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[bioontology-support] [bioontology-webmaster] Bioportal's Ontology tree widget is broken

Michael Shipway mshipwa1 at
Mon Aug 27 15:15:50 PDT 2012

I am getting the error as soon as I clicked the ontology selection
dropdown's arrow.

I just tested the Tree widget on other browsers and another OS and it works
fine there, but still breaks on my original setup.


I apologize for not including my browser and OS in my initial email.

I'm having the trouble on Windows 7 Professional, using Firefox 10.0.2

This browser has Shockwave Flash version 11.3.300.217 installed, last
updated Aug. 15, 2012.

I know the browser is out of date, but the Tree widget was working on this
configuration earlier (last tested about 2 months ago).


On the same system, so probably the same Flash version, it works in Internet
Explorer 9, version 9.0.8112.16421, Update versions 9.0.9(KB2722913), 
with Adobe Flash 11.3.300.271 installed.

This Windows system installed an update package this morning.


It also works on Ubuntu Linux 12.04 LTS using 

Firefox 14.0.1 with Adobe Flash Player and 

Chrome version 21.0.1180.81 with Adobe Flash Player


According to the Adobe web site, the Flash versions on the Linux machine are
up to date, but on the Windows machine both are a little behind and should
be the 11.4.402.265 version.



Michael Shipway-


From: Trish Whetzel [mailto:whetzel at] 
Sent: Monday, August 27, 2012 4:36 PM
To: Michael Shipway
Cc: support at Support
Subject: Re: [bioontology-webmaster] Bioportal's Ontology tree widget is


I'm not currently seeing an issue with the Tree widget. Which ontology and
term are you selecting?




PS - adding the NCBO User support forum to the Cc field




On Aug 27, 2012, at 12:55 PM, Michael Shipway wrote:

Bioportal's Ontology tree widget is broken, specifically it is calling a web
site which is not responding.

You can see the problem on the example page at:


if you try to select an ontology using the down arrow at the top left, you
get the message:
"Connection Error
Couldn't retrieve the list of Ontologies from the


Do you want to try again?"


I got this example link from this wiki page.



Michael Shipway

Sr. Software Engineer

Center for Cardiovascular Bioinformatics and Modeling

Institute for Computational Medicine

The Johns Hopkins University

3400 North Charles Street

Hackerman Hall 214

Baltimore, MD 21218-2686


bioontology-webmaster mailing list
bioontology-webmaster at


Trish Whetzel, PhD

Outreach Coordinator

The National Center for Biomedical Ontology

Ph: 650-721-2378


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