Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Feedback

Trish Whetzel whetzel at
Sat Feb 28 16:15:04 PST 2009

Ok, thought it was somewhere in the namespace area since the rdf:ID part
looked ok. I can add the last bit now about the other ontologies.


>-----Original Message-----
>From: Natasha Noy [mailto:noy at]
>Sent: Saturday, February 28, 2009 3:20 PM
>To: Trish Whetzel
>Cc: bioontology-support at
>Subject: Re: [bioontology-support] Feedback
>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:
>     xmlns=""
>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

More information about the bioontology-support mailing list