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[bioontology-support] annotation ontology selection menu

Madani,Sina AHMadani at mdanderson.org
Tue Oct 11 11:01:48 PDT 2011


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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>>
>> The National Center for Biomedical Ontology
>>
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