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[bioontology-support] SIO

Michel Dumontier michel.dumontier at gmail.com
Wed Sep 22 12:20:09 PDT 2010


> 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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