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[bioontology-support] SIO

Natasha F. Noy noy at stanford.edu
Wed Sep 22 13:12:21 PDT 2010


I see -- so you are talking about displaying OWL properties, and their  
domain, ranges, etc. Got it. We'll put it on the list. Again,  
WebProtege is where they are more likely to show up first. In fact,  
they already do.

Natasha


On Sep 22, 2010, at 12:20 PM, Michel Dumontier wrote:

>> Can you clarify the relationship part though? Other than  
>> restrictions, what
>> other relationships would you like to see?
>
> The object/datatype relations are described:
>
> http://semanticscience.org/resource/SIO_000008
> http://semanticscience.org/resource/SIO_000300
>
> i would like to see them listed :-)
>
> m.
>
> On Wed, Sep 22, 2010 at 1:48 PM, Natasha F. Noy <noy at stanford.edu>  
> wrote:
>> 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.
>>
>
>>
>> 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
>>
>>
>
>
>
> -- 
> Michel Dumontier
> Associate Professor of Bioinformatics
> Carleton University
> http://dumontierlab.com




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