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[bioontology-support] [bioontology-info] Flash Bioportal Ontology Tree javascript functions

Paul R Alexander palexander at
Thu Sep 2 11:13:53 PDT 2010


The preferred method of embedding is using Javascript (as stated in the 
wiki). The HTML embed method provides inconsistent results, especially 
when trying to use Javascript to interact with the embedded object.

As for the Javascript helper functions described on the wiki, these are 
actually not included in the Flash object and you will need to do a 
copy/paste and either embed them in a Javascript file or directly in the 
HTML. Once they are included in your page, you should be able to call 
the helper functions as needed. If you are already doing this and still 
having problems please let me know.

In addition, you can look at the source for a test page provided by our 
Flash developer to see more code examples and comments: Note that 
the code works properly on this page for me using Firefox 3.6.

Please let me know if you have other questions or if I can help with 
anything else.

Paul R Alexander
Web / UI Developer
NCBO BioPortal <>
Stanford Center for Biomedical Informatics Research

On 8/31/10 6:55 PM, Trish Whetzel wrote:
> Thanks, we are investigating this further.
> Trish
> On Aug 30, 2010, at 1:28 PM, Ilias Gerostathopoulos wrote:
>> I am trying to use the FMA ontology. I am not sure but I think the 
>> same problem exists with other ontologies as well.
>> Ilias
>> 2010/8/30 Trish Whetzel <whetzel at 
>> <mailto:whetzel at>>
>>     Which ontology are you trying to use with the Ontology Tree Widget?
>>     Trish
>>     On Aug 30, 2010, at 10:37 AM, Ilias Gerostathopoulos wrote:
>>>     Dear Sir,
>>>     in our effort to make use of a NCBO widget, namely the
>>>     OntologyTree Widget documented in the NCBO wiki
>>>     (
>>>     as part of the theses we are working on concerning the "Semantic
>>>     Medical Image Annotation" area we jumped into a problem and need
>>>     your advice and help.
>>>     Our goal is to interact with the Flash Bioportal Ontology Tree
>>>     using the javascript functions you provide in the wiki page. The
>>>     problem is that these functions will not work both in case of
>>>     embedding the Flash Application using javascript and using html
>>>     (with <object> tag). For example, when the function
>>>     getOntologyName() is fired the javascript console informs us
>>>     that the app.getOntologyName function of the embedded object
>>>     does not exist (even though the "app" object exists meaning that
>>>     the getApp() function works properly). Please note that the
>>>     problem takes place only in the javascript functions that call a
>>>     flash object's function (like the getOntologyName() mentioned
>>>     above) and not in the javascipt functions that listen to the
>>>     flash object's events like the appComplete(swfID) which work fine.
>>>     We would be grateful if you could check the above functions and
>>>     tell us if they work properly, so that we can be sure we make
>>>     the fault in the way we use them. If that is the case, could you
>>>     provide us more specific details regarding the way to embed them
>>>     in our web app?
>>>     It is very important for us to make use of the extra
>>>     functionality you provide though these functions as this will be
>>>     a serious boost to the functionality of our theses application
>>>     as a whole.
>>>     Thank you in advance,
>>>     Ilias Gerostathopoulos
>>>     - Προβολή αναφερ. κειμ. -
>>>     _______________________________________________
>>>     bioontology-info mailing list
>>>     bioontology-info at
>>>     <mailto:bioontology-info at>
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