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[bioontology-support] BIM ontology update/delete help

Paul R Alexander palexander at stanford.edu
Wed Oct 1 16:56:20 PDT 2014


Ok, somehow the ontology had been made a view of itself. Views are not shown by default on the browse page. I’ve fixed this and it’s now showing up properly.

I’m not sure what you are seeing in the tree view that looks incorrect. I downloaded the 1.2 version of your ontology and loaded it using Protege. It looks identical to the version we have as near as I can tell. Can you tell me what is wrong? Maybe send a screen shot so I can see what you are seeing?

Thanks,
Paul


On Sep 30, 2014, at 7:59 PM, Ahmad Chan <ahmadchan at gmail.com> wrote:

> Hi Paul,
> 
> I can view the ontology page by clicking on http://bioportal.bioontology.org/ontologies/BIM. What I was saying, I did not find my ontology link in search results. If you click to browse tab and select the ontology category  -Imaging. Two days ago, my ontology was in the search results.
> Second, I would be thankful, if you could help me to update the tree view, http://bioportal.bioontology.org/ontologies/BIM?p=classes&conceptid=root. The system is still displaying, my first uploaded ontology here, I also have noticed if I type any term (into Jump to box) from the updated ontology the view gets changed. . Thanks You
> 
> On Tue, Sep 30, 2014 at 8:50 PM, Paul R Alexander <palexander at stanford.edu> wrote:
> I’m not sure why you can’t see it. The ontology is available here:
> http://bioportal.bioontology.org/ontologies/BIM
> 
> You can add a submission here (you will need to be logged into your BioPortal account):
> http://bioportal.bioontology.org/ontologies/BIM/submissions/new
> 
> Paul
> 
> 
> On Sep 30, 2014, at 4:34 PM, Ahmad Chan <ahmadchan at gmail.com> wrote:
> 
>> Hi,
>> 
>> Now, I can not see my ontology in search results therefore I cannot edit. I tried to add, my ontology, as new ontology and the system is generating the following error.
>> Errors On Form
>> {"error":" Ontology already exists, see http://data.bioontology.org/ontologies/BIM\n To add a new submission, POST to: /ontologies/BIM/submission.\n To modify the resource, use PATCH.\n"}
>> 
>> 
>> On Tue, Sep 30, 2014 at 1:38 PM, Paul R Alexander <palexander at stanford.edu> wrote:
>> Ok, please upload the version you would like to have as a new submission and let me know when you have done that. After that you want all other versions removed?
>> 
>> Paul
>> 
>> 
>> On Sep 29, 2014, at 6:44 PM, Ahmad Chan <ahmadchan at gmail.com> wrote:
>> 
>>> Thanks for reply Paul. Yes, I like to remove all the old versions and also I would like to display a tree view  (http://bioportal.bioontology.org/ontologies/BIM?p=classes&conceptid=root) of my updated ontology. The current review belongs to ontology which I have added to test the uploading service. 
>>> 
>>> On Mon, Sep 29, 2014 at 10:28 PM, Paul R Alexander <palexander at stanford.edu> wrote:
>>> Ahmad,
>>> 
>>> Can you check again? I think this has been fixed. I show the version uploaded on 9/28 (version 1.1) as being the most recent and it was successfully processed and is now available. There is an older version also marked as 1.1 and several marked as 1.0. Do you want these extra/duplicate versions removed?
>>> 
>>> Paul
>>> 
>>> 
>>> On Sep 27, 2014, at 4:56 PM, Ahmad Chan <ahmadchan at gmail.com> wrote:
>>> 
>>>> Hi, 
>>>> 
>>>> Could you please help? I like to update my ontology located at (http://bioportal.bioontology.org/ontologies/BIM). I have tried with edit the submission option and to add new ontology but when I click on http://purl.bioontology.org/ontology/BIM I can see the previous version only. How can I delete all my previous versions of the ontology? Thanks
>>>> 
>>>> Ahmad Chan
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> 
>> 
>> 
> 
> 

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