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[bioontology-support] annotation ontology selection menu

Trish Whetzel whetzel at stanford.edu
Tue Oct 11 12:14:15 PDT 2011


Hi Sina, 

In the past, to remove ontologies from being displayed in the Annotator pop-up window the status field in the OBS (Annotator) database table obs_ontology can be set to 99. The other methods Paul mentioned can be explored to remove these ontologies from the Annotator database.

Trish 


On Oct 11, 2011, at 2:01 PM, 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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>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> 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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>>> 
>>> 
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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

Now on Twitter: http://twitter.com/#!/bioontology
and "Like" us on Facebook: http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153

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