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[bioontology-support] annotation ontology selection menu

Paul R Alexander palexander at stanford.edu
Tue Oct 11 12:15:07 PDT 2011


Sina,

If you go ahead and delete the ontology record from the obs_ontology 
table, my guess is that it will no longer appear. I haven't tested 
this, but it's the logical next step if setting the status to 3 does 
not prevent it from showing.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On Tue Oct 11 11:01:48 2011, Madani,Sina wrote:
> I did them already as I mentioned. These scripts revert the ontology status from 28 to 14 and then from 14 to 3.
> So the ontology metadata row with the status 3 remains in that table after running the mentioned scripts
>
> Sina
>
> -----Original Message-----
> From: Paul R Alexander [mailto:palexander at stanford.edu]
> Sent: Tuesday, October 11, 2011 12:59 PM
> To: Madani,Sina
> Cc: support at bioontology.org; Trish Whetzel
> Subject: Re: [bioontology-support] annotation ontology selection menu
>
> Sina,
>
> If that fails there is a manual option to remove them using SQL
> queries. Please see:
> http://www.bioontology.org/wiki/index.php/Annotator_Dataset_Workflow_Howto#Data_Clean-Up
>
> Replace the 39545 from the first line of the queries with the version
> of the ontology to remove, and then run the subsequent commands:
> set @var_ontology_version_id := '39545';
>
> Paul R Alexander
> Web / UI Developer
> NCBO BioPortal
> Stanford Center for Biomedical Informatics Research
>
>
> On Tue Oct 11 10:50:57 2011, Madani,Sina wrote:
>> I did that (old,list,remove) a couple of times but still ontologies remain in the obs_ontology table (if that is the location where the annotation ontologies list is coming from )
>>
>> I even revert them back from status 28 to 14 and then from 14 to 3.
>>
>> Thanks
>> Sina
>>
>> -----Original Message-----
>> From: Paul R Alexander [mailto:palexander at stanford.edu]
>> Sent: Tuesday, October 11, 2011 12:46 PM
>> To: Madani,Sina
>> Cc: support at bioontology.org; Trish Whetzel
>> Subject: Re: [bioontology-support] annotation ontology selection menu
>>
>> Sina,
>>
>> Removing ontologies from Annotator does not happen automatically when
>> they are deleted using the Admin tool. Please see Step 1 here for
>> information on how to do this:
>> http://www.bioontology.org/wiki/index.php/Annotator_Dataset_Workflow_Howto#Synchronize_Hierarchy_Database_with_Ontology_Services
>>
>> Paul R Alexander
>> Web / UI Developer
>> NCBO BioPortal
>> Stanford Center for Biomedical Informatics Research
>>
>>
>> On Tue Oct 11 10:21:10 2011, Madani,Sina wrote:
>>> Yes. Some of the ontologies in this list are completely deleted
>>> through bioportal_admin and their annotation status was set back to 3
>>> though included SQL scripts
>>>
>>> *From:*Trish Whetzel [mailto:whetzel at stanford.edu]
>>> *Sent:* Tuesday, October 11, 2011 11:58 AM
>>> *To:* Madani,Sina
>>> *Cc:* support at bioontology.org
>>> *Subject:* Re: [bioontology-support] annotation ontology selection menu
>>>
>>> Hi Sina,
>>>
>>> Which pop-up windows are you referring to, e.g. the "Ontologies" menu
>>> on the Annotator page?
>>>
>>> Trish
>>>
>>> On Oct 11, 2011, at 9:50 AM, Madani,Sina wrote:
>>>
>>>
>>>
>>> Hi,
>>>
>>> Some of the previously removed/deprecated ontologies in our local
>>> instance are still showing up in the pop up windows when selecting
>>> ontologies for annotation services. How can I refresh that list or
>>> perhaps manually remove the deprecated ontologies from that list?
>>>
>>> Thanks
>>>
>>> Sina
>>>
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>>>
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