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[bioontology-support] Owl issue

Robert Boden rboden at rsna.org
Fri Nov 20 07:31:15 PST 2015


It's sort of working actually.  If I log in, I actually DO see the 3.13.1 submission.  Also our webservice calls are pulling down the new 3.13.1 submission, so our website is working correctly(www.radlex.org<http://www.radlex.org>).  If you could just fix it so the public also sees the 3.13.1 submission, I think we'll be OK.

From: Michael Dorf [mailto:mdorf at stanford.edu]
Sent: Friday, November 20, 2015 8:57 AM
To: Robert Boden
Cc: Samson Tu; Jennifer Leigh Vendetti; support at bioontology.org; Beverly' 'Collins; Brendan Wright
Subject: Re: [bioontology-support] Owl issue

Hi Robert,

I've taken a quick look at the ontology in our system, and something does appear to be happening that prevents the latest submission (3.13.1) from appearing correctly. It requires a further investigation on our end. I've created an issue in our internal bug tracking system to keep track of this ticket, and we'll have it addressed as soon as possible.

Thank you for providing a useful information. I believe we have all we need at this point to troubleshoot this problem on our end.

Thanks!

Michael Dorf



On Nov 17, 2015, at 09:26, Robert Boden <rboden at rsna.org<mailto:rboden at rsna.org>> wrote:

OK, we figured it out on our end, and were able to get a valid OWL file to export.  We've since uploaded this to Bioportal, but I'm running into a new issue, that I could use some assistance with.

The latest submission of radlex (3.13) seems to be parsing, but after submission I noticed that we missed configuring some of the details on the ontology submission screen.  Specifically we need to set the following:

Prefered name property: http://www.owl-ontologies.com/Ontology1447433679.owl#Preferred_name
Synonym Property: http://www.owl-ontologies.com/Ontology1447433679.owl#Synonym
Definition Property: http://www.owl-ontologies.com/Ontology1447433679.owl#Definition

I've tried editing these myself using the "edit Submission Information (3.13)" link, but the changes don't seem to take when I submit the form, and I'm just taken back to the bioportal homepage, and logged out.  I also tried to do a brand new 3.13 submission with the proper information this time, and that showed up initially as "uploaded", but now when I revisit the radlex bioportal page, I don't see my new submission anymore, just the original 3.13 submission, with the incorrect properties (which messes up the display, showing Radlex ID's instead of names).

Once this is resolved, all the non-working submissions with the 11/03/2015 release date should be removed as well, leaving just 3.11, 3.12, and 3.13 remaining.

Thanks for your assistance





From: Samson Tu [mailto:swt at stanford.edu]
Sent: Tuesday, November 10, 2015 7:42 PM
To: Jennifer Leigh Vendetti
Cc: Samson Tu; Brendan Wright; Robert Boden; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Owl issue

Hi,

I looked at the Protege frame files and saw that the ontology has very complex metaclasses and property/inverse properties. Because of these property/inverse properties, there are a lot of circularities in the ontology. When I tried to export the ontology to OWL/XML, Protege throws an exception and generated an incomplete owl file. More than 10000 lines of the 10898-line file is the expansion of a single class. The exception is

Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError

Either there are circularities that Protege couldn't resolve or we have a situation where all of the classes are reachable from one single class (or both).

I dropped the ISA and HasSubtype properties (because they are the superclass/subclass relationships) and Has_Part and Has_Regional_Part properties (because they can be inferred from Part_Of and Regional_Part_Of properties)  from the radlex_metaclass and got Protege to complete its export to OWL. The result is a 34.7 MB OWL file that can be read into Protege 4/5.

Because the use of metaclasses and property value assertions made at class level in the frame ontology, radlex classes are punned as individuals and these assertions become individual-level assertions. You can probably converts them to class expression programmatically when appropriate.

With best regards,
Samson



On Nov 10, 2015, at 3:47 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Brendan,

I've looked at this a little further.  The OWL file won't open in Protege or parse in BioPortal because the file is incomplete.  If you open the OWL file in a text editor and scroll to the bottom, you'll see what I mean.  This is the cause of the error "XML document structures must start and end within the same entity" - essentially the document is missing closing elements.

I imagine the OWL file ended up incomplete because the conversion from Frames to OWL failed.  What tool are you using to do the conversion?  Is it Protege?  Or, do you have your own conversion scripts?  If it's Protege, I suggest examining the console window when you perform the conversion to see if there are any stack traces that occur.

If you're using Protege for the conversion and you notice stack traces and the process fails, please send the details of which menu items you selected to do the conversion (there are a couple of different options for converting), and also include the full stack trace from the console window.  I could probably hand these over to someone on the Protege team and they may be able to figure out why the conversion fails.

Best,
Jennifer



On Nov 10, 2015, at 12:17 PM, Brendan Wright <bwright at rsna.org<mailto:bwright at rsna.org>> wrote:

Thanks any help would be greatly appreciated.  Also can I get the email for John Graybeal?

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Tuesday, November 10, 2015 1:29 PM
To: Brendan Wright
Cc: support at bioontology.org<mailto:support at bioontology.org>; Robert Boden
Subject: Re: [bioontology-support] Owl issue

Sorry - I just noticed that you already included the source files below, which answers a few of the questions I posed to you just now.  Perhaps I need a second cup of coffee.  :)

I'm going to try to meet up with a member of the Protege team and see if we can get the conversion to work and load the OWL file into the Protege application w/out getting any parsing errors.  If we can do that, I think it would also work in BioPortal.

I'll report back as soon as I have a chance to get to this.

Best,
Jennifer


On Nov 10, 2015, at 11:26 AM, Jennifer Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Brendan,

Firstly I wanted to mention that Ray is no longer at Stanford.  John Graybeal is the new Technical Program Manager for the BioPortal team (and also the CEDAR project at BMIR [1]).

Secondly, we did notice that the latest two versions of RADLEX failed to parse.  Both the BioPortal software and the Protege Desktop application report the same error:

"org.xml.sax.SAXParseException; systemId: file:radlex.owl; lineNumber: 10898; columnNumber: 35; XML document structures must start and end within the same entity."

I noticed in your email below you describe a process that sounds to me like this ontology is developed in an older version of Protege?  (PPRJ files were abandoned after the Protege 3.x series).  Is this a Frames ontology that you are converting to OWL?  Are you using Protege to do this?

Thanks in advance for providing us with these additional details.  It would also be helpful if you could send me all of the files that you mention below.  You can post them to the support list, or if you prefer, you can send them directly to me (vendetti at stanford.edu<http://stanford.edu/>).

Best,
Jennifer

[1] http://www.metadatacenter.org/



On Nov 10, 2015, at 6:15 AM, Brendan Wright <bwright at rsna.org<mailto:bwright at rsna.org>> wrote:

Hi I am looking for some help with loading my owl file into bioportal radlex as outlined below.  I tried emailing Ray but haven't heard back so any help you can give me would be much appreciated.  Please feel free to email myself or Robert Boden if you have questions.

From: Brendan Wright
Sent: Thursday, November 05, 2015 1:14 PM
To: ray.fergerson at stanford.edu<mailto:ray.fergerson at stanford.edu>
Subject: Owl issue


Hi Ray we are trying to load a new version of radlex into bioportal but are having an issue with the owl file.
Attached is a zip of the files.
in step1 is the src pprj files, they work fine.
In step2 you will see the flattened pprj files they seems to work fine as well.
In step three we convert to owl file but the file will not open in Protégé without an error. I'm unsure as to how to proceed.
It errors as well when we tried to load it into bioportal.

Any advice on how we can test /debug these issues w/o your help would be much appreciated.






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