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[bioontology-support] Visualization tab

Eric Verbeek eric.l.verbeek at gmail.com
Fri Feb 22 09:31:45 PST 2013


Hi Erick,

The calls that the visualization makes are passing very sparse 
information; concept ids, ontology ids. Nothing large or detailed is 
sent out. I would suggest that you satisfy your users' concerns by 
looking at the relevant pieces of javascript, but it's all been 
generated from Java by GWT, and is not very readable.

All of the calls are for BioPortal REST services, and all are tring to 
fetch additional data (such as mappings, of cocnept details) from 
identifiers such as concept and ontology ids. I don't think there is any 
need for concern about data or ontology information leaking out.

Cheers,
~Eric

On 22/02/2013 1:47 AM, Erick Antezana wrote:
> Hi,
>
> does it mean that my local bioportal (appliance) is sending some data 
> so that the visualisation could be rendered? My users are a 
> bit paranoid with their data/ontologies. This could be an issue...if 
> so, is there a way to close/block it without loosing functionalities?
>
> cheers,
> Erick
>
>
> On 7 February 2013 19:49, Eric Verbeek <eric.l.verbeek at gmail.com 
> <mailto:eric.l.verbeek at gmail.com>> wrote:
>
>     Hi Sina and Ray,
>
>     The visualization is in JavaScript, and makes calls to the REST
>     services from there to the public BioPortal servers. I haven't
>     worked with the VM yet. Does the VM have internet access? Does the
>     configuration for BioPortal in the VM have different connectivity
>     paths or requirements to the REST servers than the visualization uses?
>
>     Sina, could you check a JavaScript error log or developer console
>     for errors? If you are using Chrome, you can access it with
>     Ctrl-Shift-J, or through Chrome's menu (the one with three stacked
>     horizontal lines, on all OSes). There might be some hints for me
>     in the JS errors.
>
>     ~Eric
>
>
>     On 07/02/2013 10:32 AM, Ray Fergerson wrote:
>>
>>     Sina,
>>
>>     Copying Eric (the visualization guy). I don’t understand this at
>>     all. I can confirm that difference between what you see in your
>>     VM and what we see. I believe that we are all pointing that the
>>     same instance of the visualization software though.
>>
>>     Eric, any idea why this is happening? What would cause this
>>     visualization configuration item to not show up?
>>
>>     Ray
>>
>>     *From:*bioontology-support-bounces at lists.stanford.edu
>>     <mailto:bioontology-support-bounces at lists.stanford.edu>
>>     [mailto:bioontology-support-bounces at lists.stanford.edu] *On
>>     Behalf Of *Madani,Sina
>>     *Sent:* Thursday, February 07, 2013 5:56 AM
>>     *To:* support at bioontology.org <mailto:support at bioontology.org>
>>     *Cc:* Riben,Michael Warren
>>     *Subject:* [bioontology-support] Visualization tab
>>
>>     Hi,
>>
>>     We noticed that the visualization widget of our local instance is
>>     not working properly. Comparing to your environment, apparently
>>     the “Show SNOMED Clinical term” from the drop down configuration
>>     menu is missing in our instance’s UI.
>>
>>     Is there a configuration file that I can set this in order to
>>     operationalize the Visualization tab?
>>
>>     Thanks!
>>
>>     Sina
>>
>>     *_Our local instance_*
>>
>>     *_Stanford instance _*
>>
>
>
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>
>

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