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[bioontology-support] Feedback

Natasha Noy noy at
Sat Feb 28 15:19:45 PST 2009

This is the http: in the name problem. We don't have a solution yet.  
However, she can fix her file to avoid having this prefix. All she  
needs to do is add the following line at the top of the file, in the  
block where all xml namespaces are declared:


It will load fine.

I guess you can also mention to her (I don't think you have) that we  
have loaded all the ontologies on our internal server and they should  
all look fine on Monday on production. This one she needs to fix or we  
can fix it for her. She needs to know what the fix is though so that  
it works fine in the following versions.


On Feb 28, 2009, at 2:11 PM, Trish Whetzel wrote:

> I too uploaded all of Yu Lin's ontologies to stage last night. All  
> loaded
> fine, except Ontology of Geographical Region - any ideas why that  
> one is not
> able to be explored? Loading in Protégé 3.4 (build 519) the terms are
> displayed as
> but the
> OWL file has rdf:ID="Asia_Central".
> Trish
>> -----Original Message-----
>> From: bioontology-support-bounces at
>> [mailto:bioontology-support-bounces at] On Behalf Of
>> Natasha Noy
>> Sent: Saturday, February 28, 2009 10:48 AM
>> To: Nick Griffith
>> Cc: bioontology-support at; admin at
>> Subject: Re: [bioontology-support] Feedback
>> Just to clarify for everyone. Last night, after we received the
>> request, I downloaded the ontology from the production site and
>> uploaded to stage. It is parsed and searchable now. I suspect that
>> the anonymous class fix has fixed most, if not all, of the Yu Lin's
>> ontologies. So, Trish will write to her (as she already got in touch
>> with her earlier) telling her that we fixed the problem and will have
>> the fix on our production site on Monday. She can then either upload
>> everything herself again or ask us to do so.
>> Natasha
>> On Feb 28, 2009, at 10:44 AM, Nick Griffith wrote:
>>> for this one, the ontology isnt parsed yet for when you respond.
>>> On Feb 27, 2009, at 9:48 PM, admin at wrote:
>>>> Name : Lin
>>>> Email : linikujp at
>>>> Comment:
>>>> The function of "Search All ontologies" seems can not search all
>>>> the ontologies listed in the "Browse" window. For example, if I
>>>> search "gene", and my ontolgy "Ontology of Genetic Interval",
>>>> which includes the term of gene, will not come out.
>>>> Could you please tell me why? Or could you please tell me how can
>>>> I make my ontology searchable through your "Search" Function.
>>>> Thank you!
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at
>>> Nick Griffith
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at

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