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[bioontology-support] Re-submission of Surgical Secondary Events ontology

Ray Fergerson ray.fergerson at stanford.edu
Mon Jul 15 16:56:06 PDT 2013


I'm going to move this off list and give it to our Protégé  4 expert to look 
at. He may be able to figure out what is going on and provide some direction 
about how best to get this thing loaded...

Ray

-----Original Message-----
From: bioontology-support-bounces at lists.stanford.edu 
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of 
RobyE at MSKCC.ORG
Sent: Monday, July 15, 2013 1:18 PM
To: palexander at stanford.edu
Cc: rodriguj at MSKCC.ORG; support at bioontology.org
Subject: Re: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

Do you have any suggestions for us on how to fix the problem from our end?

-----Original Message-----
From: Paul R Alexander [mailto:palexander at stanford.edu]
Sent: Monday, July 15, 2013 4:11 PM
To: Roby, Elizabeth/Surgery
Cc: support at bioontology.org; Rodriguez, Juan C./Surgery
Subject: RE: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

We use Protege 3.5 to parse ontologies. We don't typically have a problem 
loading ontologies from 4.x, though. In fact, we have a process to make sure 
these ontologies work correctly.

Paul

----- Original Message -----
From: RobyE at MSKCC.ORG
To: palexander at stanford.edu
Cc: support at bioontology.org, rodriguj at MSKCC.ORG
Sent: Mon, 15 Jul 2013 12:26:43 -0700 (PDT)
Subject: RE: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

Hi Paul,
Thank you for fixing the download. What version of Protégé are you using? I 
was looking at the ontology with version 4.3 and couldn't find the problems 
you mention. Could you point me in the right direction? We definitely want 
the ontology to parse correctly and be searchable.
Thanks for your help,
Elizabeth

From: Paul R Alexander [mailto:palexander at stanford.edu]
Sent: Monday, July 15, 2013 2:22 PM
To: Roby, Elizabeth/Surgery
Cc: support at bioontology.org
Subject: Re: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

Elizabeth,

I fixed the download error. However, the ontology itself appears to have 
some errors in it as I have problems when trying to open it with Protege. 
Though it doesn't fail to open outright in Protege, it does have problems 
displaying the Metadata and Properties tab due to problems in the sae.owl 
file.

Paul


On Jul 15, 2013, at 8:26 AM, RobyE at MSKCC.ORG<mailto:RobyE at MSKCC.ORG> wrote:


Hi Paul,
It says there is a parsing error on Version 
1.2<http://bioportal.bioontology.org/ontologies/3252>. The download gives 
the error below:

<?xml version="1.0" encoding="UTF-8" ?>
-<http://rest.bioontology.org/bioportal/ontologies/download/50477?apikey=4ea81d74-8960-4525-810b-fa1baab576ff&userapikey=> 
<errorStatus> 
<accessedResource>/bioportal/ontologies/download/50477</accessedResource>
 <accessDate>2013-07-15 08:14:20.269 PDT</accessDate> 
<shortMessage>Forbidden</shortMessage>
 <longMessage>This ontology is either private or licensed. Please go 
tohttp://bioportal.bioontology.org/ontologies/3252?p=terms to get access to 
the ontology.</longMessage>  <errorCode>403</errorCode>  </errorStatus>

Can you help?
Thanks,
Elizabeth

From: Roby, Elizabeth/Surgery
Sent: Thursday, July 11, 2013 3:25 PM
To: 'Paul R Alexander'
Cc: 'support at bioontology.org<mailto:support at bioontology.org>'
Subject: RE: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

Great!

From: Paul R Alexander [mailto:palexander at stanford.edu]
Sent: Thursday, July 11, 2013 3:25 PM
To: Roby, Elizabeth/Surgery
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

I've merged the two entries and used the preferred abbreviation.

Paul


On Jul 11, 2013, at 12:23 PM, RobyE at MSKCC.ORG<mailto:RobyE at MSKCC.ORG> wrote:

Thank you!

From: Paul R Alexander [mailto:palexander at stanford.edu<http://stanford.edu>]
Sent: Thursday, July 11, 2013 3:14 PM
To: Roby, Elizabeth/Surgery
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Re-submission of Surgical Secondary 
Events ontology

Elizabeth,

I can remove the version with the SSE abbreviation. However, should the 
public one actually have the SSE abbreviation? We would prefer to have the 
formal names and abbreviations in the system.

Paul


On Jul 11, 2013, at 12:09 PM, RobyE at MSKCC.ORG<mailto:RobyE at MSKCC.ORG> wrote:



Hello,
Please remove the earlier (Licensed) submission of the Surgical Secondary 
Events (Memorial Sloan-Kettering Surgical Secondary Events) ontology.
The correct one should be public (abbreviated SURSE).
Thanks for your help,
Elizabeth




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