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

Trish Whetzel whetzel at
Mon Sep 20 17:06:46 PDT 2010

Hi Ilias,

We do plan to provide access to ICD10 via the Hierarchy web services  
in the near future, possibly as soon as the end of this week.

For FMA, the designated property for the preferred name was selected  
by the ontology developers. Is your preference to be able to display  
the FMA tree hierarchy with only the labels versus the namespace  
abbreviation added to the labels?


On Sep 19, 2010, at 8:15 AM, Ilias Gerostathopoulos wrote:

> Trish,
> I would like to ask you about the hierarchy rest services of  
> Bioportal. In our project we are using the FMA and the ICD10  
> (virtual id: 1516) ontology as reference ontologies to enhance our  
> annotation and search web tool on medical images. We found out that  
> the hierarchy rest services you offer for the FMA ontology are very  
> useful as we can search in greater depth in this specific ontology,  
> something very crucial for our search tool. Unfortunately, you do  
> not offer these services for every ontology of Bioportal and - to  
> our concern - for the above mentioned ICD10. Is it in your plans for  
> the near future to include the ICD10 in the in the list of  
> ontologies processed for use with the hierarchy services? That would  
> be of great assistance to us.
> As we are using the FMA ontology (v. id 1053), we found out that  
> there was an update to version 3.1 lately (version id: 44507). We  
> would like to point out that probably a mistake was made when  
> configuring this ontology version: rendering of the ontology tree  
> was made using the "id" attribute, where the "label" attribute  
> should be used. This can easily be noticed if you try to explore the  
> ontology. We feel that you would like to know and corrent this  
> mistake.
> I am looking forward to your reply,
> Ilias Gerostathopoulos,
> Biomedical Simulations and Imaging Laboratory
> National Technical University of Athens
> Greece
> 2010/9/1 Trish Whetzel <whetzel at>
> 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>
>> 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

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