Nabble - Protégé

Re: Reg: Choosing whether OWL.

2008-10-11T14:06:48Z

Please review the following:

OWL vs. Frames - side by side.

http://protege.stanford.edu/conference/2006/submissions/abstracts/7.2_Wang_Hai_Protege_conf.pdf

Ron

On Sat, Oct 11, 2008 at 5:27 AM, sapna pg <sapnapga@...> wrote:

Greetings!

I am new in the area of ontologies and have been reading up material from the web on the area and tools available. At the end of it, I understand that I am confused as to what is the right options to choose.
I need to build an ontology of an application and query data stored. I went thru the Protege website but am unable to decide whether to use Protege Frames Editor/OWL. Further doubt includes whether it will suffice to use RDQL and SPARQL or OWL and which of them gives better features. If there is any site that clearly specifies use of these or distinguishes these, I would be happy if you could give me directions.

With thanks
Sapna

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--
Ron Schultz

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From forum: Protege - General

Reg: Choosing whether OWL.

2008-10-11T03:27:48Z

Greetings!

I am new in the area of ontologies and have been reading up material from the web on the area and tools available. At the end of it, I understand that I am confused as to what is the right options to choose.
I need to build an ontology of an application and query data stored. I went thru the Protege website but am unable to decide whether to use Protege Frames Editor/OWL. Further doubt includes whether it will suffice to use RDQL and SPARQL or OWL and which of them gives better features. If there is any site that clearly specifies use of these or distinguishes these, I would be happy if you could give me directions.

With thanks
Sapna

From forum: Protege - General

ClassNotFoundException: org.protege.editor.owl.model.hierarchy.roots.Relation

2008-10-11T03:20:55Z

Hello All,
Does anybody know why the following error emitted, from owlModel = ProtegeOWL.createJenaOWLModelFromURI(uri);
It works before build 130, now i got this error with all latest builds.

Thank you,
Weishan

java.lang.NoClassDefFoundError: org/protege/editor/owl/model/hierarchy/roots/Relation
    at edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.<init>(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.parser.GlobalParserCache.getTripleProcessor(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriples(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(Unknown Source)
    at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown Source)
    at edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Unknown Source)
    at edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.create(Unknown Source)
    at edu.stanford.smi.protegex.owl.ProtegeOWL.createJenaOWLModelFromURI(Unknown Source)
    at com.eu.hydra.flamenco.ruleprocessing.OntologyData.<init>(OntologyData.java:38)
    at com.eu.hydra.flamenco.ruleprocessing.OntologyData.getOntologyDataInstance(OntologyData.java:50)
    at com.eu.hydra.flamenco.ruleprocessing.OntologyData.main(OntologyData.java:57)
Caused by: java.lang.ClassNotFoundException: org.protege.editor.owl.model.hierarchy.roots.Relation
    at java.net.URLClassLoader$1.run(URLClassLoader.java:200)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:276)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
    at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
    ... 12 more

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From forum: Protege - OWL

Re: Ontology

2008-10-10T17:11:10Z

Hi Aashique,

The answer to your question is: depends on your problem.

Using ontologies can be useful in many domains, but you have to
understand that using an ontology just for the sake of it does not make
too much sense. After you understand what ontologies are and what is
your problem you try to solve, you can investigate whether or not
ontologies can be useful for you.
If you know nothing or very little about ontologies maybe you should
start with reading the wikipedia entry on this topic
http://en.wikipedia.org/wiki/Ontology_(computer_science)
and following the pointers of interest from there. The following article
is also very good:
http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html

If you are in doubt how to apply ontologies by using Protege, you can
find very good help in the Protege website's documentation section:
http://protege.stanford.edu/doc/users.html

I hope this helps,
Csongor

Aashique wrote:
> Hello,
>
> Would somebody please explain to me How to apply ontology once it is
> created? I just started working in this field and would appreciate help.
>
> Thanks,
>
> Aashique
>

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From forum: Protege - General

Re: (no subject)

2008-10-10T10:26:15Z

Hi all,

I accidentally hit “Send” before I finish the email.

Here is the complete version:

Have anyone tried to trigger an external event upon document save/change? I would like to notify an external application about changes made in Protégé.

One way to do is when user hits “save” button, a JMS message is triggered to notify such event.

Another alternative would be creating a plugin that has the ability to make an http request to another server?

Have anyone done anything like that? Does protégé have any API/plugins for external event notification?

Thanks a lot

Jun

From: protege-owl-bounces@... [mailto:protege-owl-bounces@...] On Behalf Of Ni, Jun (FindLaw)
Sent: Thursday, October 09, 2008 4:17 PM
To: protege-owl@...
Subject: [protege-owl] (no subject)

Hi all,

Have anyone tried to trigger an external event upon document save/change?

From forum: Protege - OWL

Ontology

2008-10-10T08:52:58Z

Hello,

Would somebody please explain to me How to apply ontology once it is created? I just started working in this field and would appreciate help.

Thanks,

Aashique

From forum: Protege - General

Re: Modeling Problem

2008-10-10T07:48:52Z

On 10 Oct 2008, at 4:49 AM, Michael Lodemann wrote:

>>> This one is a great hint. But I need sth like:
>>>
>>> curr_position(?sign, ?pos) ^ onRoadSection(?sign, ?road_sec) ^
>>> road_sec_start(?start_pos, ?road_sec) ^ road_sec_end(?end_pos, ?
>>> road_sec) ^
>>> swrlb:greaterThanOrEqual(?pos, ?start_pos) ^
>>> swrlb:lessThanOrEqual(?pos, ?end_pos) -> CorrectlyPlacedSign(?sign)
>>>
>>> Is this possible?
>>
>> Ah, you are now beyond my experiences with SWRL; I'm not actively
>> using it. I hope others can help here.
>
> You already helped me a lot!
>
>>> And do "curr_position", "onRoadSection", "road_sec_start" and
>>> "road_sec_end" have to be (object)-properties in my ontology?
>>
>> They would have to be properties, but not object properties.
>
> But what else? There only do exist object- datatype- and
> annotation-properties, right? "onRoadSection" for me is clearly an
> object-property with domain "Sign" and range "RoadSection".
> But with "curr_position" it is not so clear, because domain is
> "Sign" but
> range is "Sign.Position" which actually is a Datatype-property of
> Sign,
> correct?
> Can anyone tell me how to model such a property in an owl-ontology
> with
> protege?

I think it's simpler than you are suggesting. I see it as this:

:curr_position rdf:type owl:DatatypeProperty ;
rdfs:domain :Sign ;
rdfs:range xsd:integer .

:curr_position is a Datatype Property, with a domain of :Sign and a
range of integer. I'm not sure what Sign.position would mean, in an
owl world; a property is not 'attached' to a Class, as it is with
Object Oriented programming. If you wanted the position to be another
Individual (in the OWL sense), with a class of :SignPlacement then it
would be an object property (note the conventional change in the URI,
using Capitalization rather than underscore to show an ObjectProperty):

:currPosition rdf:type owl:ObjectProperty ;
rdfs:domain :Sign ;
rdfs:range :SignPlacement .

btw, remember that the first version here means that the reasoner can
infer that anything that has a :curr_position property is a :Sign and
the second version would have that and the inference that anything the
property "points to" is a :SignPlacement

>>> And "CorrectlyPlacedSign" is a class as you described before, right?
>>
>> Yup, should result in adding statements of the form:
>>
>> ?sign rdf:type :CorrectPlacedSign .
>>
>> (I think, again I'm far from an expert, or even competent with
>> SWRL :)
>
> But shouldn't "CorrectlyPlacedSign" be an infered class - so that
> statements (or instances of sign) are added by applying the SWRL-
> Rule(s)?

Yeah, we are agreeing. I'm just pointing out that "an inferred
class" (for the URI) is indicated by adding a statement to the
reasoned Model, such that any individual (a URI) that matched ?sign
will now feature in a new statement:

eg, you assert:

:ind1 rdf:type owl:Resource ;
rdf:type :Sign .

You write an SWRL rule which concludes with CorrectlyPlacedSign(?
sign), where ?sign matched :ind1, and an OWL+SWRL aware reasoner (eg
Pellet) now makes available a new statement (which exists alongside
all the asserted statements).

:ind1 rdf:type :CorrectlyPlacedSign .

<snip>

>> SWRL is a way of
>> writing templates for triples. So you can think about
>> curr_position(?
>> sign, ?pos) taking each statement like:
>>
>> :ind1 :curr_position "some_pos" .
>>
>> and setting ?sign to :ind1 and ?pos to "some_pos" for use in the rest
>> of the rule.
>
> What do you mean with ":ind1"?

It's just shorthand for yourNS:individual1, probably I should have
used :sign1. It's any URI.

Sounds like you are well on your way.

hth,
James

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From forum: Protege - OWL

Protege-OWL api: method for getting inferred property values

2008-10-10T05:17:32Z

Hi all,
Does anybody knows a method in Protege-OWL api to get inferred property values
of an individual?

thanks n regards,
Suja

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From forum: Protege - OWL

Re: protege owl api :outofmemory exception

2008-10-10T05:13:36Z

Hii,

I solved the problem by connecting to Pellet reasoner via the OWL_API
method(Previously i was using Jena method)

Thanks everybody,
--Suja

Quoting Luigi Iannone <iannone@...>:

> Hi,
>
> I am afraid I cannot help with the protege-owl api, but in order to
> further circumscribe the problem
> why don't you try the OWL API http://owlapi.sourceforge.net/
> it should be more up-to-date with the OWL most recent specs plus it
> can give you a third opinion
> on your ontology.
> If the problem persists, there is definitely something weird in your
> ontology
> if not it was the protege-owl API.
>
> Finally, if the former is the case I suggest also to have a look at
> pellint (http://pellet.owldl.com/pellint). Maybe that will help you in
> isolating the problem
>
>
> Hope it helps,
>
> Luigi
>
>
> On 1 Oct 2008, at 12:58, sujaram@... wrote:
>
> > Hi Luigi,
> >
> > Really sorry for confusing you too :), and thanks for taking the
> > trouble..
> > My problem is:
> >
> > 1)In Protege GUI i can execute rules and use reasoner without any
> > errors.
> >
> > 2) Now I am developing an ontology application using the same
> > ontology with
> > protege-owl api.In the application, when i cam using the reasoning
> > API and use
> > methods such as "reasoner.getInferredTypes" the "Outofmemory"
> > exception appears.
> >
> > Quoting Luigi Iannone <iannone@...>:
> >
> >> Hi,
> >>
> >> On 1 Oct 2008, at 12:08, sujaram@... wrote:
> >>
> >>> Hi Luigi,
> >>>
> >>> Thanks for the help. I checked with the OWL validator. It is giving
> >>> messages
> >>> about swrl rules such as
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#arguments
> >>> # Untyped Object Property:
> >> http://www.w3.org/2003/11/swrl#propertyPredicate
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#classPredicate
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#head
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#builtin
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#argument1
> >>> # Untyped Object Property:
> http://www.w3.org/1999/02/22-rdf-syntax-ns#rest
> >>> # Untyped Object Property:
> >> http://www.w3.org/1999/02/22-rdf-syntax-ns#first
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#argument2
> >>> # Untyped Object Property: http://www.w3.org/2003/11/swrl#body
> >>>
> >>
> >> The only explanation I can think of is that you are not importing any
> >> ontology that defines the names above.
> >> I would have not thought that the validator is SWRL aware
> >>
> >>> Also, there are messages like
> >>>
> >>> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid103
> >>> Not an
> >>> intersection/union/oneof
> >>> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid494
> >>> Not an
> >>> intersection/union/oneof
> >>> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid355
> >>> Not an
> >>> intersection/union/oneof
> >>> # Bad list first/rest subject: http://www.barc.gov.in/ISMS.owl#genid256
> >>> Not an
> >>> intersection/union/oneof
> >>
> >> Can't advise on that. Do such ids appear at all in your serialised
> >> ontology?
> >
> > ----No, they dont appear.
> >>
> >>
> >>>
> >>>
> >>> Also, it is giving some errors which i think do not exist, such as
> >>>
> >>> # http://www.barc.gov.in/ISMS.owl#isOwnedBy used as Individual and
> >>> Property
> >>> # http://www.barc.gov.in/ISMS.owl#hasSystemResource used as
> >>> Individual and Property
> >>> # http://www.barc.gov.in/ISMS.owl#hasCriticality used as Individual
> >>> and Property
> >>>
> >>> I am sure these are not true.
> >>
> >> What makes you so sure?
> >
> > --I haven't defined them like tat!!! Protege GUI also show them as
> > properties..
> >>
> >>>
> >>> The validator conclusion is tat it is not an OWL-DL ontology.
> >>>
> >>> In the Protege GUI, I could execute swrl rules and do reasoner
> >>> classifcation
> >>> without any problems.
> >>
> >> But you said you could not in your initial email
> >>
> >>> Now where can be the problem? I feel really confused.
> >>>
> >>
> >> So do I :-)
> >>
> >>> thanks n regards,
> >>> Suja
> >>
> >> Luigi
> >
> > thanks,
> >
> > --Suja.
> >>
> >>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Quoting Luigi Iannone <iannone@...>:
> >>>
> >>>> Hi Suja,
> >>>>
> >>>> It may be the case that your ontology is really tough and
> >>>> challenges
> >>>> the reasoner.
> >>>> Increasing the heap size beyond the physical limit of what you have
> >>>> available will only slow it down further. It is very likely that
> >>>> your OS
> >>>> will resort to disk space in order to emulate the extra RAM, and
> >>>> disk
> >>>> access is much slower than RAM access.
> >>>>
> >>>> You might want to check that everything is alright with the
> >>>> ontology
> >>>> itself. For that I suggest http://www.mygrid.org.uk/OWL/Validator
> >>>> with
> >>>> the caveat that if it uses OWL2
> >>>> the validator will not cope with its latest features
> >>>>
> >>>> Hope this helps,
> >>>>
> >>>> Luigi
> >>>> On 1 Oct 2008, at 11:30, sujaram@... wrote:
> >>>>
> >>>>>
> >>>>>
> >>>>> Hii,
> >>>>> I am using protege owl api for developing an ontology application,
> >>>>> in eclipse.
> >>>>> Problem is that while executing Pellet reasoner, i am getting an
> >>>>> "outOfMemory"
> >>>>> exception. I tried increasing heap size using "-Xmx500M" flag. But
> >>>>> then system
> >>>>> is getting hanged.
> >>>>>
> >>>>> Can anyone plzz help me to proceed? My RAM size is just 256 MB. Is
> >>>>> that the
> >>>>> cause of problem? Should I upgrade?
> >>>>>
> >>>>> regards,
> >>>>> suja.
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> -------------------------------------------------
> >>>>>
> >>>>> _______________________________________________
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> >>>>>
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> >>>> _______________________________________________
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> >>>
> >>>
> >>>
> >>>
> >>> -------------------------------------------------
> >>>
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From forum: Protege - OWL

Re: Modeling Problem

2008-10-10T02:01:44Z

>> curr_position(?sign, ?pos) ^ onRoadSection(?sign, ?road_sec) ^
>> road_sec_start(?start_pos, ?road_sec) ^ road_sec_end(?end_pos, ?
>> road_sec) ^
>> swrlb:greaterThanOrEqual(?pos, ?start_pos) ^
>> swrlb:lessThanOrEqual(?pos, ?end_pos) -> CorrectlyPlacedSign(?sign)
>
> I haven't really worked with SWRL, but this all seems like it should
> be a valid rule.

That sounds great, because I just started to try out SWRL the day before
yesterday.

>> Is this possible?
>> And do "curr_position", "onRoadSection", "road_sec_start" and
>> "road_sec_end" have to be (object)-properties in my ontology?
>> And "CorrectlyPlacedSign" is a class as you described before, right?
>> What about "?pos", "?star_pos" and "?end_pos"? In my ontology they
>> currently are Datatype-properties of "Sign" and "RoadSection"
>> respectively.
>> Is it possible to handle it like this?
>
> You can use a mix of object and datatype properties. For the
> arithmetic and comparison built-ins, you would need to use datatype
> properties to get appropriate values for them to operate on.

How would you model for example the "curr_position"-Property? The thing
is, it has a domain "Sign" and a range "Sign.Position", which is a
datatype-property. So "curr-position" cannot be an object-property, right?
But what else? Same proplem with "road_sec_start" D:"RoadSection"
R:"RoadSection.Start" and "road_sec_end" D:"RoadSection"
R:"RoadSection.End".

Should I consider to model "Position" as a class so that "Sign" has a
postion and "RoadSection" has two positions (start, end)? Are there
aliases? ... like RoadSection.(Postion as Start), RoadSection(Postion as
End)? How do I model this?

>> That brings me to the next problem - negotiation.
>> I can't model in SWRL that all not CorrectlyPlaced-Signs are
>> MisPlaced-Signs, can I?
>
> Correct. This is a consequence of open-world reasoning. There is no
> "failure as negation" reasoning allowed.
>
>> So do I have to create rules for every possible misplacement?
>
> That is one possible method. With your specific example, it shouldn't
> be too hard, since with the 1-dimensional model, you only have two
> possibilities for an incorrectly placed sign. It is either before the
> road segment or after it. Now, your full model may have other ways
> signs could be incorrectly placed, so this may not be completely
> practical. But you do have to essentially come up with the negated
> rules yourself, especially since a number of the rule clauses really
> exist only to bind variables and are not directly part of the correct
> placement test.

Ok, that is what I thought. Thanks for the clearance.

> The other option is to do something procedural, like using Java code
> to take the set-difference between all signs and all correctly-placed
> signs. That allows you to introduce your own "closed world"
> assumption outside of the OWL+SWRL reasoning system.

I would like to have it all together in one OWL-file. So I would like to
avoid the usage of jena etc.

Thanks for your help! Perhaps you can help me going further with
modeling the mixed-up-property "curr_position(Sign, Sign.Position)".

Bye,
Michael

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From forum: Protege - OWL

Re: Modeling Problem

2008-10-10T01:49:45Z

>> This one is a great hint. But I need sth like:
>>
>> curr_position(?sign, ?pos) ^ onRoadSection(?sign, ?road_sec) ^
>> road_sec_start(?start_pos, ?road_sec) ^ road_sec_end(?end_pos, ?
>> road_sec) ^
>> swrlb:greaterThanOrEqual(?pos, ?start_pos) ^
>> swrlb:lessThanOrEqual(?pos, ?end_pos) -> CorrectlyPlacedSign(?sign)
>>
>> Is this possible?
>
> Ah, you are now beyond my experiences with SWRL; I'm not actively
> using it. I hope others can help here.

You already helped me a lot!

>> And do "curr_position", "onRoadSection", "road_sec_start" and
>> "road_sec_end" have to be (object)-properties in my ontology?
>
> They would have to be properties, but not object properties.

But what else? There only do exist object- datatype- and
annotation-properties, right? "onRoadSection" for me is clearly an
object-property with domain "Sign" and range "RoadSection".
But with "curr_position" it is not so clear, because domain is "Sign" but
range is "Sign.Position" which actually is a Datatype-property of Sign,
correct?
Can anyone tell me how to model such a property in an owl-ontology with
protege?

>> And "CorrectlyPlacedSign" is a class as you described before, right?
>
> Yup, should result in adding statements of the form:
>
> ?sign rdf:type :CorrectPlacedSign .
>
> (I think, again I'm far from an expert, or even competent with SWRL :)

But shouldn't "CorrectlyPlacedSign" be an infered class - so that
statements (or instances of sign) are added by applying the SWRL-Rule(s)?

>> What about "?pos", "?star_pos" and "?end_pos"? In my ontology they
>> currently are Datatype-properties of "Sign" and "RoadSection"
>> respectively.
>> Is it possible to handle it like this?
>
> I don't think that SWRL is restricted to Object properties, otherwise
> what would swrlb:greaterThanOrEqual work with?

Of course you are right!

> SWRL is a way of
> writing templates for triples. So you can think about curr_position(?
> sign, ?pos) taking each statement like:
>
> :ind1 :curr_position "some_pos" .
>
> and setting ?sign to :ind1 and ?pos to "some_pos" for use in the rest
> of the rule.

What do you mean with ":ind1"?

>> That brings me to the next problem - negotiation.
>
> You mean negation?

Yes I do - sorry.

>> I can't model in SWRL that all not CorrectlyPlaced-Signs are
>> MisPlaced-Signs, can I?
>
> You might be able to, but I'd model misplacement directly, so you can
> tell if you have any corner cases left out.

Nice, what Thomas said about this issue.

>> So do I have to create rules for every possible misplacement?
>
> That's why I was suggesting a two-step approach, creating an
> intermediate property (:correct_position) for each :Sign. It might
> make the individual rules for each class of sign more simple.

Yes, now I understand this attempt a bit more.

>>> which requires a way of calculating the correct_position for
>>> each :Sign. For some that might be possible using the swrl math
>>> transforms to generate a new statement (ie a SWRL result of ->
>>> correct_position(?sign, ?calculated) )
>>
>> Sorry, I don't really get the need for the "correct_position"-Term.
>
> It's an attempt to decomposition of the problem and so end up with
> simpler SWRL rules that are semantically clearer.
>
>> Hmm, I like SWRL, because you can store it together with the
>> ontology in
>> one owl-file. What is the advantage of using sth. like Jena? Why not
>> declarative programming? Just because of its complexity?
>
> Yup, SWRL is good for that, and I encourage you to push on with it
> (perhaps sharing your experiences here when it works ;)

Yes, when I got my example running I will post the whole OWL-file here.
Might be a good starting-point for others.
> , but if you
> are under a tight deadline working procedurally might be more
> familiar; it is for me.

I agree, it is for me as well. But I want to have all things together in
on OWL-file.

> Also remember that using SWRL is going to
> require an SWRL capable reasoner; if your knowledge base + RAM needed
> for reasoning is greater than RAM for Java, you won't be able to load
> it into something like Pellet. Probably not a limitation unless you
> are doing 100,000s of signs :) Furthermore the speed can be a problem
> (although see Pellint for help there). Procedural moves on the RDF
> (eg using CONSTRUCT sparql queries) are a sometimes a clunky, but good
> enough, way around such problems.

That is an important thought although I'm far away from dealing with such
big ammount of data.

Thanks again. I would appreciate if you can help me going further with
this mixed-up-property "curr_position(Sign, Sign.Position)".

Bye,
Michael
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From forum: Protege - OWL

Re: SWRLQueryAPI - invalid query name

2008-10-09T17:47:21Z

Can you send me a code snippet and sample ontology and I can have a look
at it. This API has been out there for over a year so either the latest
build is broken or there is something in the ontology causing a bug.

Martin

Shepherd, Michael wrote:

>OK, great thanks! We are doing that now and are hitting a different problem. When we programmatically create our rule
>
>SWRLImp _imp_ = factory.createImp("Query", "Box(?p)-> sqwrl:select(?p)");
>
>Then when we runSQWRLQueries and then getSQWRLResult, the following error from Jess is returned...
>
> while executing (invokeSWRLBuiltIn "Query-1" "http://sqwrl.stanford.edu/ontologies/built-ins/3.4/sqwrl.owl#select" 0 false ?http://www.semanticweb.org/ontologies/2008/8/Ontology1222717988080.owl#p)
> while executing rule LHS (Node2)
> while executing rule LHS (TECT)
> while executing (assert (MAIN::http://www.semanticweb.org/ontologies/2008/8/Ontology1222717988080.owl#Box (name http://www.semanticweb.org/ontologies/2008/8/Ontology1222717988080.owl#Golf1GloveBoxA))).
> Message: error invoking built-in from Jess: exception thrown by built-in 'sqwrl:select' in rule 'Query-1': attempt to add data beyond the end of a row.
> Program text: ( assert ( http://www.semanticweb.org/ontologies/2008/8/Ontology1222717988080.owl#Box ( name http://www.semanticweb.org/ontologies/2008/8/Ontology1222717988080.owl#Golf1GloveBoxA ) ) ) at line 1.
>Oct 8, 2008 3:24:42 PM com.xerox.packont3.SqwrlTest main
>SEVERE: error running SQWRL queries: Jess reported an error in routine invokeSWRLBuiltIn
>
>Thoughts on this one?
>
>~ Mike
>
>
>-----Original Message-----
>From: protege-owl-bounces@... [mailto:protege-owl-bounces@...] On Behalf Of Martin O'Connor
>Sent: Wednesday, October 08, 2008 1:25 PM
>To: User support for the Protege-OWL editor
>Cc: protege-owl@...
>Subject: Re: [protege-owl] SWRLQueryAPI - invalid query name
>
>You need to run the queries first:
>
>queryEngine.runSQWRLQueries();
>
>I think this exception is a little confusing. I should probably just
>return an empty result in this case.
>
>Martin
>
>
>Shepherd, Michael wrote:
>
>
>
>>I have a question about the SWRLQueryAPI. I'm trying to use based on
>>web doc http://protege.cim3.net/cgi-bin/wiki.pl?SQWRLQueryAPI.
>>
>>So I use my code using the latest jars from build 506 and the latest
>>jess.jar. I try to invoke the QueryEngine with a rule I created via
>>the code.
>>
>>SWRLFactory factory = *new* SWRLFactory(owlModel);
>>
>>SWRLImp _imp_ = factory.createImp("Query", "Box(?p)-> sqwrl:select(?p)");
>>
>>SQWRLResult result = queryEngine.getSQWRLResult("Query");
>>
>>When executing the above rule in the SWRLTab in Protégé 3.4 beta, I
>>get the results I expect (10 individual of type Box). When I execute
>>via the API, I get the following error in the last line above:
>>
>>Oct 7, 2008 3:30:05 PM com.xerox.packont3.SqwrlTest main
>>
>>SEVERE: invalid query name 'Query'
>>
>>_edu.stanford.smi.protegex.owl.swrl.sqwrl.exceptions.InvalidQueryNameException_:
>>invalid query name 'Query'
>>
>>at
>>edu.stanford.smi.protegex.owl.swrl.bridge.impl.AbstractSWRLRuleEngineBridge.getSQWRLResult(Unknown
>>Source)
>>
>>at com.xerox.packont3.SqwrlTest.main(_SqwrlTest.java:159_)
>>
>>_edu.stanford.smi.protegex.owl.swrl.sqwrl.exceptions.InvalidQueryNameException_:
>>invalid query name 'Query'
>>
>>at
>>edu.stanford.smi.protegex.owl.swrl.bridge.impl.AbstractSWRLRuleEngineBridge.getSQWRLResult(Unknown
>>Source)
>>
>>at com.xerox.packont3.SqwrlTest.main(_SqwrlTest.java:159_)
>>
>>Should I need to do something with the SWRLImp? The web documentation
>>doesn't state so.
>>
>>Thoughts?
>>
>>Thanks!
>>
>>* *
>>
>>~ Mike
>>
>>*Michael Shepherd*
>>Research Technical Staff, Xerox Corporation
>>michael.shepherd@... <mailto:michael.shepherd@...>
>>*http://www.linkedin.com/in/michaelshepherd*
>>*http://www.facebook.com/profile.php?id=634126333*
>>
>>
>>
>>See who we know in common <http://www.linkedin.com/e/wwk/6125599/>
>>
>>
>>
>>Want a signature like this? <http://www.linkedin.com/e/sig/6125599/>
>>
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>>
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>>
>>
>>
>
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>

From forum: Protege - OWL

Re: Trigger external events upon save

2008-10-09T16:26:17Z

Hi all,

I accidentally hit “Send” before I finish the email.

Here is the complete version:

Have anyone tried to trigger an external event upon document save/change? I would like to notify an external application about changes made in Protégé.

One way to do is when user hits “save” button, a JMS message is triggered to notify such event.

Another alternative would be creating a plugin that has the ability to make an http request to another server?

Have anyone done anything like that? Does protégé have any API/plugins for external event notification?

Thanks a lot

Jun

From: Ni, Jun (FindLaw)
Sent: Thursday, October 09, 2008 4:17 PM
To: protege-owl@...
Subject:

Hi all,

Have anyone tried to trigger an external event upon document save/change?

From forum: Protege - OWL

(no subject)

2008-10-09T16:17:15Z

Hi all,

Have anyone tried to trigger an external event upon document save/change?

From forum: Protege - OWL

Re: abstract language to describe ontology

2008-10-09T11:24:28Z

Protege 4 will render an owl file in many different formats. When the
"Save As" menu is invoked it will ask you for the format that you
desire. Of these various renderings, I think that the Manchester owl
syntax and the latex mode are possibilities. If you use LaTeX for your
thesis (a much better choice than word), then the LaTeX rendering will
use a syntax that is appropriate for a formal dl paper. The manchester
owl syntax is a bit less formal looking but it is a favorite for easy
reading and understanding.

-Timothy

The manchester owl syntax is one possibility. Protege 4 will write out
your owl files in this and in several other

On Thu, 2008-10-02 at 17:19 +0200, emanu.storti@... wrote:

> Hi everybody, actually this isn't a question concerning protégé, but I
> hope you can give me an help anyway.
> I'm developing an ontology and I
> was thinking about using a formalism to describe it. First of all, I
> would like to define concept, relations, restrictions using this
> language and then I'd like to translate it into OWL language: all this
> in order to have a high level abstract representation of my future owl
> ontology, and also to describe it in my thesis in a human-readable
> syntax (unlike RDF/XML).
>
> 1) Should I use some DL abstract language?
>
> 2) What is the most commonly used solution?
> 2bis) Where can I find some
> resources to learn how to express concepts and logic rules in that
> language?
> 3) Are there any tools (Protégé plugins, for example) to
> translate from this abstract language into owl?
>
> Thank you in advance,
>
> Emanuele Storti
>
>
> Con Tiscali Adsl 8 Mega navighi SENZA LIMITI e GRATIS PER I PRIMI TRE MESI. In seguito paghi solo € 19,95 al mese. Attivala subito, l’offerta è valida fino al 02/10/2008! http://abbonati.tiscali.it/promo/adsl8mega/
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From forum: Protege - OWL

Re: Modeling Problem

2008-10-09T10:32:31Z

On Oct 9, 2008, at 4:58 AM, Michael Lodemann wrote:

> This one is a great hint. But I need sth like:
>
> curr_position(?sign, ?pos) ^ onRoadSection(?sign, ?road_sec) ^
> road_sec_start(?start_pos, ?road_sec) ^ road_sec_end(?end_pos, ?
> road_sec) ^
> swrlb:greaterThanOrEqual(?pos, ?start_pos) ^
> swrlb:lessThanOrEqual(?pos, ?end_pos) -> CorrectlyPlacedSign(?sign)

I haven't really worked with SWRL, but this all seems like it should
be a valid rule.

> Is this possible?
> And do "curr_position", "onRoadSection", "road_sec_start" and
> "road_sec_end" have to be (object)-properties in my ontology?
> And "CorrectlyPlacedSign" is a class as you described before, right?
> What about "?pos", "?star_pos" and "?end_pos"? In my ontology they
> currently are Datatype-properties of "Sign" and "RoadSection"
> respectively.
> Is it possible to handle it like this?

You can use a mix of object and datatype properties. For the
arithmetic and comparison built-ins, you would need to use datatype
properties to get appropriate values for them to operate on.

> That brings me to the next problem - negotiation.
> I can't model in SWRL that all not CorrectlyPlaced-Signs are
> MisPlaced-Signs, can I?

Correct. This is a consequence of open-world reasoning. There is no
"failure as negation" reasoning allowed.

> So do I have to create rules for every possible misplacement?

That is one possible method. With your specific example, it shouldn't
be too hard, since with the 1-dimensional model, you only have two
possibilities for an incorrectly placed sign. It is either before the
road segment or after it. Now, your full model may have other ways
signs could be incorrectly placed, so this may not be completely
practical. But you do have to essentially come up with the negated
rules yourself, especially since a number of the rule clauses really
exist only to bind variables and are not directly part of the correct
placement test.

The other option is to do something procedural, like using Java code
to take the set-difference between all signs and all correctly-placed
signs. That allows you to introduce your own "closed world"
assumption outside of the OWL+SWRL reasoning system.

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From forum: Protege - OWL

Re: Modeling Problem

2008-10-09T08:22:43Z

On 9 Oct 2008, at 7:58 AM, Michael Lodemann wrote:

>> Well first you need to figure out the features of the sign which
>> determine its correct placement (with reference to the :Road
>> or :RoadSection). I'm not sure how you do that with "Beware of
>> Kangaroos", unless you have other information about where a sign
>> should go.
>
> It's because it doesn't matter what is written on that sign. It
> might be a
> "No Parking"- or a "Beware of Kangaroos"-sign or whatever. I just
> want to
> make sure, that a sign belonging to a road-section is placed correctly
> somewhere on the road-section. Like: Sign.Pos >= RoadSection.Start-
> Pos AND
> Sign.Pos <= RoadSection.End-Pos
>
>> With the distance to all the data you need to do the math
>> to determine whether the current placement of the sign (or the
>> position attribute of the sign) is correct.
>>
>> You want to get to here (untested and illustrative):
>>
>> curr_position(?sign, ?pos) ^ correct_position(?sign, ?correct) ^
>> swrlb:equal(?pos, ?correct) -> CorrectlyPlacedSign(?sign)
>
> This one is a great hint. But I need sth like:
>
> curr_position(?sign, ?pos) ^ onRoadSection(?sign, ?road_sec) ^
> road_sec_start(?start_pos, ?road_sec) ^ road_sec_end(?end_pos, ?
> road_sec) ^
> swrlb:greaterThanOrEqual(?pos, ?start_pos) ^
> swrlb:lessThanOrEqual(?pos, ?end_pos) -> CorrectlyPlacedSign(?sign)
>
> Is this possible?

Ah, you are now beyond my experiences with SWRL; I'm not actively
using it. I hope others can help here.

> And do "curr_position", "onRoadSection", "road_sec_start" and
> "road_sec_end" have to be (object)-properties in my ontology?

They would have to be properties, but not object properties.

> And "CorrectlyPlacedSign" is a class as you described before, right?

Yup, should result in adding statements of the form:

?sign rdf:type :CorrectPlacedSign .

(I think, again I'm far from an expert, or even competent with SWRL :)

> What about "?pos", "?star_pos" and "?end_pos"? In my ontology they
> currently are Datatype-properties of "Sign" and "RoadSection"
> respectively.
> Is it possible to handle it like this?

I don't think that SWRL is restricted to Object properties, otherwise
what would swrlb:greaterThanOrEqual work with? SWRL is a way of
writing templates for triples. So you can think about curr_position(?
sign, ?pos) taking each statement like:

:ind1 :curr_position "some_pos" .

and setting ?sign to :ind1 and ?pos to "some_pos" for use in the rest
of the rule.

>
> That brings me to the next problem - negotiation.

You mean negation?

> I can't model in SWRL that all not CorrectlyPlaced-Signs are
> MisPlaced-Signs, can I?

You might be able to, but I'd model misplacement directly, so you can
tell if you have any corner cases left out.

> So do I have to create rules for every possible misplacement?

That's why I was suggesting a two-step approach, creating an
intermediate property (:correct_position) for each :Sign. It might
make the individual rules for each class of sign more simple.

>> which requires a way of calculating the correct_position for
>> each :Sign. For some that might be possible using the swrl math
>> transforms to generate a new statement (ie a SWRL result of ->
>> correct_position(?sign, ?calculated) )
>
> Sorry, I don't really get the need for the "correct_position"-Term.

It's an attempt to decomposition of the problem and so end up with
simpler SWRL rules that are semantically clearer.

>> You might find that calculating the correct_position is best done
>> procedurally, accessing the knowledge base (ontology) via Jena or
>> similar. That said by the time you are working procedurally you
>> could
>> do the generation of the CorrectlyPlacedSign and MisPlacedSign
>> statements procedurally too, taking SWRL out of the equation.
>
> Hmm, I like SWRL, because you can store it together with the
> ontology in
> one owl-file. What is the advantage of using sth. like Jena? Why not
> declarative programming? Just because of its complexity?

Yup, SWRL is good for that, and I encourage you to push on with it
(perhaps sharing your experiences here when it works ;), but if you
are under a tight deadline working procedurally might be more
familiar; it is for me. Also remember that using SWRL is going to
require an SWRL capable reasoner; if your knowledge base + RAM needed
for reasoning is greater than RAM for Java, you won't be able to load
it into something like Pellet. Probably not a limitation unless you
are doing 100,000s of signs :) Furthermore the speed can be a problem
(although see Pellint for help there). Procedural moves on the RDF
(eg using CONSTRUCT sparql queries) are a sometimes a clunky, but good
enough, way around such problems.

--J

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From forum: Protege - OWL

Protege

2008-10-09T07:34:39Z

Hi,

I have to write a report describing the functions beyond creating the ontology that Protege and TopBraid composer can support.

Ontologies can be created in both software packages, but please describe what we can then do with the ontologies once they are created.

Does Protege support functions and processes for ontology applications? Does it for example allow data integration from two different sources?

Thanks,

AC

From forum: Protege - General

Reminder - Semantic Web Applications and Tools for Life Sciences (SWAT4LS)

2008-10-09T06:11:37Z

International Workshop on
Semantic Web Applications and Tools for Life Sciences (SWAT4LS)
28th November 2008, Edinburgh, UK
http://www.swat4ls.org/
Call for Papers

Submission deadline: 13 October 2008!

A selection of papers will be published in a BMC Bioinformatics
supplement devoted to the workshop

Overview
--------
The workshop is organized in sessions and open discussions. Invited
speakers will present state-of-theart,
provocative lectures on the workshop's main topic, while a number of
submissions will be accepted as
oral presentations and posters on all workshop's topics.

Workshop Description
--------------------
Semantic Web technologies, tools and applications are starting to
emerge in Life Sciences. In recent
years, systems have been introduced and an increasing interest among
researchers is arising. This
workshop will provide a venue to present and discuss benefits and
limits of the adoption of these
technologies and tools in biomedical informatics and computational biology.
It will showcase experiences, information resources, tools development
and applications. It will bring
together researchers, both developers and users, from the various
fields of Biology, Bioinformatics and
Computer Science, to discuss goals, current limits and some real use
cases for Semantic Web
technologies in Life Sciences.

Keynote Speakers
------------------------
+ Semantic web technology in translational cancer research,
Michael Krauthammer, Department of Pathology, Yale University School
of Medicine, USA
+ Using Ontologies to bring Web Services on to the Semantic Web
Mark Wilkinson, Dept. of Medical Genetics, University of British
Columbia, Canada

Workshop Venue and Format
------------------------
The workshop will take place in Edinburgh, Scotland, on 28 November
2008, and is hosted by the e-
Science Institute of the UK's National e-Science Centre (NeSC).
SWAT4LS will be a one-day workshop and will consist of two invited
talks, regular paper and poster
presentations. The workshop will conclude with a panel discussion on
the strength and weaknesses of the
Semantic Web for the Life Sciences.

Deadlines
---------
* Submission deadline (both papers and posters): 13 October 2008
* Notification of acceptance: 20 October 2008
* Camera-ready submission: 3 November 2008

Topics of Interest
------------------
Topics of interest include, but are not limited to:
* Standards, Technologies, Tools for the Semantic Web
o Semantic Web standards (RDF, OWL, ...)
o RDF/OWL, SKOS, .... and their applicability to bioinformatics
o RDF Schemas and Query systems
o Biomedical Ontologies and related tools
o Formal approaches to large biomedical controlled terminologies
and vocabularies
* Systems for a Semantic Web for Bioinformatics
o Bio-ontologies, RDF stores, Semantic Web Services
o RDF repositories and query systems for life sciences
o Semantically aware biomedical Web Services
o Semantic Biological Data Integration Systems
* Existing and perspective applications of the Semantic Web for Bioinformatics
o Semantic browsers, Semantic collaborative research
o Case studies, use cases, and scenarios
o Semantic Web applications in life sciences

Type of contributions and instructions
----------------------
The following possible original contributions are sought:
* Oral communications (regular papers)
* Posters
* Software demos

All contributions must be in English and must be submitted through the
EasyChair review system at:
http://www.easychair.org/conferences/?conf=swat4ls.
Please upload all submissions as PDF files in LNCS format (see
http://www.springer.de/comp/lncs/authors.html ).
To ensure high quality, submitted papers will be carefully
peer-reviewed by at least three members of the
Scientific Committee.
* Submissions for Oral communications should be between 10 and 15 pages.
* Posters submissions should be between 4 and 8 pages.
* Software demo proposals should also be between 4 and 8 pages.

All accepted oral communications and posters will be published with
the CEUR-WS.org Workshop
Proceedings service (see http://ceur-ws.org/).

Furthermore, a selection of papers will be published in a special
issue of the BMC Bioinformatics journal
devoted to the SWAT4LS workshop.

To this end, a special Call will be launched shortly after the
workshop, for extended and revised versions
of contributions submitted to the workshop and accepted either as oral
communication or poster.
For any information, refer to info@... .

Workshop Chairs
----------------
+ Albert Burger, School of Mathematical and Computer Sciences,
Heriot-Watt University, and Human
Genetics Unit, Medical Research Council, Edinburgh, United Kingdom
+ Adrian Paschke, Corporate Semantic Web, Free University Dresden, Germany
+ Paolo Romano, Bioinformatics, National Cancer Research Institute,
Genova, Italy
+ Andrea Splendiani, Medical Informatics Department, University of
Rennes 1, Rennes, France

Programme Committee
----------------
+ Giulio Armano, University of Cagliari, Italy
+ Christopher Baker, Institute for Infocomm Research (I2R), Singapore
+ Pedro Barahona, New University of Lisboa, Portugal
+ Liliana Barrio-Alvers, Transinsight GmbH, Germany
+ Virendra C. Bhavsar, University of New Brunswick, Canada
+ Olivier Bodenreider, National Library of Medicine, Bethesda, USA
+ Matt-Mouley Bouamrane, University of Machester, United Kingdom
+ Werner Ceusters, University at Buffalo, USA
+ Kei Cheung, Yale Center for Medical Informatics, USA
+ Marie-Dominique Devignes, LORIA, Vandoeuvre les Nancy, France
+ Michel Dumontier, Carleton University, Canada
+ C. Maria Keet, Free University of Bozen-Bolzano, Italy
+ Graham Kemp, Chalmers University of Technology, Sweden
+ Jacob Tilman Koehler, University of Tromsø, Norway
+ Ludwig Krippahl, New University of Lisboa, Portugal
+ Patrick Lambrix, Linköping University, Sweden
+ Phillip Lord, University of Newcastle, United Kingdom
+ M. Scott Marshall, University of Amsterdam, The Netherlands
+ Lyndon Nixon, STI International, Austria
+ Stephan Philippi, University of Koblenz-Landau, Germany
+ Alan Ruttenberg, Science Commons, USA
+ Matthias Samwald, DERI, Galway, Ireland, and Semantic Web Company, Austria
+ Nigam Shah, Center for Biomedical Informatics Research, USA
+ Michael Schröder, TU Dresden, Germany
+ Robert Stevens, University of Manchester, United Kingdom
+ Luca Toldo, Merck Serono, Germany
+ Tetsuro Toyoda, RIKEN, Japan
+ Jano van Hemert, University of Edinburgh, United Kingdom

=====================================================================
In Co-operation with:
- National Cancer Research Institute, Genova, Italy
- Biotechnology Centre, TU Dresden, Dresden, Germany
- School of Mathematical and Computer Sciences, Heriot-Watt
University, Edinburgh, United Kingdom
- Université de Rennes 1, Rennes, France
- e-Science Institute, Edinburgh, Scotland, United Kingdom
- SeaLife Project, European Commission Information Society and Media
- Laboratory for Interdisciplinary Technologies in Bioinformatics
(LITBIO), Italy
=====================================================================

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From forum: Protege - OWL