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

Yongqun He yongqunh at
Mon Apr 26 09:59:25 PDT 2010

Hi Trish,

>>> Trish Whetzel <whetzel at> 4/26/2010 12:47 PM >>>
Thanks! I put in a tracker item to request that AEO be added to the automatic pull process.


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


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?


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? 

>>> Trish Whetzel <whetzel at> 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  
and will resolve to the 'visualize' page of the latest version of VO  
loaded into BioPortal.

Best regards,

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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