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[bioontology-support] [bioontology-info] PURL service

Trish Whetzel whetzel at stanford.edu
Wed Dec 2 17:31:33 PST 2009


Hi Shahim,

Ok, thanks for trying that out. I'll look into the provenance of  
making edits to PURLs a bit further.

With respect to loading an OWL2 ontology into BioPortal, BioPortal  
uses the Protege 3.4.x for OWL ontologies and therefore should reflect  
the same information as what is seen directly from Protege. There is a  
development version of BioPortal at: http://stage.bioontology.org if  
you would like to test load your ontology without having it be public.

Also, there is work on the Notes feature to provide additional  
structure to the Notes. The current requirements list is at: http://www.bioontology.org/wiki/index.php/Ontology_Notes 
. Let us know if you have any comments/requests.

Thanks,
Trish


On Dec 2, 2009, at 1:54 PM, Shahim Essaid wrote:

> I was able to find two PURLs:
>
> /biositemaps/biositemap_NCBC_NCBO.rdf
> /biositemaps/Biositemap_CTSA_Stanford.rdf
>
> I was able to click on the modify record icon and the edit form did  
> show up. There is a submit button but I didn't try to make any  
> changes to see what happens.
>
> On an unrelated issue, if I upload an ontology to BioPortal, will I  
> be able to delete it in a way where BioPortal will not keep any  
> traces of the ontology?  I am asking this so that I can try to  
> upload an OWL2 test ontology to see how BioPortal will handle OWL2  
> axioms but I would like to quickly remove this ontology once I  
> understand the consequences of using OWL2 in BioPortal.  I opened an  
> OWL2 test ontology using Protege 3.4 and it was able to show the  
> named classes but it had trouble showing the OWL2 class  
> descriptions.  Even though Protege 3.4 couldn't parse the OWL2  
> axioms, it was able to maintain all the axioms even when the  
> ontology was reexported using Protege 3.4  (probably because it  
> dealt with them as RDF triples even if it couldn't understand  
> them).  Based on this, I am wondering if BioPortal can behave in a  
> similar fashion.  All I need from BioPortal at this time is for it  
> to be able to show/navigate the named class hierarchy for an OWL2  
> ontology and for users to be able to make comments on named entities.
>
> Thanks,
> Shahim
>
>
> Trish Whetzel wrote:
>> I don't believe that one can damage an existing PURL. In the worse  
>> case, I think that it is tombstoned and will therefore still be  
>> accessible.  When you login, can you search for a PURL with  
>> Maintainer ID 'whetzel' and let me know if it looks like you can  
>> edit the PURL?
>>
>> As for domains, after I new domain is requested I should be  
>> notified and can approve the domain and then you can create PURLs  
>> within the domain.
>>
>> Cheers,
>> Trish
>>
>>
>> On Dec 1, 2009, at 3:01 PM, Shahim Essaid wrote:
>>
>>> Thanks, that worked.
>>>
>>> I am new to PURL and I need to read the documentation.  In the  
>>> mean time, is it possible that I will damage the existing  
>>> records?  The user interface doesn't make it clear what type of  
>>> actions I am allowed to take and what actions are restricted.  I  
>>> am assuming that if I attempt to delete or modify a PURL by  
>>> mistake (a PURL I didn't create), the system will not allow this  
>>> to happen.  Also, can I freely create my own domains and start  
>>> adding PURLs to them or is there some sort of review process for  
>>> any/all changes?
>>>
>>> Thanks,
>>> Shahim
>>>
>>>
>>>
>>> Trish Whetzel wrote:
>>>> Sorry about that - the original pwd should allow you to login now.
>>>>
>>>> Trish
>>>>
>>>
>>
>

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
whetzel at stanford.edu
http://www.bioontology.org



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