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[bioontology-support] [Diseaseontology-discussion] [BioPortal] Human Disease Ontology Parsing Failed

Ray Fergerson ray.fergerson at
Wed Aug 21 17:34:27 PDT 2013

The strange thing is that it appears to have worked before (judging by the 
old version). It broke in mid April. I don’t think that we have changed 
anything on our side.


From: Lynn Schriml [mailto:lynn.schriml at]
Sent: Wednesday, August 21, 2013 3:46 PM
To: Ray Fergerson
Cc: support
Subject: Re: [bioontology-support] [Diseaseontology-discussion] [BioPortal] 
Human Disease Ontology Parsing Failed

Thank you Ray!!

How odd, any idea why this is happening ?

I've been looking at the file and haven't been able to figure this out.

Much appreciated !!


Sent from my iPhone

On Aug 21, 2013, at 6:32 PM, Ray Fergerson <ray.fergerson at> 


The problem seems to be that the download link returns HTML rather than an 
OWL file. Perhaps it is using HTML to redirect, but this does not work. An 
excerpt of the text that we are seeing is given below. You can see the 
entire page that we retrieve if you download the ontology from the link on 
the bioportal page.


<!DOCTYPE html>

<!-- Server: sfn-web-4 -->

<!--[if lt IE 7 ]> <html lang="en" class="no-js ie6"> <![endif]-->

<!--[if IE 7 ]>    <html lang="en" class="no-js ie7"> <![endif]-->

<!--[if IE 8 ]>    <html lang="en" class="no-js ie8"> <![endif]-->

<!--[if IE 9 ]>    <html lang="en" class="no-js ie9"> <![endif]-->

<!--[if (gt IE 9)|!(IE)]>--> <html lang="en" class="no-js"> <!--<![endif]-->


    <meta content="text/html; charset=UTF-8" http-equiv="content-type"/>


  Disease Ontology / Code

    / [r2607]


<meta id="webtracker" name="webtracker" content='{"event_id": 
"99b61464-09fd-11e3-a85e-0200ac1d2936", "project": 
"diseaseontology", "action_type": "svn"}' />

From: bioontology-support-bounces at 
[mailto:bioontology-support-bounces at] On Behalf Of Lynn 
Sent: Monday, August 19, 2013 7:27 AM
To: support
Subject: Re: [bioontology-support] [Diseaseontology-discussion] [BioPortal] 
Human Disease Ontology Parsing Failed


   I see that the DO load has a parsing error.

If you can send me the error, I can fix it today.

Thank you,

Lynn Schriml

On Sat, Aug 17, 2013 at 11:37 PM, <support at> wrote:

Human Disease Ontology parsing failed.

The BioPortal team is investigating the issue.

Please contact support at if you have questions.

Thank you,
The BioPortal Team
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