Using OWL API to import ontology - owl-api

I'm using the OWL API, and I have an ontology. I'm trying to import another ontology the way we do in protege, i.e. select the OWL File locally and then import it. Is this possible with the OWL API
I'm using the import declaration,
OWLImportsDeclaration importDeclaraton = ontology.getFactory().getOWLImportsDeclaration(IRI.create("/home/noor/Dropbox/TaggingCaseStudy/Programs/TextBasedMA/files/ontologies/OBMA2/photo1.owl"));
But I'm getting an error, it is not taking the file locally,
Caused by: java.io.FileNotFoundException: http://semanticweb.org/home/noor/Dropbox/TaggingCaseStudy/Programs/TextBasedMA/files/ontologies/OBMA2/photo1.owl

Your IRI is relative, not absolute - it needs to start with file: for a file to be found. Relative IRIs will be resolved against the base IRI at the time of loading, which in your case creates the URL which you can see in the error.
Try making the IRI absolute, or use indirection by using the actual ontology IRI in the import and using an IRIMapper to point at the file.
E.g., if your ontology has an IRI of http://example.com/myontology, use
OWLImportsDeclaration importDeclaraton = ontology.getFactory().getOWLImportsDeclaration(IRI.create("http://example.com/myontology"));
to create the imports declaration, and add an IRIMapper to your OWLOntologyManager for resolving it when loading the ontology:
manager.addIRIMapper(new SimpleIRIMapper(IRI.create("http://example.com/myontology"),
IRI.create("file:///actual/path/to/file.owl"));
Edit: with OWLAPI 4, this looks like:
manager.getIRIMappers().add(new SimpleIRIMapper(IRI.create("http://example.com/myontology"),
IRI.create("file:///actual/path/to/file.owl"));
Javadoc for this can be found on the GitHub page

Related

Loading .owl files in marklogic

Is it possible to load .owl files using mlcp?
I tried with -input_file_type rdf but it gives error as below:
bin/mlcp.sh import -host localhost -port 9010 -username uname
-password pwd -mode local -input_file_path /home/user/semantics/data -input_file_type rdf -input_file_pattern '.*.owl'
FATAL contentpump.RDFReader: dbpedia1.owl: Element or attribute do not
match QName production: QName::=(NCName':')?NCName. FATAL
contentpump.RDFReader: dbpedia2.owl: Element or attribute do not match
QName production: QName::=(NCName':')?NCName.
What am I missing here ?
MarkLogic documentation lists the supported triples file formats:
.rdf
.ttl
.json
.n3
.nt
.nq
.trig
Maybe you convert your .owl file to one of those formats, at which point you could use MLCP to load it. I tried plugging your example into a format converter, but that didn't work. Perhaps it's because we only have a snippet here.
MarkLogic should be able to process .owl files, but I think Joshua is right that MarkLogic is expecting .owl files to contain RDF/XML. You can also see that from the list of Mimetypes in the Admin interface. It lists the .owl extension as 'application/owl+xml', and RDF/XML seems to be the more common serialization of OWL.
Might just be that if you rename the file to .nt that it works..
HTH!

How to see yago2s ontology like dbpedia owl?

Hello I'm totally newbie in ontology.
I downloaded dbpedia ontology .owl file and open it using topbraid composer.
Topbraid composer shows dbpedia class( owl:Thing -> Activity, Agent, .. etc). Each class also has its own instances.
However, yago2s only provides many .ttl files( yagoSchema.ttl, yagoFact.ttl .. etc).
Cause I think these ttl files are similar to owl file, I also open it using topbraid composer. I expected to see the structure like dbpedia owl file, but it wasn't similar to dbpedia owl file..
They provide schema ttl file, instances ttl file, ... files respectively, but i wanna see the whole thing at once.
Should I get yago2s owl file? or is there any ways to see yago ttl files like dbpedia owl??
Thanks in advance.
The error message when I tried to open yagoTypes.ttl file is
java.lang.reflect.InvocationTargetException
at org.eclipse.jface.operation.ModalContext.run(ModalContext.java:421)
at org.eclipse.jface.dialogs.ProgressMonitorDialog.run(ProgressMonitorDialog.java:507)
at org.eclipse.ui.internal.progress.ProgressMonitorJobsDialog.run(ProgressMonitorJobsDialog.java:275)
at org.eclipse.ui.internal.progress.ProgressManager$3.run(ProgressManager.java:960)
at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70)
at org.eclipse.ui.internal.progress.ProgressManager.busyCursorWhile(ProgressManager.java:995)
at org.eclipse.ui.internal.progress.ProgressManager.busyCursorWhile(ProgressManager.java:970)
at org.topbraidcomposer.core.io.TBCIO$3.run(TBCIO.java:501)
at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35)
at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135)
at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4145)
at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3762)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine$9.run(PartRenderingEngine.java:1113)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.e4.ui.internal.workbench.swt.PartRenderingEngine.run(PartRenderingEngine.java:997)
at org.eclipse.e4.ui.internal.workbench.E4Workbench.createAndRunUI(E4Workbench.java:140)
at org.eclipse.ui.internal.Workbench$5.run(Workbench.java:611)
at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332)
at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:567)
at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:150)
at org.eclipse.ui.internal.ide.application.IDEApplication.start(IDEApplication.java:124)
at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110)
at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:354)
at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:181)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.lang.reflect.Method.invoke(Unknown Source)
at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:636)
at org.eclipse.equinox.launcher.Main.basicRun(Main.java:591)
at org.eclipse.equinox.launcher.Main.run(Main.java:1450)
at org.eclipse.equinox.launcher.Main.main(Main.java:1426)
Caused by: java.lang.NullPointerException
at org.topbraid.core.model.Classes.getMetaClasses(Classes.java:548)
at org.topbraid.core.model.Classes.computeMetaClasses(Classes.java:45)
at org.topbraidcomposer.core.session.AbstractSessionWithCache.getCachedMetaClasses(AbstractSessionWithCache.java:67)
at org.topbraid.core.model.Classes.getMetaClasses(Classes.java:166)
at org.topbraidcomposer.editors.ResourceEditorLauncher.checkVisibility(ResourceEditorLauncher.java:270)
at org.topbraidcomposer.editors.ResourceEditorLauncher.access$4(ResourceEditorLauncher.java:269)
at org.topbraidcomposer.editors.ResourceEditorLauncher$5.run(ResourceEditorLauncher.java:577)
at org.topbraidcomposer.core.io.TBCIO$2.run(TBCIO.java:482)
at org.eclipse.jface.operation.ModalContext$ModalContextThread.run(ModalContext.java:121)
and this same error occurs when I concatenate yagoTypes.ttl and yagoFacts.ttl using cat command, and try to open this concatenated file..
Where to get the data
If you got the data from YAGO2s Downloads, it says right at the beginning of the page:
You can download the entire YAGO2s ontology in one piece. (Extracted
from 2012-12-01 version of Wikipedia.)
Download YAGO2s ontology in
.ttl format! (2.2 Gb compressed, 18.5 Gb uncompressed)
That sounds like what you want. If you just want to see the class hierarchy, though, then you might want the yagoTaxonomy files:
yagoTaxonomy The entire YAGO taxonomy. These are all rdfs:subClassOf facts derived from Wikipedia and from WordNet.
The format of the data
OWL is a ontology language with an abstract structure that can be serialized in a number of different ways including OWL/XML, the OWL Functional Syntax, the Manchester Syntax, and encoded as RDF. Now, RDF is also an abstract format, and can be serialized in a number of ways, including N-Triples, N3, Turtle (ttl), and RDF/XML. Most .owl files that you find are actually RDF/XML files that are serializations of the RDF encoding of an OWL ontology. That's probably what your .owl file is. The .ttl files you're seeing are the Turtle serialization of the RDF encoding of an OWL ontology. Standard RDF processing tools should be able to process it.

Using Fat-Free PHP for Backbone.js routing with external Model.php files

I'm very new to Fat-Free and Backbone.js. I've been searching and reading articles and searching and reading articles trying to find a way to route to individual PHP files containing the database communications. The code below works, and I can use it, but it seems hackish. Is there a way to call an external PHP file (in the server/models/ directory) and a specific method from the $f3-route(...) line?
<?php
// File: /index.php
define("PATH",1);
$f3 = require('server/fatfree/lib/base.php');
$uri = explode('/', $_SERVER["REQUEST_URI"]);
require_once "server/models/{$uri[PATH]}.php";
$f3->route('GET /hello/#file', 'HelloModel->doSomething');
$f3->route('GET /project/#file', 'ProjectModel->doSomething');
$f3->route('GET /book/#file', 'BookModel->doSomething');
$f3->run();
?>
Thanks a lot for your advice.
You should add the server/models directory to the autoloader of F3 using the autoloader feature.
$f3->set('AUTOLOAD','server/models/');
That way, the required source files of your classes will be loaded on demand. However, note that the files must be named the same as your class, i.e. class Foo has to be defined in foo.php or Foo.php. The case of the filename does not matter.

Fully qualified class name while using exceptionSuper argument in CXF Wsdl2Java utilty

This is related to this question and the subsequent patch applied to cxf .
When using a WSDL-first approach to generate java stubs, is there a way to make exceptions extend RuntimeException instead of Exception?
Thanks Daniel and Piepera for the patch . But the generated code only adds the classname instead of fully qualified name and there is no import statement added for the custom exception supplied.
I have specified to use "com.google.adwords.api.AdwordsException" as exceptionSuper and wsdl2java maven plugin creates the following wsdl fault . But it didn't add an import statement for com.google.adwords.api.AdwordsException and compilation failed.
#WebFault(name = "ApiExceptionFault", targetNamespace = "https://adwords.google.com/api/adwords/billing/v201209")
public class ApiException extends AdwordsException {
Could you please fix it to either add the import statement or use the fully qualified name.
WSDL2JAVA Usage
wsdl2java -d C:\Dev\src\main\java -exceptionSuper com.google.adwords.api.AdwordsException -client -verbose -xjc-Xvalue-constructor -xjc-npa https://adwords.google.com/api/adwords/cm/v201209/CampaignService?wsdl

Querying Google AppEngine's Datastore using PHP (through Quercus) and low-level API isn't working

When I query Google AppEngine's datastore using PHP(through Quercus) and the low-level data-access API for an entity, I get an error that the entity doesn't exist, even though I've put it in the datastore previously.
The specific error is "com.caucho.quercus.QuercusException: com.google.appengine.api.datastore.DatastoreService.get: No entity was found matching the key: Test(value1)"
Here's the relevant code -
<?php
import com.google.appengine.api.datastore.DatastoreService;
import com.google.appengine.api.datastore.DatastoreServiceFactory;
import com.google.appengine.api.datastore.Entity;
import com.google.appengine.api.datastore.EntityNotFoundException;
import com.google.appengine.api.datastore.Key;
import com.google.appengine.api.datastore.KeyFactory;
import com.google.appengine.api.datastore.PreparedQuery;
import com.google.appengine.api.datastore.Query;
$testkey = KeyFactory::createKey("Test", "value1");
$ent = new Entity($testkey);
$ent->setProperty("field1", "value2");
$ent->setProperty("field2", "value3");
$dataService = DatastoreServiceFactory::getDatastoreService();
$dataService->put($ent);
echo "Data entered";
try
{
$ent = $dataService->get($testkey);
echo "Data queried - the results are \n";
echo "Field1 has value ".$ent->getProperty("field1")."\n";
echo "Field2 has value ".$ent->getProperty("field2")."\n";
}
catch(EntityNotFoundException $e)
{
echo("<br/>Entity test not found.");
echo("<br/>Stack Trace is:\n");
echo($e);
}
And here's the detailed stack-trace - link.
This same code runs fine in Java (of course after changing the syntax). I wonder what's wrong.
Thanks.
I have found the solution to my problem. It was caused by missing dependencies and I solved it by using the prepackaged PHP Wordpress application available here.
One thing is to be noted. The package overlooked a minor issue in that all files other than the src/ directory need to be in a war/ directory which stays alongside the src/ directory (this as per appengine conventions as mentioned on its documentation). So I organized the files thus myself, put the above PHP file in the war/ directory, and it's working fine on the appengine.

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