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[bioontology-support] BioPortal widgets

Paul R Alexander palexander at stanford.edu
Mon Dec 5 10:38:28 PST 2011


Pradnya,

I think you combined the instructions for the Javascript widgets with 
the ones for the Flash widgets. Also, you should use the Flex apps that 
are hosted by NCBO as the ones hosted at UVic are not guaranteed to be 
available (see my corrected code below).

I'm guessing that this is the IP address for your instance of the 
Virtual Appliance: 192.168.15.174. If so, then the code below should 
work for you. Noe that it's using ontology id 1003, so if that ontology 
doesn't exist on your Appliance then it will not work.

<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000"
             id="OntologyTree" width="300" height="100%"
             
codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab">
<param name="movie" 
value="http://bioportal.bioontology.org/flex/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=true&server=http://192.168.15.174:8080" 
/>
<embed src="http://bioportal.bioontology.org/flex/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&virtual=true"
                         
pluginspage="http://www.adobe.com/go/getflashplayer">
</embed>
</object>

Best,
Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 12/2/11 1:03 PM, Pradnya Gawade wrote:
>
> 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/swflash.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=true"/>
>
> <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&virtual=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 <mailto: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_Widget_] 
> 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_Appliance#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 
> <mailto: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_Widget
>
> 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 
> <mailto: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:* support at bioontology.org <mailto: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 fromhttp://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:* support at bioontology.org <mailto: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
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu 
>> <mailto:bioontology-support at lists.stanford.edu>
>> 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 <http://www.bioontology.org/>
>>
>> Now on Twitter: http://twitter.com/#!/bioontology 
>> <http://twitter.com/#%21/bioontology>
>>
>> and "Like" us on Facebook: 
>> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>
>> 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 
>> <http://twitter.com/#%21/bioontology>
>>
>> and "Like" us on Facebook: 
>> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>>
> 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 
> <http://twitter.com/#%21/bioontology>
>
> and "Like" us on Facebook: 
> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>
> 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 
> <http://twitter.com/#%21/bioontology>
>
> and "Like" us on Facebook: 
> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>
> 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 
> <http://twitter.com/#%21/bioontology>
>
> and "Like" us on Facebook: 
> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>
> 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 
> <http://twitter.com/#%21/bioontology>
>
> and "Like" us on Facebook: 
> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>
> 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 
> <http://twitter.com/#%21/bioontology>
>
> and "Like" us on Facebook: 
> http://www.facebook.com/pages/National-Center-for-Biomedical-Ontology/127444774011153
>
>
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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