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

RobyE at MSKCC.ORG RobyE at MSKCC.ORG
Mon Jul 15 13:18:09 PDT 2013


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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