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[bioontology-support] [BioPortal] Feedback from plostaxonomy

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 9 12:10:09 PDT 2017


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#"
xmlns:rdf ="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:xsd ="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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