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[bioontology-support] SIO

Natasha F. Noy noy at stanford.edu
Wed Sep 22 10:48:47 PDT 2010


Actually, the bug is on the restrictions side. We are not showing them  
now (we used to, in the past). It's on our list of things to do to get  
that working again.

Can you clarify the relationship part though? Other than restrictions,  
what other relationships would you like to see?

On showing/hiding axioms: yes, that would work. To be honest though,  
at the moment it is not getting very high on the queue as only a tiny  
fraction of our users needs that. We are more likely to support this  
full OWL browsing in WebProtege than in BioPortal.

Natasha


On Sep 21, 2010, at 11:53 AM, Michel Dumontier wrote:

> 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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