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[bioontology-support] SIO

Michel Dumontier michel.dumontier at gmail.com
Tue Sep 21 11:53:18 PDT 2010


Hi,
 In the link you gave me, i don't know how to see any of the relations
- i assume this is related to the bug you allude to. I also don't see
any axioms associated with the classes, even though the first three
classes are associated with existential and universal restrictions.

Perhaps you can have a show/hide feature for the axioms then. Would be
great to render the axioms using the OWL manchester syntax - which is
pretty much becoming default by those who use OWL.

Q: Are there plans to show the SVN log messages in BioPortal? Or is
there anyway that I could code the SVN messages as Bioportal notes?

m.

On Tue, Sep 21, 2010 at 12:29 PM, Natasha F. Noy <noy at stanford.edu> wrote:
> We do support relations. Some of them don't show up because of a bug, which
> we plan to fix. Basically, we will show restrictions. For the moment, we
> don't plan to show random axioms (not attached to classes) in the UI. At
> least for the moment people asking for a simpler interface, not more
> complicated one. We will reconsider if the trend changes, I guess.
>
> Natasha
>
>
> On Sep 20, 2010, at 8:42 PM, Michel Dumontier wrote:
>
>> do you plan support for OWL axioms?  what about relations?
>>
>> m.
>>
>> On Mon, Sep 20, 2010 at 7:08 PM, Natasha F. Noy <noy at stanford.edu> wrote:
>>>
>>> It's up:
>>> http://bioportal.bioontology.org/visualize/44510
>>>
>>> Please let us know if you see anything amiss.
>>>
>>> Thanks!
>>>
>>> Natasha
>>>
>>>
>>> On Sep 16, 2010, at 5:59 PM, Michel Dumontier wrote:
>>>
>>>> Hi,
>>>>  Thanks for the heads-up. The class/object property overlap is fixed.
>>>>
>>>> m.
>>>>
>>>> On Thu, Sep 16, 2010 at 6:44 PM, Natasha F. Noy <noy at stanford.edu>
>>>> wrote:
>>>>>
>>>>> Hi Michel,
>>>>>
>>>>> We are having some trouble with parsing the ontology (BioPortal uses
>>>>> Protege
>>>>> 3 to parse OWL ontologies). I know it looks fine in Protege 4. But you
>>>>> have
>>>>> a bunch of resources (e.g., SIO_000310, SIO_000219) declared both as
>>>>> owl:ObjectProperty and owl:Class. Is that the intent?
>>>>>
>>>>> Protege 3 really chokes on these :( Before we do something though,
>>>>> wanted
>>>>> to
>>>>> make sure that this is really what you meant to say.
>>>>>
>>>>> Thanks in advance for clarifications!
>>>>>
>>>>> Natasha
>>>>>
>>>>>
>>>>> On Sep 15, 2010, at 9:21 AM, Michel Dumontier wrote:
>>>>>
>>>>>> hello,
>>>>>>  i would like to register a new OWL ontology termed SIO ( i have
>>>>>> created the project description ).
>>>>>>
>>>>>> it is available at
>>>>>>
>>>>>> http://semanticscience.googlecode.com/svn/trunk/ontology/sio.owl
>>>>>>
>>>>>> and the bioportal file is at
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> http://semanticscience.googlecode.com/svn/trunk/ontology/bioportal_listing.txt
>>>>>>
>>>>>> cheers,
>>>>>>
>>>>>> m.
>>>>>>
>>>>>> --
>>>>>> Michel Dumontier
>>>>>> Associate Professor of Bioinformatics
>>>>>> Carleton University
>>>>>> http://dumontierlab.com
>>>>>> _______________________________________________
>>>>>> bioontology-support mailing list
>>>>>> bioontology-support at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Michel Dumontier
>>>> Associate Professor of Bioinformatics
>>>> Carleton University
>>>> http://dumontierlab.com
>>>
>>>
>>
>>
>>
>> --
>> Michel Dumontier
>> Associate Professor of Bioinformatics
>> Carleton University
>> http://dumontierlab.com
>
>



-- 
Michel Dumontier
Associate Professor of Bioinformatics
Carleton University
http://dumontierlab.com



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