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[bioontology-support] HIV ontology parsing issue [WAS: Ontology Upload]

Jennifer Leigh Vendetti vendetti at
Wed Apr 5 15:08:37 PDT 2017

Hello Sabrina,

On Apr 4, 2017, at 4:37 PM, Sabrina Falcon <falcos2 at<mailto:falcos2 at>> wrote:

Okay thank you this was a tremendous help.

We fixed the date, changed the part of tags, and re-uploaded. It still came up with an RDF error, so we will be very interested to hear back once you consult the API authors.

Thanks for fixing the date.  With your latest version (2.7), I’m still seeing the same parsing error for the part_of tags.

Quick question - I’m corresponding with one of the developers of the OWL API and they noticed that the first line of your file is this:

format-version: 2.6

We are only able to locate an OBO format specification of 1.4 [1], but nothing newer.  Could you offer any insight into where you got the version number from?  Are you aware of OBO format specifications later than 1.4?

Thank you,


On Apr 4, 2017, at 2:15 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hello Sabrina,

I spent some time looking at the problem you reported with the HIV ontology.  I’ve entered an issue in our tracker so that you can follow our progress if desired [1].

I’ve identified two issues:

1).  The ontology source file uses an incorrect date format that causes a parsing exception.  The OBO format guide states that dates in headers must use the format of dd:MM:yyyy HH:mm.  If you change line 2 of the ontology source file from this:

date: December 27, 2016

… to this:

date: 27:12:2016 00:00

… that particular parsing error is solved.

2).  Unfortunately, the second issue is more complicated.  In short, BioPortal and Protege both use the OWL API internally for ontology parsing.  BioPortal is using version 4.2.5 of the OWL API, which fails to parse the HIV ontology with exceptions about the “part_of” tags.  Protege is using version 4.2.8 of the OWL API, which parses the ontology without issue.  This is why you’re able to open your ontology in Protege successfully.  It’s unclear what the difference is between OWL API versions that causes the parsing failure.  I’ll need to contact the authors of the API to see if they can shed any light.

Kind regards,


On Apr 4, 2017, at 10:17 AM, Sabrina Falcon <falcos2 at<mailto:falcos2 at>> wrote:

bioontology-support at<mailto:bioontology-support at> is the link. We have always had this problem, and we don’t know how to begin to fix it.

The .OBO document format works on Protege perfectly, so I don’t know how to find the error if Protege doesn’t pick up the mistake.

On Apr 3, 2017, at 1:25 PM, Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>> wrote:

Hello Sabrina,

Your message was sent to the support list administrators (bioontology-support-owner), instead of the support list itself.  The proper email address for support questions is: bioontology-support at<mailto:bioontology-support at>.

What is the URL of your ontology page where you are seeing the RDF error status?

Thank you,

On Apr 3, 2017, at 1:05 PM, Sabrina Falcon <falcos2 at<mailto:falcos2 at>> wrote:


My name is Sabrina Falcon my BioPortal username is sabrinafalcon.

I uploaded my ontology in .OBO format. It's now on my profile and it says that there is an RDF error.

What can be done to fix this problem?

Thank you,
Sabrina Falcon

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