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[bioontology-support] BioPortal widgets

Pradnya Gawade pgawade at openclinica.com
Fri Dec 2 13:03:52 PST 2011


Hi Trish,

 

It seems defining the additional variable 'BP_SEARCH_SERVER' mentioned
at
[http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can
_I_use_widgets_with_my_Virtual_Appliance.3F] did not make difference for
me. Probably some thing additional needs to be done to associate this
new variable with the source of data to this widget. I was using html
version of the code for this widget and tried to incorporate this
variable and it which did not work. Pasting my code for reference at the
end of this email. I think basically I need to get the URL similar to
[http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf] for my
instance of BioPortal but I could not get the valid URL which shows me
some thing.

 

I also tried to use java script version of the code but I guess I am not
clear with how to use it inside the web page and thinking to put some
more efforts into it. 

Please let me know if any body has any comments on the html code I am
using. That might help me to get this done faster.

 

Thank you,

Pradnya

 

My html code for the ontology tree widget:

<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"

            id="OntologyTree" width="300" height="100%"

 
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swfla
sh.cab">

            <param name="movie"
value="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf" />

            <param name="quality" value="high" />

            <param name="bgcolor" value="#ffffff" />

            <param name="allowScriptAccess" value="always" />      

            <param name="flashVars"
value="ontology=1003&alerterrors=false&canchangeontology=false&virtual=t
rue" />

            <param name="BP_SEARCH_SERVER" value="http://192.168.15.174"
/>  

            <embed
src="http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf"
quality="high" bgcolor="#ffffff"

                        width="300" height="100%" name="OntologyTree"
align="middle"

                        play="true"

                        loop="false"

                        allowScriptAccess="always"

                        type="application/x-shockwave-flash"

 
flashVars="ontology=1003&alerterrors=false&canchangeontology=true&virtua
l=true"

 
pluginspage="http://www.adobe.com/go/getflashplayer">

            </embed>

</object>

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Wednesday, November 30, 2011 8:01 PM
To: Pradnya Gawade
Cc: support at bioontology.org
Subject: Re: [bioontology-support] BioPortal widgets

 

Hi Pradnya, 

 

The Flex/Flash-based widgets need a few extra steps, which are
documented at:

http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_
I_use_widgets_with_my_Virtual_Appliance.3F

 

Trish 

 

 

On Nov 30, 2011, at 12:14 PM, Pradnya Gawade wrote:





Hi Trish,

 

Thanks for your answer on opening the tree widget with some term
pre-populated and it seems it may not server my requirement as I do not
want to be restricted only to children of this term but would like to
see complete hierarchy with just focus on a selected term on load. 

 

The [http://{domain|ip}:8080/bioportal]  URL in case of my BioPortal VM
image does not take me any where in the browser. So I am writing this to
you as well as support at bioontology.org

Just to provide an overview, I am looking to get answer to following
question:

How to make widgets fetch the data from my instance of BioPortal?

 

I believe as mentioned at
[http://www.bioontology.org/wiki/index.php/NCBO_Widgets#OntologyTree_Wid
get] I will have to specify the value for parameters 'server' and
probably also for 'redirecturl' to achieve this. However I could not
achieve the desired effect even after doing this. Either I am missing
some thing or I am not providing the right values to these parameters.

Please comment if any body has done this in past. 

 

Thank you,

Pradnya

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Monday, November 28, 2011 11:49 AM
To: Pradnya Gawade
Subject: Re: [bioontology-support] BioPortal widgets

 

The login/pwd are listed in the VM Appliance document on the wiki at:

http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Applianc
e#Getting_Started

 

Trish 

 

 

On Nov 28, 2011, at 8:41 AM, Pradnya Gawade wrote:






Hi Trish,

 

I will check the things you have mentioned here and will get back to
you.

One other quick question for now, what is the user name, password I can
use to login to admin UI of VM image? I forgot what I entered last week
while talking to you and forgot to save our chat messages on gotomeeting
where I believe you had sent that to me.

 

Thank you,

Pradnya

 

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Monday, November 28, 2011 11:36 AM
To: Pradnya Gawade
Subject: Re: [bioontology-support] BioPortal widgets

 

Related to the widgets, the Web service endpoint will be whatever domain
or ip the machine is located on. Therefore, it would be whatever
domain/ip address you type in to get to the UI.  Here is the form it
should take:  http://{domain|ip}:8080/bioportal  

I believe that this is the form that we tried last week, however if this
does not work please email: support at bioontology.org. 

 

The Tree Widget can be opened with some term populated however this term
will then be displayed as the root of the tree and this will also
restrict the view of the ontology to this branch of the the ontology and
only children of this term will be visible in the widget. The parameter
is rootconceptid, see more here:

http://www.bioontology.org/wiki/index.php/NCBO_Widgets#OntologyTree_Widg
et

 

Trish 

 

 

On Nov 28, 2011, at 7:41 AM, Pradnya Gawade wrote:







Hi Trish,

 

Just a reminder on the stuff I am waiting about widgets:

1.	How to make widgets fetch the data from my instance of
BioPortal?
2.	How can I open the Tree Hierarchy widget with some search term
prepopulated?

 

Thank you,

Pradnya

 

________________________________

From: Pradnya Gawade 
Sent: Wednesday, November 23, 2011 2:05 PM
To: 'Trish Whetzel'
Subject: RE: [bioontology-support] BioPortal widgets

 

You might see organizer name as Ben Baumann.

 

 

 

________________________________

From: Pradnya Gawade 
Sent: Wednesday, November 23, 2011 2:04 PM
To: 'Trish Whetzel'
Subject: RE: [bioontology-support] BioPortal widgets

 

Hi Trish,

 

I just sent you the GoToMeeting invite. Please join if you can. If not
then we can try to have it next week. I will try to follow the wiki page
that you pointed out.

 

Thank s for your help.

 

- Pradnya

 

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Wednesday, November 23, 2011 1:17 PM
To: Pradnya Gawade
Subject: Re: [bioontology-support] BioPortal widgets

 

I can be available until 2:30pm ET.

 

Trish 

 

 

On Nov 23, 2011, at 8:13 AM, Pradnya Gawade wrote:

 

I am in Boston, Massachusetts, so Eastern Standard Time. Sorry for the
late response, is it still possible to have a screen sharing session?

 

Thank you,

Pradnya 

 

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Tuesday, November 22, 2011 7:19 PM
To: Pradnya Gawade
Subject: Re: [bioontology-support] BioPortal widgets

 

What timezone?

 

Trish 

 

On Nov 22, 2011, at 3:32 PM, Pradnya Gawade wrote:

 

It will be great if we could schedule some thing after 1 pm. Does that
time work for you?

Thanks in advance.

 

- Pradnya

 

________________________________

From: Trish Whetzel [mailto:whetzel at stanford.edu] 
Sent: Tuesday, November 22, 2011 4:26 PM
To: Pradnya Gawade
Subject: Re: [bioontology-support] BioPortal widgets

 

Do you have some time tomorrow we can set-up a screen share and talk in
person?

 

Trish  

Sent from my iPhone


On Nov 22, 2011, at 2:30 PM, "Pradnya Gawade" <pgawade at openclinica.com>
wrote:

	Are you talking about widgets page on my instance of BioPortal?
Sorry, I am not clear. If yes, how do I access that page? 

	 

	Thank you,

	- Pradnya

	 

	 

	
________________________________


	From: Trish Whetzel [mailto:whetzel at stanford.edu] 
	Sent: Tuesday, November 22, 2011 3:05 PM
	To: Pradnya Gawade
	Cc: <mailto:support at bioontology.org> support at bioontology.org
	Subject: Re: [bioontology-support] BioPortal widgets

	 

	When you view the Widgets page, what information do you see when
you click on the "Get Code" button? I believe that the URL should be the
same as the URL that you use to access the Admin Web page for your
instance. 

	 

	Trish 

	 

	 

	On Nov 22, 2011, at 1:33 PM, Pradnya Gawade wrote:

	
	
	
	
	
	
	

	Trish,

	 

	On the following wiki page, I see some parameters like server,
redirecturl which I thought would be useful in making the widget to
fetch the data from my instance of BioPortal but I do not see that
taking place after some trials. I am using the related html code inside
my web page. 

	Also I see that this widget probably fetches the structure from
<http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf>
http://keg.cs.uvic.ca/ncbo/ontologytree/OntologyTree.swf

	I wonder is this the URL which should be replaced with my
instance URL or it the value of 'server' parameter that is used for
getting the actual data? I tried changing both them but neither worked.

	I will highly appreciate any details on this one.

	 

	 

	Thank you, 

	Pradnya

	
________________________________


	From: Trish Whetzel [mailto:whetzel at stanford.edu] 
	Sent: Monday, November 21, 2011 3:09 PM
	To: Pradnya Gawade
	Cc: <mailto:support at bioontology.org> support at bioontology.org
	Subject: Re: [bioontology-support] BioPortal widgets

	 

	Hi Pradnya,

	 

	I think that the VM Appliance also contains the widgets and that
the code examples should provide information to use the widgets with
your instance of BioPortal. Perhaps there are other users of the VM
Appliance on the mailing list that can comment?

	 

	Trish 

	 

	 

	On Nov 21, 2011, at 8:53 AM, Pradnya Gawade wrote:

	
	
	
	
	
	
	
	

	

	Hi Trish,

	 

	I am planning to use some of the BioPortal widgets like Tree
Hierarchy, Search etc in my web application. I see that presently it
connects and gets the data probably from one of your servers. Is there
any way to make it point to our BioPortal instance so it will get the
data from there?

	Thanks in advance.

	 

	-          Pradnya

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	Trish Whetzel, PhD

	Outreach Coordinator

	The National Center for Biomedical Ontology

	Ph: 650-721-2378

	<http://www.bioontology.org/> http://www.bioontology.org
<http://www.bioontology.org/> 

	 

	Now on Twitter: <http://twitter.com/#!/bioontology>
http://twitter.com/#!/bioontology

	and "Like" us on Facebook:
<http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/1
27444774011153>
http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/12
7444774011153

	 

	 

	

	Trish Whetzel, PhD

	Outreach Coordinator

	The National Center for Biomedical Ontology

	Ph: 650-721-2378

	<http://www.bioontology.org/> http://www.bioontology.org
<http://www.bioontology.org/> 

	 

	Now on Twitter: <http://twitter.com/#!/bioontology>
http://twitter.com/#!/bioontology

	and "Like" us on Facebook:
<http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/1
27444774011153>
http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/12
7444774011153

	 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org <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/12
7444774011153

 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org <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/12
7444774011153

 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org <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/12
7444774011153

 

 

Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378

http://www.bioontology.org <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/12
7444774011153

 

 

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/12
7444774011153

 

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