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[bioontology-support] [BioPortal] Feedback from plostaxonomy

Eric Lopatin elopatin at plos.org
Wed May 10 21:22:52 PDT 2017


Hi Jennifer,

As Artur is out of the office until Friday, I just wanted to send a note to mention that the PLOS Thesaurus entry<http://bioportal.bioontology.org/ontologies/PLOSTHES/?p=classes&conceptid=root> is indeed accessible. Perhaps it was a minor outage as you suspected.

Best,
Eric
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From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Date: Wednesday, May 10, 2017 at 11:54 AM
To: Artur Arikainen <aarikainen at plos.org>
Cc: "support at bioontology.org" <support at bioontology.org>, Taxo Team <taxoteam at plos.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from plostaxonomy

Hello Artur,

I’m not able to reproduce that error on our side.  It may have been a temporary / brief outage of our software.  Let us know if you are still experiencing that behavior.

Kind regards,
Jennifer


[cid:image001.png at 01D2C9D3.94B99B40]



On May 10, 2017, at 6:46 AM, Artur Arikainen <aarikainen at plos.org<mailto:aarikainen at plos.org>> wrote:

Hi Jennifer,

Thanks for this!

The software we use to manage our taxonomy didn’t automatically include that declaration, which I wasn’t aware of until now. However, I’ll keep make sure to add that manually for future updates for now, but I’ll also let our software provider know, in case they can add this to a future release.

I’m not sure if the problem is related, but I’m currently not able to access our entry<http://bioportal.bioontology.org/ontologies/PLOSTHES> (error screenshot below). I can access other entries. Would you be able to have a look at this issue as well?

<image001.jpg>

Best wishes,

Artur


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From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 09 May 2017 20:10
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Taxo Team <taxoteam at plos.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from plostaxonomy

Hello Artur,


On May 9, 2017, at 6:16 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

I tried uploading a submission (plosthes.2016-4), but I got an error message, so I assumed the upload didn't work. I therefore uploaded it again, but now there are two entries for the same taxonomy version.
Could you please delete plosthes.2016-4 dated released 03/22/2016? This was the incorrect release date anyway.



I deleted the intermediary submission as you requested.

The ontology file you submitted failed to parse because it’s invalid.  Parsing resulted in this error:

org.xml.sax.SAXParseException; lineNumber: 81; columnNumber: 44; The prefix "foaf" for element "foaf:homepage" is not bound.

This error indicates that the file is missing the foaf prefix declaration.  I manually edited your ontology file to add the declaration, i.e.:

<rdf:RDF
xmlns ="&local;"
xml:base ="&local;"
xmlns:skos ="http://www.w3.org/2004/02/skos/core#<http://www.w3.org/2004/02/skos/core>"
xmlns:rdf ="http://www.w3.org/1999/02/22-rdf-syntax-ns#<http://www.w3.org/1999/02/22-rdf-syntax-ns>"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#<http://www.w3.org/2000/01/rdf-schema>"
xmlns:xsd ="http://www.w3.org/2001/XMLSchema#<http://www.w3.org/2001/XMLSchema>"
xmlns:foaf="http://xmlns.com/foaf/0.1/"
xmlns:local ="&local;”>

I reprocessed the corrected ontology file, and it’s now available to browse in BioPortal.  If you upload new submissions in the future, you’ll need to fix the issue with the missing declaration in order for parsing to complete successfully.

Kind regards,
Jennifer

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