Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Chen Yang Chen.Yang at UGent.be
Fri Aug 24 16:00:23 PDT 2018


Hi Michael,
Thanks a lot. I will follow what you suggested. Thanks again.
Best regards,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 25 August 2018 00:57
To: Chen Yang <Chen.Yang at UGent.be>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

Hi Chen,

Thank you for working with us on this issue. I’ve checked your updated NEST.owl file, and it still has a number of declarations such as:

    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00057"/>
    </Declaration>
    <Declaration>
        <AnnotationProperty IRI="http://one.ugent.be/00061"/>
    </Declaration>

The best thing for you to do before uploading a new submission to BioPortal is to open your updated file in Protege client and do “File => Save as… => RDF/XML Syntax”. If the ontology is not parsing correctly, you will see a dialog with a list of errors:

[cid:image001.png at 01D43C0E.FFD93260]

If you still see any of these errors in Protege, that means that BioPortal will not be able to successfully process this ontology. Once these errors have been displayed, you can click on the little red triangle (!) icon in the top right corner of the Protege client to see the exact messages from the log. This will help you narrow down the declarations that still need to be fixed.

I hope this helps in getting your errors straightened out.

Thanks!

Michael



On Aug 24, 2018, at 7:49 AM, Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>> wrote:

Hi Michael,
I modified my ontology and uploaded again (e.g. 00073 --> ne00073). It seemed ok after uploading on 22/08, however, it is finally marked as error rdf today.
Best,
Chen

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: 21 August 2018 23:44
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: Chen Yang <Chen.Yang at UGent.be<mailto:Chen.Yang at UGent.be>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be<mailto:chen.yang at ugent.be>

Hi Chen,

I’ve gotten some more insight on why your ontology isn’t processing correctly in BioPortal.
http://one.ugent.be/00057 is both an Annotation and a Class in the NEST OWL file. (You can see this in Protege, if you know the little purple things are Annotations and the little orange circles are Classes.) When an OWL file is converted to RDF/XML, it is necessary to convert the properties (which Annotations are) to QNames. The QName is the last fragment of the URI, so in the case above, the QName is evaluated to 00057.
Unfortunately, in addition to QNames not being able to include colons (#16<https://github.com/ncbo/bioportal-project/issues/16> problem), QNames also can not start with a digit. So the resulting transformation produces an RDF/XML which can not be parsed.
The full QNames spec can be found here: https://www.w3.org/2001/tag/doc/qnameids

You can reproduce this issue if you open NEST.owl in Protege and then attempt to save it as RDF/XML Syntax. The resulting error in Protege log is:

2018-08-21 14:38:03.927 [AWT-EventQueue-0] ERROR OWLEditorKit    An error occurred whilst saving the http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00028
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_40]
Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName): http://one.ugent.be/00061

The easiest solution to this issue is to add a letter in front of the QName for the annotations.

Hope this helped clarify the issue.

Thanks!

Michael



On Aug 20, 2018, at 3:45 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Chen,

Thanks for contacting us. I’ve looked at your ontology, and it did fail to process in BioPortal. It seems that the underlying issue is:

Caused by: org.semanticweb.owlapi.rdf.rdfxml.renderer.IllegalElementNameException: Illegal Element Name (Element Is Not A QName):
http://one.ugent.be/00061
http://one.ugent.be/00073
http://one.ugent.be/00051
http://one.ugent.be/00068
http://one.ugent.be/00057
http://one.ugent.be/00077
http://one.ugent.be/00067
http://one.ugent.be/00023
http://one.ugent.be/00001
http://one.ugent.be/00034
http://one.ugent.be/00028

I’ve created an issue in our Github tracker that details our progress on working to resolve it:

https://github.com/ncbo/bioportal-project/issues/87

There is a similar issue in our system with an identical error, but I haven’t found the exact solution in the tracker history.

https://github.com/ncbo/bioportal-project/issues/16

I need to consult on this further with my colleagues, one of which, unfortunately, is on vacation until August 30th. I’ll try to keep you posted on what further I find out.

Thanks!

Michael



----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------



On Aug 20, 2018, at 3:13 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FNEST

Feedback:
Dear,
I submitted the newest version of NEST ontology. I tested it before uploading, no error was detected. However, it is marked as error rdf in BioPortal.http://bioportal.bioontology.org/ontologies/NEST
Best,
Chen

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180824/62de5c14/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 62931 bytes
Desc: image001.png
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180824/62de5c14/attachment-0001.png>


More information about the bioontology-support mailing list