owlapi-developer — Development discussion list

Re: [OWLAPI-developer] Bugs/ suggestions to OWL API

[Sean B. <se...@cs...>]

Aditya A Kalyanpur wrote:

> Hi,
> 
> Firstly, I must comment on how useful this API has been to us in
> developing our ontology editor - SWOOP, at the MINDSWAP research group at
> UMD, given it's apt OWL-centric design (esp. ontology change handling was
> a breeze)..Thanks Sean et al

Glad to hear it :-)
> 
> Anyway, here is a list of extensions (some to the core stuff) we would
> love to have in the API - most of these are probably known to developers,
> please correct me in case any of the stuff below works or has been fixed after
> release:
> 
> - Mainly Remove(Individual/PropertyAxiom/Domain/Range/Imports/
> AnnotationInstance) haven't been defined under OntologyChange in the
> API..while this list isn't exhaustive, the other removal changes are minor
> and not particularly useful for now
> 
> - RemoveClassAxiom interface has been defined but code for it hasn't been
> implemented yet

> 
> - OntologyReplicator code hasn't been implemented
> 
> And here are some bugs we encountered:
> 
> - RemoveEntity doesn't remove all references of the entity in the ontology

There are (at least) two solutions -- either pull out all the references 
when an entity is removed, or simply prevent the removal of an entity 
that's used. The latter is the approach I took in the original OilEd 
implementations -- it's *much* easier to do. For example, you don't have 
to worry about what to do when someone removes a class that's used in a 
restriction that happens to be the RHS of a subclass axiom. It does kind 
of put the onus on the remover to do stuff in the right order, but in my 
opinion that's no bad thing.

I've got some way towards tackling this with some better "find where 
this is used" functionality which can then be used to catch dangling 
removals.

> - Serializing individual assertions where property URI's are in FOAF style
> (URIs with no frgament ID). A QName cannot be generated for these
> properties and invalid XML is generated.

Yes. Bit nasty this one, though I note that Ron Alford has provided a 
solution.

	Sean

-- 
Sean Bechhofer
se...@cs...
http://www.cs.man.ac.uk/~seanb

[OWLAPI-developer] RDF Renderer corrections

[Ron A. <ro...@um...>]

Hello,
I'm working on the save functionality for Swoop, specifically being able 
to edit remote ontologies via webdav.
Since a bunch of our stuff is foaf derived, we've been having problems 
saving anything that has individuals in it.

I've attached a QName generator that should be fairly robust, along with 
a version of Renderer that uses it.

Both of these are in the development copy of Swoop until owlapi comes 
out with a release that fixes the problem.


I've attached the LGPL notice to the qname provider, but if people want 
to use it to patch up code they're using until a new release comes out, 
I can shove a BSD or MIT or what not on it.


Next up is fixing the ontology information (imports, annotations, etc).

-Ron

[OWLAPI-developer] Re: [OWLAPI-interest] Is there a bug in parsing?

[Sean B. <se...@cs...>]

sevki kayir wrote:

> Hi there, I have an OWL weapon ontology and I use
> OWLAPI to parse and use this ontology as a
> knowledgebase. The problem is that I get a top level
> class of the ontology as a subclass of another class
> although it is not... For example I have charge and
> fuse classes at the top level. When I parse and try to
> get the charge types within the ontology I also get
> the fuse as a subclass of the charge. The problem does
> not occur among other classes. I would appreciate if
> you could help me in solving this problem. If required
> I can send the code I wrote to access the ontology...

You need to supply a little more context here. Perhaps you could provide 
a URL of the ontology?

	Sean

-- 
Sean Bechhofer
se...@cs...
http://www.cs.man.ac.uk/~seanb

[OWLAPI-developer] Is there a bug in parsing?

[sevki k. <ut...@ya...>]

Hi there, I have an OWL weapon ontology and I use
OWLAPI to parse and use this ontology as a
knowledgebase. The problem is that I get a top level
class of the ontology as a subclass of another class
although it is not... For example I have charge and
fuse classes at the top level. When I parse and try to
get the charge types within the ontology I also get
the fuse as a subclass of the charge. The problem does
not occur among other classes. I would appreciate if
you could help me in solving this problem. If required
I can send the code I wrote to access the ontology...


	
		
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Re: [OWLAPI-developer] Error parsing OWL file..

[Sean B. <se...@cs...>]

Aditya A Kalyanpur wrote:
> Hi,
>   There's an error parsing this file using the OWL API (seems valid XML
> and opens in IE w/o any probs):
> 
> http://www.biopax.org/release/biopax-level1.owl
> 
> java.lang.RuntimeException: Parsing failed due to XML Problem: Document
> root element is missing.

There seems to be some kind of funny control character at the beginning 
of the file (before the <?xml...?>) -- I can see this if I open in 
Mozilla, or wget and then look at it with an editor. My guess is that 
this is what's confusing the parser, although why other validators/IE 
don't mind is a mystery to me....

	Sean

-- 
Sean Bechhofer
se...@cs...
http://www.cs.man.ac.uk/~seanb

[OWLAPI-developer] Error parsing OWL file..

[Aditya A K. <ad...@Gl...>]

Hi,
  There's an error parsing this file using the OWL API (seems valid XML
and opens in IE w/o any probs):

http://www.biopax.org/release/biopax-level1.owl

java.lang.RuntimeException: Parsing failed due to XML Problem: Document
root element is missing.

Cheers,
Aditya

[OWLAPI-developer] Bugs/ suggestions to OWL API

[Aditya A K. <ad...@Gl...>]

Hi,

Firstly, I must comment on how useful this API has been to us in
developing our ontology editor - SWOOP, at the MINDSWAP research group at
UMD, given it's apt OWL-centric design (esp. ontology change handling was
a breeze)..Thanks Sean et al

Anyway, here is a list of extensions (some to the core stuff) we would
love to have in the API - most of these are probably known to developers,
please correct me in case any of the stuff below works or has been fixed after
release:

- Mainly Remove(Individual/PropertyAxiom/Domain/Range/Imports/
AnnotationInstance) haven't been defined under OntologyChange in the
API..while this list isn't exhaustive, the other removal changes are minor
and not particularly useful for now

- RemoveClassAxiom interface has been defined but code for it hasn't been
implemented yet

- OntologyReplicator code hasn't been implemented

And here are some bugs we encountered:

- RemoveEntity doesn't remove all references of the entity in the ontology

- Serializing individual assertions where property URI's are in FOAF style
(URIs with no frgament ID). A QName cannot be generated for these
properties and invalid XML is generated.

- Missing imports information. Since imports statements are not generated,
class and property declarations are duplicated in the importing ontology
(which is not really an error but increases the size of the output).

Cheers,
Aditya

[OWLAPI-developer] the properties a class object for

[sevki k. <ut...@ya...>]

Hi,
I have another problem of accessing the ontology and I
tried to look it up from some other renderer files but
due to lack of time I could not find the solution. The
problem is how I can reach to the properties and the
property values (which are some other classes) of a
class object for. I can get the properties and its
ranges for some super classes but not for the class
itself. Thanks for your kind help.

Sevki



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[OWLAPI-developer] Properties of a class itself

[sevki k. <ut...@ya...>]

Hi,
I have another problem of accessing the ontology and I
tried to look it up from some other renderer files but
due to lack of time I could not find the solution. The
problem is how I can reach to the properties and the
property values (which are some other classes) of a
class itself. Thanks for our kind help.


		
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[OWLAPI-developer] Re: [OWLAPI-interest] how to get the object values

[Sean B. <se...@cs...>]

sevki kayir wrote:

> Hi there! 
> Can any of you help me in getting the object values of
> an owl ontology. I am a new user of OWLApi and I want
> to parse an OWL ontology and get the object values of
> an individual in that ontology. The situation is that
> the object values are also individuals to which I can
> not reach. I can get the properties for the
> individuals but not the individuals that are the
> fillers of those properties. Maybe its solution is to
> parse the triples but I also can't do that. Could you
> please help me in my problem? Can you provide a sample
> code to access the triples and get the object values ?

You should be able to get the object values of an individual through the

getObjectPropertyValues(OWLOntology o)

method on OWLIndividual. This returns a Map which is keyed on 
properties, with values sets of individuals. Some sample code (taken 
from the RDF renderer) is as follows:

OWLIndividual ind;
OWLOntology ontology;

...

Map propertyValues = ind.getObjectPropertyValues( ontology );
  for (Iterator it = propertyValues.keySet().iterator();
       it.hasNext();) {
   OWLObjectProperty prop = (OWLObjectProperty) it.next();
   Set vals = (Set) propertyValues.get(prop);
   for (Iterator valIt = vals.iterator(); valIt.hasNext();) {
    OWLIndividual oi = (OWLIndividual) valIt.next();
    pw.println(INDENT + "<"
	       + shortForm(prop.getURI())
	       + " rdf:resource=\""
	       + oi.getURI()
	       + "\"/>");
   }
}

The Renderer implementations are a good place to look, in general to see 
how one can access information within an ontology.

	Sean

-- 
Sean Bechhofer
se...@cs...
http://www.cs.man.ac.uk/~seanb

[OWLAPI-developer] how to get the object values

[sevki k. <ut...@ya...>]

Hi there! 
Can any of you help me in getting the object values of
an owl ontology. I am a new user of OWLApi and I want
to parse an OWL ontology and get the object values of
an individual in that ontology. The situation is that
the object values are also individuals to which I can
not reach. I can get the properties for the
individuals but not the individuals that are the
fillers of those properties. Maybe its solution is to
parse the triples but I also can't do that. Could you
please help me in my problem? Can you provide a sample
code to access the triples and get the object values ?


		
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