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[bioontology-support] New ontology submission - file upload error

Jennifer Leigh Vendetti vendetti at
Mon May 8 16:34:51 PDT 2017

Hello Jade,

I found two issues that prevented your ontology from parsing in BioPortal:

1).  The pull URL was specified incorrectly (pointing to an HTML page on GitHub rather than the ontology source file).

2).  Seven occurrences of invalid values in xml:lang attributes.

I downloaded your ontology file from GitHub and corrected the xml:lang attributes in my local copy.  I created a new submission for your ontology (with all the same metadata, except that I specified a file upload instead of a pull URL).  The corrected ontology file parsed successfully and is now fully available for you to browse in BioPortal [1].

I noticed that you specified a viewing restriction of “private”, so I’ll contact you off the support list with more specific information with regard to fixing your ontology.

Kind regards,


On May 5, 2017, at 3:46 AM, Jade Hotchkiss <giant.plankton at<mailto:giant.plankton at>> wrote:


I successfully submitted the SCDO ontology into BioPortal (restricted to private). It is now available here:, but it shows that there was an upload error with the file submitted. And when I click on the "Classes" tab I get this message: "Problem retrieving classes".

Is this because of the delay in the ontology being visible on the site or is there really something wrong with the file I provided?
I tried two different ways of providing access to the file, but I get the same result:
1) file path in github
2) uploaded file from my PC

Thank you in advance for your help.

Kind Regards,
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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