[bioontology-support] Error rdf

classic Classic list List threaded Threaded
5 messages Options
Reply | Threaded
Open this post in threaded view
|

[bioontology-support] Error rdf

Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN]

I tried updating our ontology with a new version downloaded directly from WebProtege, but it’s given “rdf error” message in BioPortal twice now…. Can you give more detail?

 

http://bioportal.bioontology.org/ontologies/RBO

Thanks

 

 

Dan Berrios, MD PhD MPH

USRA/NASA Ames Research Center

650 604 0470 (office)

415 902 5099 (cell)

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] Error rdf

jvendetti
Hello Dan,

I looked at the processing log files on our production server. BioPortal can’t load RBO.owl because the ontology source file has 26 occurrences of invalid values in xml:lang attributes. One such example can be found on line 53,078 (DNA microarray class):

    …        
    <obo:IAO_0000119 xml:lang="2008/03/03">Web:&lt;http://en.wikipedia.org/wiki/DNA_microarray&gt;</obo:IAO_0000119>
    <rdfs:label xml:lang="en">DNA microarray</rdfs:label>
</owl:Class>

All of these occurrences need to be corrected to use a valid value, e.g., xml:lang=“en”. After making these changes, I believe the system will be able to consume the ontology without issues.

Kind regards,
Jennifer


On Sep 18, 2020, at 3:54 PM, Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]> wrote:

I tried updating our ontology with a new version downloaded directly from WebProtege, but it’s given “rdf error” message in BioPortal twice now…. Can you give more detail?
 
 
 
Dan Berrios, MD PhD MPH
USRA/NASA Ames Research Center
650 604 0470 (office)
415 902 5099 (cell)
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] Error rdf

Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN]

OK yeah I see those in Protégé.  I wonder how they got there? These classes were imported using OBO Robot.  Maybe a bug in Robot.

 

Thanks

 

 

Dan Berrios, MD PhD MPH

USRA/NASA Ames Research Center

650 604 0470 (office)

415 902 5099 (cell)

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, September 18, 2020 4:21 PM
To: Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]>
Cc: [hidden email]
Subject: [EXTERNAL] Re: [bioontology-support] Error rdf

 

Hello Dan,

 

I looked at the processing log files on our production server. BioPortal can’t load RBO.owl because the ontology source file has 26 occurrences of invalid values in xml:lang attributes. One such example can be found on line 53,078 (DNA microarray class):

 

 <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400148">

    …        

    <obo:IAO_0000119 xml:lang="2008/03/03">Web:&lt;http://en.wikipedia.org/wiki/DNA_microarray&gt;</obo:IAO_0000119>

    <rdfs:label xml:lang="en">DNA microarray</rdfs:label>

</owl:Class>

 

All of these occurrences need to be corrected to use a valid value, e.g., xml:lang=“en”. After making these changes, I believe the system will be able to consume the ontology without issues.

 

Kind regards,

Jennifer

 



On Sep 18, 2020, at 3:54 PM, Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]> wrote:

 

I tried updating our ontology with a new version downloaded directly from WebProtege, but it’s given “rdf error” message in BioPortal twice now…. Can you give more detail?

 

 

 

Dan Berrios, MD PhD MPH

USRA/NASA Ames Research Center

650 604 0470 (office)

415 902 5099 (cell)

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] Error rdf

Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN]
In reply to this post by jvendetti

I loaded a new version of our RBO ontology last night. After it processed, there was no particular error message in the status column, but it won’t show the classes (“Problem retrieving classes”).  It does show properties.  WebProtege has not reported any problems with this version….  Can you help?


 

 

Dan Berrios, MD PhD MPH

USRA/NASA Ames Research Center

650 604 0470 (office)

415 902 5099 (cell)

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, September 18, 2020 4:21 PM
To: Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]>
Cc: [hidden email]
Subject: [EXTERNAL] Re: [bioontology-support] Error rdf

 

Hello Dan,

 

I looked at the processing log files on our production server. BioPortal can’t load RBO.owl because the ontology source file has 26 occurrences of invalid values in xml:lang attributes. One such example can be found on line 53,078 (DNA microarray class):

 

 <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0400148">

    …        

    <obo:IAO_0000119 xml:lang="2008/03/03">Web:&lt;http://en.wikipedia.org/wiki/DNA_microarray&gt;</obo:IAO_0000119>

    <rdfs:label xml:lang="en">DNA microarray</rdfs:label>

</owl:Class>

 

All of these occurrences need to be corrected to use a valid value, e.g., xml:lang=“en”. After making these changes, I believe the system will be able to consume the ontology without issues.

 

Kind regards,

Jennifer

 



On Sep 18, 2020, at 3:54 PM, Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]> wrote:

 

I tried updating our ontology with a new version downloaded directly from WebProtege, but it’s given “rdf error” message in BioPortal twice now…. Can you give more detail?

 

 

 

Dan Berrios, MD PhD MPH

USRA/NASA Ames Research Center

650 604 0470 (office)

415 902 5099 (cell)

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] Error rdf

John Graybeal-2
Dan,

I am seeing RBO's classes without a problem now. I think this was likely a temporary cacheing issue. When a new ontology is submitted, it can sometimes take hours for all the new data to percolate several layers of cache that our system includes (and then to be updated on your browser cache). In the meantime the browser can cache the error page for a little while.

If you are still having trouble, can you try another browser or do a hard refresh of your classes page?  You can perform a hard refresh of the page with Cmd + Shift + R on the Mac, or Ctrl + Shift + R on Windows.

Let us know if you are still seeing a problem. Thanks!

John

On Dec 1, 2020, at 9:49 AM, Berrios, Daniel C. (ARC-SCR)[UNIVERSITIES SPACE RESEARCH ASSN] <[hidden email]> wrote:

I loaded a new version of our RBO ontology last night. After it processed, there was no particular error message in the status column, but it won’t show the classes (“Problem retrieving classes”).  It does show properties.  WebProtege has not reported any problems with this version….  Can you help?


 
 
Dan Berrios, MD PhD MPH
USRA/NASA Ames Research Center
650 604 0470 (office)
415 902 5099 (cell)

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support