontology-support mailing list
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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