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[bioontology-support] Visualization tab

Erick Antezana erick.antezana at gmail.com
Wed Feb 27 01:01:10 PST 2013


Hi Eric,

thanks for clarifying this "issue".

cheers,
Erick

On 22 February 2013 18:31, Eric Verbeek <eric.l.verbeek at gmail.com> wrote:

>  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> 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<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
>> *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 *
>>
>>
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>
>
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