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[bioontology-support] [BioPortal] Ontology for Biomedical Investigations Parsing Failed

Jie Zheng jiezheng at pcbi.upenn.edu
Tue Apr 10 07:16:38 PDT 2012


Hi,

Does anyone Bioportal developer look at parsing error of OBI that caused 
by ClassCastException? It still shows 'parsing error' on the Bioportal 
website.  Any progress on fixing the error? We uploaded the ontology 10 
days ago.

Thanks,

Jie

>
> On 4/5/2012 4:39 PM, Trish Whetzel wrote:
>> Hi Jie,
>>
>> Yes, the issue is being reviewed. A ClassCastException error was 
>> found. I don't yet have more details on what needs to be done to 
>> resolve the issue.
>>
>> Trish
>>
>>
>> On Apr 5, 2012, at 1:08 PM, Jie Zheng wrote:
>>
>>> Is anyone in charge of the parsing error issue of OBI? Any issue we 
>>> need to fix in the submitted ontology?
>>>
>>> Thanks,
>>>
>>> Jie
>>>
>>> On 4/2/2012 10:39 AM, Jie Zheng wrote:
>>>> Hi,
>>>>
>>>> The new version of OBI uploaded on March 30 is the version that 
>>>> imports BFO 2.0 (prerelease) 
>>>> (http://purl.obolibrary.org/obo/bfo.owl) which has problem to be 
>>>> opened by Protege 3.4. The one uploaded on April 1 merged BFO to 
>>>> OBI. It is no problem to be opened using Protege v3.4 and Protege 
>>>> v4.1. Reasoning using Hermit on Protege 4.1 works fine as well. 
>>>> Please let me know if you find any issue.
>>>>
>>>> Thanks,
>>>>
>>>> Jie
>>>>
>>>> On 4/2/2012 2:34 AM, support at bioontology.org 
>>>> <mailto:support at bioontology.org> wrote:
>>>>> Ontology for Biomedical Investigations parsing failed.
>>>>>
>>>>> The BioPortal team is investigating the issue.
>>>>>
>>>>> Please contact support at bioontology.org 
>>>>> <mailto:support at bioontology.org> if you have questions.
>>>>>
>>>>> Thank you,
>>>>> The BioPortal Team
>>>>
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>>>> <mailto:bioontology-support at lists.stanford.edu>
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>>>
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>>
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> http://www.bioontology.org
>>
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>
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