[bioontology-support] [BioPortal] Load from URL failure for Plant Ontology

[Jennifer Leigh Vendetti]

Hi Laurel,

We had an issue with our PURL server (it went down for a period of time over the weekend).  It’s back up as of this morning - I tested your PURL and it’s working fine now.  Apologies for the inconvenience.  The PURL server is normally very stable, so this was somewhat of an unusual event.

Best,
Jennifer


On Oct 17, 2016, at 5:11 PM, Laurel Cooper <cooperl at science.oregonstate.edu<mailto:cooperl at science.oregonstate.edu>> wrote:


Hi

Thanks for the reply- I get this message when I click on the http://purl.bioontology.org/ontology/PTO

"We're sorry but something has gone wrong. We have been notified of this error."

I will check it again in the morning,
Laurel

On 10/17/16 4:09 PM, Jennifer Leigh Vendetti wrote:
Hi Laurel,

Sorry - I’m not sure what you mean when you say the ontology isn’t working.  I went to the metadata and classes pages for the September 2016 version you mentioned and all the data looks like it’s displaying fine (screen shots below).

Ontologies that have download URLs specified are pulled on a nightly basis.  If you edited the download URL today, BioPortal would check for a new version of your ontology overnight tonight and you should be able to see it tomorrow.  If you need it immediately, let us know and I can manually process it now for you.

Best,
Jennifer




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On Oct 17, 2016, at 3:40 PM, Laurel Cooper <cooperl at science.oregonstate.edu<mailto:cooperl at science.oregonstate.edu>> wrote:


Thanks for your help with the PO, I am also having issues with this one:

http://bioportal.bioontology.org/ontologies/PTO

http://bioportal.bioontology.org/ontologies/PTO?p=classes&conceptid=root

I had uploaded new version back in September and still not working- updated the submission info today to point at http://purl.obolibrary.org/obo/to/subsets/to-basic.obo

Thanks for your help

Laurel

On 10/17/16 12:07 PM, Jennifer Leigh Vendetti wrote:
Hi Laurel,

Apologies for the delay.  The latest version of the Plant Ontology is now parsed and available in BioPortal:

http://bioportal.bioontology.org/ontologies/PO

Best,
Jennifer




On Oct 14, 2016, at 11:33 AM, Laurel Cooper <cooperl at science.oregonstate.edu<mailto:cooperl at science.oregonstate.edu>> wrote:


Hi

I fixed the link for the Plant Ontology by replacing the url below with the PURL:  http://purl.obolibrary.org/obo/po.obo

But the download links are still pointing at the previous version.

Thanks, Laurel Cooper


-------- Forwarded Message --------
Subject:        [BioPortal] Load from URL failure for Plant Ontology
Date:   Thu, 13 Oct 2016 18:09:05 -0700
From:   admin at bioontology.org<mailto:admin at bioontology.org>
To:     cooperl at science.oregonstate.edu<mailto:cooperl at science.oregonstate.edu>


BioPortal failed to load Plant Ontology (PO) from URL: https://cdn.rawgit.com/Planteome/plant-ontology/master/po-release-files/plant-ontology-21.obo.

Please verify the URL you provided for daily loading of your ontology:

  1.  Make sure you are signed in to BioPortal.
  2.  Navigate to your ontology summary page: http://bioportal.bioontology.org/ontologies/PO.
  3.  Click the "Edit submission information" link.
  4.  In the Location row, verify that you entered a valid URL for daily loading of your ontology in the URL text area.

If you need further assistance, please contact us<mailto:support at bioontology.org> via the BioPortal support mailing list.

Thank you,
The BioPortal Team
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--
**********************************************************
Laurel (Lol) Cooper, PhD
Bioinformatics Scientist, The Planteome Project
Dept. of Botany and Plant Pathology
Rm 3086, Cordley Hall
Oregon State University
Corvallis, OR 97331
Web: www.planteome.org<http://www.planteome.org/>

Phone: 541-737-5272
Fax: 541-737-3573
Skype: cooperlol910
***********************************************************



--
**********************************************************
Laurel (Lol) Cooper, PhD
Bioinformatics Scientist, The Planteome Project
Dept. of Botany and Plant Pathology
Rm 3086, Cordley Hall
Oregon State University
Corvallis, OR 97331
Web: www.planteome.org<http://www.planteome.org/>

Phone: 541-737-5272
Fax: 541-737-3573
Skype: cooperlol910
***********************************************************

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