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[bioontology-support] Display error in BioPortal. Re: Automatic ontology pull

Trish Whetzel whetzel at stanford.edu
Mon Apr 26 09:47:07 PDT 2010


Thanks! I put in a tracker item to request that AEO be added to the  
automatic pull process.

Trish


On Apr 26, 2010, at 9:11 AM, Allen Zuoshuang Xiang wrote:

> Hi Trish,
>
> I have included the metadata file. It can also be downloaded from https://aeo.svn.sourceforge.net/svnroot/aeo/trunk/src/ontology/ontologies.txt 
> .
>
> Thanks,
> Allen
>
>
>
> On 4/25/2010 9:06 PM, Trish Whetzel wrote:
>>
>> Yes, I noticed that and have a question/tracker item into Natasha  
>> to help resolve the issue regarding the display of the term labels.
>>
>> We can certainly set-up AEO to pull automatically. Can you generate  
>> an ontology metadata file in the same format as used for VO and  
>> then send us the full path to the location to where this file has  
>> been uploaded?
>>
>> Thanks!
>> Trish
>>
>>
>>
>> On Apr 25, 2010, at 3:53 PM, Yongqun He wrote:
>>
>>> Hi Trish,
>>>
>>> I am glad to hear from you again. It appears that VO is displayed  
>>> well in BioPortal. One note is that some terms like  
>>> obo:OBI_0000047 (processed material) and CHEBI:CHEBI_23367  
>>> (molecular entity) do not show the labels. I am not sure why.
>>>
>>> Also, recently I submitted another ontology AEO: Adverse Event  
>>> Ontology to BioPortal. Can I also use the automatic update  
>>> mechanism?
>>>
>>> Thanks!
>>> Oliver
>>>
>>> >>> Trish Whetzel <whetzel at stanford.edu> 4/25/2010 3:00 PM >>>
>>> Hi Oliver,
>>>
>>> I am writing to update you on a few items related to BioPortal and  
>>> the
>>> Vaccine ontology.  In cases where the hierarchy is displayed as a  
>>> flat
>>> list, we have found that this is due to one of the imported  
>>> ontologies
>>> not being available via the web at the time of loading the Vaccine
>>> ontology. We are able to correct the display if an imported ontology
>>> is not accessible via the web when loading VO and are monitoring new
>>> uploads of VO.
>>>
>>> We have also generated PURLs that can be used to refer to ontologies
>>> in BioPortal. For VO, this is http://purl.bioontology.org/ontology/ 
>>> VO
>>> and will resolve to the 'visualize' page of the latest version of VO
>>> loaded into BioPortal.
>>>
>>> Best regards,
>>> Trish
>>>
>>>
>>>
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and  
>>> should not be used for urgent or sensitive issues
>>
>
> <ontologies.txt>

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