Wanted: Simple example for RDF file-based reconciliation

[Tim Williams]

Hello OpenRefiners,

I just started using OpenRefine and have successfully imported a spreadsheet and am on my way to converting it to RDF. The next step is reconciliation and that is where I have hit a problem.  When trying to reconcile against online endpoints the reconciliation wheel spins and spins without resolution.  This may be a problem with my company's firewall not allowing OpenRefine to reach out to the web. I have found the same problem if I download an ontology like sio, stato or others and use file-based reconciliation ( these ontologies of course also reach out to other various web addresses).

To help me trouble-shoot I want to try reconciling against a very simple and self-contained RDF file with no external references.  Is there a description somewhere of the RDF structure that OpenRefine expects?  I tried creating a minimalist ontology with Protege but even the simplest still reaches out to various sources for owl, xsd, rdfs, etc. and once again the "Add file-based reconciliation" activity wheel spins and spins....

Any help would be greatly appreciated.

Cheers,

Tim 

[Martin Magdinier]

Hello Tim

Two questions to better understand what you are trying to achieve.

1. Which version of refine are you using?

2. Against which service are you trying to reconcile your dataset?

Martin

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[Tom Morris]

Hi Tim.  Sorry for the delayed response.  The RDF reconciliation service (both SPARQL and local RDF file) is provided by a separate extension.

It has its own website where you can find more information about it:

http://refine.deri.ie/

They have an example of reconciling against a local RDF dump here:

http://refine.deri.ie/dumpRecon

Tom

[Tim Williams]

Thank you Tom!   I will follow up with the links you provided.

- Tim

[Tim Williams]

In response to Martin's question:

OS: Windows Vista
JAVA_HOME=jdk1.7.0_60
OpenRefine 2.6 Beta 1
RDF Refine 0.8

Trying to use the organizations.rdf file as part of the online example here:

http://refine.deri.ie/dumpRecon

From the command window I see the following Java error:

10:20:24.519 [ org.mortbay.log] Error for /command/rdf-extension/uploadFileAndAddService (905ms)
java.lang.NoClassDefFoundError: com/ibm/icu/text/StringPrepParseException
at com.hp.hpl.jena.iri.impl.SchemeSpecification.<init>(SchemeSpecification.java:68)
at com.hp.hpl.jena.iri.ViolationCodes$Initialize.<clinit>(ViolationCodes.java:1360)

I tested this using a machine on which I am admin and on a guest wireless account at work where I am not behind a restrictive firewall. I even added the http:// addresses in the RDF file to the Java security site exceptions, just in case.

No one else getting this problem with the example?

Cheers,

Tim

[Tim Williams]

Additional clarification:

The problem occurs when I clicked the "OK" button on the "Add file-based reconciliation service" , at which point the Java error is shown in the command window from which I launched open refine (refine.bat) and the application shows the "Adding new reconciliation service" while the progress wheel spins indefinitely.

[Tom Morris]

On Tue, Apr 29, 2014 at 11:12 AM, Tim Williams <novas...@gmail.com> wrote:

In response to Martin's question:

OS: Windows Vista
JAVA_HOME=jdk1.7.0_60
OpenRefine  2.6 Beta 1
RDF Refine 0.8

Always useful information to include in any discussion of software behavior!

 

Trying to use the organizations.rdf file as part of the online example here:

http://refine.deri.ie/dumpRecon

From the command window I see the following Java error:

10:20:24.519 [          org.mortbay.log] Error for /command/rdf-extension/uploadFileAndAddService (905ms)
java.lang.NoClassDefFoundError: com/ibm/icu/text/StringPrepParseException
        at com.hp.hpl.jena.iri.impl.SchemeSpecification.<init>(SchemeSpecification.java:68)
        at com.hp.hpl.jena.iri.ViolationCodes$Initialize.<clinit>(ViolationCodes.java:1360)

The RDF extension depended on Refine bundling ICU4J which we've removed in 2.6 to help get the kit size down (we were only using a trivial piece of an enormous chunk of code).

If you're using OpenRefine 2.6, you need at least 0.9 of the RDF extension, referred to in this news post of theirs:

"2014-03-06: a test version compatible with Open Refine 2.6 beta is released!"

Tom

[Tim Williams]

Tom,

Case closed! I had overlooked the obvious note on the RDF extension webpage about version compatibility.

I downgraded to version 2.5 of Google Refine and installed the 0.8 version of the extension.  I have successfully added file-based reconciliation.  I will upgrade to 2.6 OpenRefine and 0.9 of RDF extension once 0.9 moves past alpha source code. I found the 0.9 instructions a bit cryptic for a newbie like me.

THANK YOU!!

Tim