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[bioontology-support] [BioPortal] Feedback from Brian Aevermann

Scheuermann, Richard RScheuermann at jcvi.org
Thu Jul 18 13:39:24 PDT 2019


Jennifer,

I just updated my BioPortal profile with my current jcvi email address.  My username is:  scheuerm.

Thanks,

Richard


--------------------------------------------
Richard H. Scheuermann, Ph.D.
Director, La Jolla Campus
J. Craig Venter Institute
4120 Capricorn Ln.
La Jolla, CA 92037
www.jcvi.org<http://www.jcvi.org>

rscheuermann at jcvi.org<mailto:rscheuermann at jcvi.org>
858-200-1876


From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Thursday, July 18, 2019 at 1:36 PM
To: "Richard H. Scheuermann" <RScheuermann at jcvi.org>
Cc: "Aevermann, Brian" <baeverma at jcvi.org>, NCBO User Support <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Brian Aevermann

Hi Richard,

Sure, no problem. You’ll need to let us know your BioPortal account name or email address that you used to set up an account. I searched our backend for a user object associated with your jcvi.org<http://jcvi.org> email address, but couldn’t find anything. If you haven’t signed up for an account yet, you can do so here:

https://bioportal.bioontology.org/accounts/new<https://bioportal.bioontology.org/accounts/new>

Kind regards,
Jennifer



On Jul 18, 2019, at 1:30 PM, Scheuermann, Richard <RScheuermann at jcvi.org<mailto:RScheuermann at jcvi.org>> wrote:

While we are at it, could I have read/write privileges as well?


--------------------------------------------
Richard H. Scheuermann, Ph.D.
Director, La Jolla Campus
J. Craig Venter Institute
4120 Capricorn Ln.
La Jolla, CA 92037
www.jcvi.org<http://www.jcvi.org/>

rscheuermann at jcvi.org<mailto:rscheuermann at jcvi.org>
858-200-1876


From: "Richard H. Scheuermann" <RScheuermann at jcvi.org<mailto:RScheuermann at jcvi.org>>
Date: Thursday, July 18, 2019 at 1:24 PM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>, "Aevermann, Brian" <baeverma at jcvi.org<mailto:baeverma at jcvi.org>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Brian Aevermann

Thanks Jennifer.  That seems to have resolved the problem!


--------------------------------------------
Richard H. Scheuermann, Ph.D.
Director, La Jolla Campus
J. Craig Venter Institute
4120 Capricorn Ln.
La Jolla, CA 92037
www.jcvi.org<http://www.jcvi.org/>

rscheuermann at jcvi.org<mailto:rscheuermann at jcvi.org>
858-200-1876


From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Thursday, July 18, 2019 at 1:20 PM
To: "Aevermann, Brian" <baeverma at jcvi.org<mailto:baeverma at jcvi.org>>
Cc: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>, "Richard H. Scheuermann" <RScheuermann at jcvi.org<mailto:RScheuermann at jcvi.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Brian Aevermann

Hi Brian,

I think the problem may have been a corrupt value in our cache that stores the root classes. I reprocessed the latest submission of PCL and flushed our application caches. The class tree is now displaying without issue in BioPortal. Feel free to contact us again if you see any further issues.

Kind regards,
Jennifer


<image001.png>







On Jul 18, 2019, at 12:51 PM, Aevermann, Brian <baeverma at jcvi.org<mailto:baeverma at jcvi.org>> wrote:

Jennifer,

Much appreciated! I will hold off for the moment as we are deliberating on the content of our next update. If you could please take a look at the current version and investigate why the classes are no longer displaying (they were displaying previously), it would be a big help to us.

Thanks again!!

Brian Aevermann


—
Brian Aevermann
Bioinformatics Analyst
J. Craig Venter Institute
4120 Capricorn Lane
La Jolla, CA 92037
858-200-1873

From: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Date: Thursday, July 18, 2019 at 12:47 PM
To: NCBO User Support <support at bioontology.org<mailto:support at bioontology.org>>
Cc: "Aevermann, Brian" <baeverma at jcvi.org<mailto:baeverma at jcvi.org>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Brian Aevermann

Hello Brian,

Yes - I just gave you administrative access to PCL. You may have to refresh your browser to see the edit buttons.

I took a quick look at the parsing log file for the last submission of this ontology and it wasn’t immediately clear to me what the issue was. Were you planning to upload a new version? If so, I’ll hold off on further investigation. If not, let me know, as we’ll need to troubleshoot the current version in BioPortal.

Kind regards,
Jennifer







On Jul 18, 2019, at 12:12 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Brian Aevermann
Email: baeverma at jcvi.org<mailto:baeverma at jcvi.org>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FPCL

Feedback:
Hello,
The ontology located at http://bioportal.bioontology.org/ontologies/PCL/?p=summary<http://bioportal.bioontology.org/ontologies/PCL/?p=summary> is not displaying the classes properly. A colleague of mine was maintaining it; however he has left my institute. Can I get Read/write permission assigned to me so I can try to fix it?
Thanks!
Brian Aevermann

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