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[bioontology-support] HIV ontology parsing issue [WAS: Ontology Upload]
Jennifer Leigh Vendetti
vendetti at stanford.edu
Thu Apr 6 14:09:31 PDT 2017
Hello again Sabrina,
Just a quick follow-up to the question I posed yesterday:
According to the OBO Flat File Format Guide , the "format-version" tag is used to denote the OBO specification version that the ontology files uses, whereas the “data-version” tag gives the version of the ontology. I suppose that you used the format-version tag to give the version of the ontology, when what you really meant was something like this:
I’m not really sure which version of the OBO specification you wanted your ontology file to conform to.
On Apr 5, 2017, at 3:08 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
On Apr 4, 2017, at 4:37 PM, Sabrina Falcon <falcos2 at unlv.nevada.edu<mailto:falcos2 at unlv.nevada.edu>> 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:
We are only able to locate an OBO format specification of 1.4 , 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?
On Apr 4, 2017, at 2:15 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
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 .
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.
On Apr 4, 2017, at 10:17 AM, Sabrina Falcon <falcos2 at unlv.nevada.edu<mailto:falcos2 at unlv.nevada.edu>> wrote:
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu> 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 stanford.edu<mailto:vendetti at stanford.edu>> wrote:
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 lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>.
What is the URL of your ontology page where you are seeing the RDF error status?
On Apr 3, 2017, at 1:05 PM, Sabrina Falcon <falcos2 at unlv.nevada.edu<mailto:falcos2 at unlv.nevada.edu>> 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?
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