Hung Le | 1 Oct 04:46 2011
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Question about SWRL Tab: negative rules to delete instances

Dear Martin J. O'Connor,

 

We are very impressed with SWRL Tab tool that you developed.

We are currently using it for our research to define Information Access Control rules. However, it does not allow us to define negative rules that can delete instances from OWL,

 

We would like to extend your work to implement negative rules, but are not sure if that makes sense nor foresee any issues and challenges that might make you not to do that. Could you please give us some advices?

 

Thank you very much.

 

-Hung

 

Hung Le, Ph.D
Biomedical Informatics Research and Development (BIRD) Center,
Department of Biostatistics & Computational Biology,
University of Rochester Medical Center,
601 Elmwood Avenue - P.O. Box 630,
Rochester, New York 14642.

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nada | 1 Oct 10:56 2011
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call another servlet in a web application

I have two servlets in my web application (SQAES) this is the name of my java 
web app.

1) the main servlet: SQAServlet  (in the package SQA.Learning.System) 
it has  <at> WebServlet ("/SQASystem")

2) LOServlet (in tha package RelatedLOs)
I did not use  <at> WebServlet in this servlet

The doPost method of the SQAServlet calls the LOServlet.
I tried different ways to handle this but I got the following error

The requested resource not available

these are the ways I tried to call the LOServlets:

out.println("<a href=\"http://localhost:8080/SQAES/RelatedLOs/LOServlet?
queryStr="+concept+"\">"+concept+"</a><br>");

out.println("<a href=\"http://localhost:8080/SQAES/LOServlet?
queryStr="+concept+"\">"+concept+"</a><br>");

out.println("<a href=\"http://localhost:8080/SQASystem/LOServlet?
queryStr="+concept+"\">"+concept+"</a><br>");

any suggestions where I'm wrong? I'm using Eclipse and Tomcat7

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Adrian Paschke | 1 Oct 11:31 2011
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CFP: Semantic Web Applications and Tools for the Life Sciences (SWAT4LS 2011) - Deadline October 7th

                   Call for Papers

 

          4th International Workshop on

  Semantic Web Applications and Tools for the Life Sciences

                   SWAT4LS 2011

            http://www.swat4ls.org/2011/

            Dec 7th-9th, 2011, London, UK

 

    In cooperation with ACM SIG Bioinformatics, W3C

 

 ++++ Submission Deadline in one Week - Oct 7, 2011   ++++

 

News:

*********************************************************************

* Proceedings will be published and listed in the ACM ICP Series    *

* SWAT4LS in cooperation with the ACM SIG Bioinformatics            *

* SWAT4LS supported by W3C                                          *

* Journal Special Issue for extended and revised accepted papers    *

* Program includes Hackathon, Tutorials, Keynotes, Demos, Panel     *

* http://www.swat4ls.org/workshops/london2011/scientific-programme/ *

* Sponsored by BBSRC, NCBO, BioMed Central                          *

*********************************************************************

 

 

Overview

======================================================

 

Since 2008, SWAT4LS is a workshop that has provided a platform for the presentation and discussion of the benefits and limits of applying web-based information systems and semantic technologies in Biomedical Informatics and Computational Biology.

 

Growing steadily each year as Semantic Web applications become more widespread, SWAT4LS has been in Edinburgh 2008, Amsterdam 2009, and Berlin 2010, with London planned for 2011. The last edition of SWAT4LS was held in Berlin, on December 10th, 2010 with more than 100 attendees. It was preceded by two days of tutorials and other associated events.

 

We are confident that the next edition of SWAT4LS will provide the same open and stimulating environment that continues to bring together researchers, both developers and users, from domains spanning health care, life sciences, clinical research and translational medicine, to discuss goals, current limits and real experiences in the use of Semantic Web technologies in Life Sciences.

 

Rationale

======================================================

 

The Web is a key medium for information publishing, and Web-based information systems play a key role in biomedical information exchange and integration. At the same time, the variety and complexity of biomedical information call for the adoption of semantic-based solutions. The Semantic Web provides a set of technologies and standards that are key to supporting semantic markup, ontology development, distributed information resources and collaborative social environments. Altogether the adoption of the Web-based semantic-enabled technologies in the Life Sciences has a potential impact on the future of publishing, scientific communication, and biomedical research. 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 serve as a showcase for experiences, information resources, tools development and applications.

 

Topics

======================================================

 

Topics of interest include, but are not limited to:

 

- Standards, Technologies, Tools for the Semantic Web

 

o Semantic Web standards and new proposals (e.g.: RDF, OWL, SKOS, SPIN, RuleML)

o Tools for ontology management, editing and versioning

o RDF stores, Reasoners, query and visualization systems

o Formal approaches to large biomedical knowledge bases

o Tools for semantic-enabled web publication

o Alternative approaches to integrate semantic representations and web based solutions

 

- Systems for a Semantic Web for Bioinformatics

 

o Biomedical knowledge bases on the Semantic Web

o EHR and clinical research data interoperability and reuse

o Clinical data pipelines for supporting tailored therapy and molecular medicine

o Tracking genotype and phenotype assertions with provenance

o Semantic biomedical Web Services

o Semantics aware Biological Data Integration Systems

o Semantic-enabled biomedical information systems and solutions

o Linked Data for biomedical research, drug development and discovery

 

- Existing and prospective applications of the Semantic Web for Bioinformatics

 

o Semantic Wikis

o Semantic collaborative research environments

o Semantic crowdsourcing and collective intelligence

o Alternative approaches to biomedical metadata generation and management

o Case studies, use cases, and scenarios

 

Type of contributions

======================================================

 

The following possible contributions are sought:

 

- Research papers

- Position papers

- Posters

- Software demos

 

Proceedings

======================================================

 

Accepted papers will be published as proceedings in the ACM ICP Series (The publication will be available under the following ISBN number: 978-1-4503-1076-5).

 

Special issue

======================================================

 

Authors of accepted contributions to the upcoming edition of SWAT4LS will be invited to submit an extended and revised version of their contributions for a special issue of an international peer-reviewed scientific journal (under definition, special issues of SWAT4LS have appeared in the past in BMC Bioinformatics and in the BMC Journal of Biomedical Semantics.)

 

Deadlines

======================================================

 

- Papers submission deadline: 7 October 2011

- Posters and demo submission deadline: 31 October 2011

- Communication of acceptance: 7 November 2011

- Camera ready: 21 November 2011

 

Instructions

======================================================

 

All papers and posters must be in English, formatted according to ACM IPCS guidelines (http://www.acm.org/sigs/publications/proceedings-templates) and submitted in pdf format.

 

- Submissions for papers should report original research, and should be between 4 and 8 pages.

- Submissions for position papers should report qualified opinions, recommendations or conclusions, and should be between 1 and 3 pages.

- Submissions for posters should be between 1 and 2 pages.

- Submissions for software demo proposals should also be between 1 and 2 pages.

 

Submission

======================================================

 

All submissions are handled via the EasyChair submission system ( https://www.easychair.org/conferences/?conf=swat4ls2011).

To ensure high quality, submitted papers will be carefully peer-reviewed by at least three members of the Scientific Committee.

 

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Agnieszka.Lawrynowicz | 1 Oct 12:55 2011
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[ANN] Opening of the DMO (Data Mining Ontology) Foundry

Dear Colleagues,

We are happy to announce the opening of the *DMO (Data Mining Ontology)
Foundry* (http://www.dmo-foundry.org/),  an initiative designed to promote
the development of ontologies representing the data mining domain. The DMO
Foundry will gather the most significant ontologies concerning data mining
and the different algorithms and resources that have been developed to
support the knowledge discovery process.

Each ontology in the DMO Foundry is freely available for browsing and open
discussion, as well as collaborative development, by data mining
specialists all over the world.  We cordially welcome all interested
researchers and practitioners to join the initiative.  To find out how you
can participate in ontology development, click on the "How to join" tab at
the top of the DMO-Foundry page.

To access and navigate an ontology, and contribute to it, click on the
"Ontologies" tab, then on your selected ontology and its OWL Browser tool.
As you browse, you can click on the "Comment" button to share your
insights,  criticisms, and suggestions on the concept or relation you are
currently exploring. For more general comments, go the the "Forum" tab and
post a message to initiate a discussion thread.
Please note that until the end of March 2012, this site is being
road-tested on the Data Mining OPtimization (DMOP) Ontology developed in
the EU FP7 ICT project e-LICO (2009-2012).  We are in contact with authors
of other DM ontologies, but if you are developing a relevant ontology that
you think we are not aware of, please set up a post in the Forum.
You are also invited to contact us by writing to an email address
info <at> dmo-foundry.org.

Kind regards,

Melanie Hilario, Agnieszka Lawrynowicz, Phong Nguyen, Raul Palma
(DMO Foundry Management Board members)

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Martin O'Connor | 2 Oct 00:31 2011
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Re: Question about SWRL Tab: negative rules to delete instances


Hung,

Unfortunately, the provision of negation (or, strictly speaking, negation as failure) in SWRL is
problematic. See the 
following entry in the language FAQ for an explanation of why:

http://protege.cim3.net/cgi-bin/wiki.pl?SWRLLanguageFAQ#nidA3Q

Also, since SWRL supports monotonic inference only, ontology modifications are not supported:

http://protege.cim3.net/cgi-bin/wiki.pl?SWRLLanguageFAQ#nid9TR

The SQWRL query language does support a form of negation as failure with it collection operators:

http://protege.cim3.net/cgi-bin/wiki.pl?CollectionsSQWRL#nidBJC

However, this negation works for SQWRL queries only. It does not work for SWRL rules.

Martin

On 9/30/2011 7:46 PM, Hung Le wrote:
>> We would like to extend your work to implement negative rules, but are not sure if that makes sense nor
foresee any 
>> issues and challenges that might make you not to do that. Could you please give us some advices?
>>
>> Thank you very much.
>>
>> -Hung
>>
>> Hung Le, Ph.D
>> Biomedical Informatics Research and Development (BIRD) Center,
>> Department of Biostatistics & Computational Biology,
>> University of Rochester Medical Center,
>> 601 Elmwood Avenue <x-apple-data-detectors://2> - P.O. Box 630, <x-apple-data-detectors://3>
>> Rochester, New York 14642 <x-apple-data-detectors://3>.
>>
>
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Hung Le | 2 Oct 03:12 2011
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Re: Question about SWRL Tab: negative rules to delete instances

Martin,

Thanks a lot for your email and URLs. It did help me to understand lots of
things. That's quite interesting.

However, I could not get a clear answer for what I really needed. For
example, I'd like to define this rule:

	hasRevocation(userA, perm) --> (*neg*) hasPermission(userA, perm).
	i.e. userB is revoked a permission 'perm' (assuming that an instance
hasPermission(userB, perm) exists in OWL.

If this rule is executed, it should delete the instance hasPermission(userB,
perm) from OWL file.

I am not sure if that is possible in SQWRL or any other OWL plugins? If not,
is it possible to extend SWRLTab/SQWRLTab to do that?

Thanks
-Hung

-----Original Message-----
From: protege-owl-bounces <at> lists.stanford.edu
[mailto:protege-owl-bounces <at> lists.stanford.edu] On Behalf Of Martin O'Connor
Sent: Saturday, October 01, 2011 6:31 PM
To: protege-owl <at> lists.stanford.edu
Subject: Re: [protege-owl] Question about SWRL Tab: negative rules to delete
instances

Hung,

Unfortunately, the provision of negation (or, strictly speaking, negation as
failure) in SWRL is problematic. See the following entry in the language FAQ
for an explanation of why:

http://protege.cim3.net/cgi-bin/wiki.pl?SWRLLanguageFAQ#nidA3Q

Also, since SWRL supports monotonic inference only, ontology modifications
are not supported:

http://protege.cim3.net/cgi-bin/wiki.pl?SWRLLanguageFAQ#nid9TR

The SQWRL query language does support a form of negation as failure with it
collection operators:

http://protege.cim3.net/cgi-bin/wiki.pl?CollectionsSQWRL#nidBJC

However, this negation works for SQWRL queries only. It does not work for
SWRL rules.

Martin

On 9/30/2011 7:46 PM, Hung Le wrote:
>> We would like to extend your work to implement negative rules, but 
>> are not sure if that makes sense nor foresee any issues and challenges
that might make you not to do that. Could you please give us some advices?
>>
>> Thank you very much.
>>
>> -Hung
>>
>> Hung Le, Ph.D
>> Biomedical Informatics Research and Development (BIRD) Center, 
>> Department of Biostatistics & Computational Biology, University of 
>> Rochester Medical Center,
>> 601 Elmwood Avenue <x-apple-data-detectors://2> - P.O. Box 630, 
>> <x-apple-data-detectors://3> Rochester, New York 14642
<x-apple-data-detectors://3>.
>>
>
> _______________________________________________
> protege-owl mailing list
> protege-owl <at> lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: 
> http://protege.stanford.edu/doc/faq.html#01a.03

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Joujou Ro | 2 Oct 19:19 2011
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sparql in protege

Hi,
I would like to know if if information generated by SPARQL query in protégé can be extracted under any
format like (.txt,.doc..).
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Bruce Whealton | 2 Oct 19:24 2011

WebProtege questions

Hello all,
      I was wondering about the differences between installing WebProtege in Local Mode versus External Server Mode? 
Does the External Server mode use the servers at Stanford.edu? 
Or how does this work?  What are the benefits of each?
Is one easier to use than the other?
Thanks,
Bruce
++++++++++++++++++++++++++++++++++++++++++++++++++
Bruce Whealton, Owner Future Wave Designs
FOAF: http://whealton.info/BruceWhealtonJr/foaf.rdf
Vcard: http://whealton.info/BruceWhealtonJr/brucewhealtonvcard.html
Web Design and Development http://FutureWaveDesigns.com
http://futurewavedesigns.com/wordpress/
Web Technology wiki: http://futurewavedesigns.com/w/
++++++++++++++++++++++++++++++++++++++++++++++++++
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Brice Sommacal | 3 Oct 15:17 2011
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Re: ProtegeReasonner /DatatypeProperty and getAncestorProperties - Expected result is wrong

Hello Tania, 


In my last message, I was asking few questions on how to build a custom model from a inferred model made by ProtegePelletJenaReasoner.
Althought, I have resolved the problem on super properties, the last upgrade to P3.4.7 makes failed my program. 

My issue is not about super-properties; but super classes.

I mean that in 3.4.6 I was using the following to retrieve all the super classes from a current class: reasoner.getAncestorClasses((OWLClass)curInd.getDirectType())

But the program fails at this line. (with no traces)

Instead of this, from now, I am using the following line: curInd.getDirectType().getSuperclasses(); 
The plugin is working fine but I wonder why this behavior is happening. 

Do you have an idea why the program breaks using getAncestorClasses?

So, for this method, the resonner is not useful anymore. 

regards, 


Brice



2011/7/29 Tania Tudorache <tudorache <at> stanford.edu>
On 07/27/2011 09:39 AM, Brice Sommacal wrote:
Hello Tania, 

Sorry I missed my reasonner name. I'm using ProtegePelletJenaReasoner. But, changing the reasonner didn't change anything. 

Thanks for pointing me out these two functions. I'm sure they will be pretty useful in the next future, but not yet in this specific case.

If my understanding of what you are doing is right, then these methods give you back exactly what you need.




In fact, I used a deprecated function: myOWLProp.getSuperproperties(true);

This one is from the Protege-OWL API, and it will only return you the asserted super properties.


This one returns all the super properties of a datatype properties. But the recommended function (getAncestorProperties) doesn't.

The getAncestorProperties comes from Jena and the reasoner, and should return also the inferred super properties (probably you don't care about these). It might be that they are not implemented in the Jena implementation of Pellet 1.5.2.



I checked "Get inferred property values" by Protege UI, and I did not retrieve the assertions for super datatype properties...

I wonder why. I also did a test and they worked fine. The UI uses the ProtegePelletOWLAPIReasoner implementation. I did not try the ProtegePelletJenaReasoner in the UI.

Anyway, I'm glad you fixed your problem.

Tania




Thanks for your help :-)


Brice

2011/7/27 Tania Tudorache <tudorache <at> stanford.edu>
Hi Brice,

You did not tell us which reasoner you are using. The ProtegeReasoner is just an interface, and there are several implementation of it (ProtegePelletOWLAPIReasoner, DefaultJenaReasoner, ProtegePelletJenaReasoner). How did you initialize the reasoner?

The result of the getAncestorProperties comes directly from the reasoner, and if you don't get back the ancestor, then there is not much we can do.

Rather than doing yourself the inference for the new model, you could use the methods from the ProtegeReasoner interface:
public Collection<OWLIndividual> getRelatedIndividuals(OWLIndividual subject, OWLObjectProperty objectProperty) throws ProtegeReasonerException;
public Collection getRelatedValues(OWLIndividual subject, OWLDatatypeProperty datatypeProperty) throws ProtegeReasonerException;

that would give you the assertions back: S-B-O, S-A-O both for object and datatype properties. I just tested this in the Protege UI using the Protege Pellet reasoner, and it works fine. (in the Individuals Tab, right click on an individual and then select from the context menu: "Get inferred property values".

Tania



On 07/26/2011 07:13 AM, Brice Sommacal wrote:
Hello, 

I'm using ProtegeReasonner to retrieve all the super "objects" for :
  - class (by using getAncestorClasses)
  - properties (by using getAncestorProperties)

I made 2 functions. 
The first one retrieves all ancestor classes for all the instances, and then add them as type in a new model.  

I then replicate the same function in order to apply quite the same process with the properties. 
This is working well when I manipulate Object Property, but when using Datatype Propeties, I don't retrieve the expected result. 

I mean: if A is super property of B.
If the 2 properties are object properties, I will retrieve A and B as ancestors of B.

But, if A and B are datatype properties, I will only retrieve B as an ancestor. 

I use this line to get a collection of ancestor
Collection<OWLProperty> temp = reasoner.getAncestorProperties(myOWLProp);

My goal is to add a new statement like this:
 if I encounter a triple Subject - B - Object, I will then add the triple Subject - A - Object. 

I wonder if am I using the wrong functions or the right reasonner... Do you have a hint on this?

Thanks, 


Brice 
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Help with datatype restrictions in Protégé 3.4.7

Hello everybody,

 

Is it possible in Protege 3.4.7 to create DataType restrictions bounded to a range of integers just like in Protege 4. ?, i.e has_value some integer[>=100]

 

Thank you in advance for your help

 

Cecilia

 

 

--

=======================================================

Cecilia Zanni-Merk

INSA de Strasbourg

24 Bd de la Victoire - 67084 Strasbourg - France

Phone: +33 3 88 14 47 71

 

"Beware of bugs in the above code; I have only proved

it correct, not tried it". Donald Knuth

 

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Gmane