Ernesto,
I looked into the ProSE
manual and your article.
This looks very interesting and will require from me more reading.
> ProSE plugin is obsolete and it should be updated
When do you plan to do this? Will this work for the Protege3.4.2
(OWL)?
Thank you so much,
Jeff
From: Ernesto
Jimenez-Ruiz [mailto:ernesto.jimenez.ruiz@xxxxxxxxx]
Sent: Monday, July 26, 2010 4:53 AM
To: Ian Horrocks
Cc: Zhuk, Yefim; Peter Yim; ontolog-forum@xxxxxxxxxxxxxxxx; Bernardo
Cuenca Grau
Subject: Re: owl and scalability
Dear all,
I updated the module extractor for the OWL API 3
http://krono.act.uji.es/people/Ernesto/safety-ontology-reuse/locality-module-extractor
However the ProSE plugin is obsolete and it should be updated to the last
version of the OWL API and Protege 4 (it is in my TODO list).
Nevertheless the module extractor provides an OWL containing the module
entituies as output, which could be directly loaded into Protege.
Ernesto.
2010/7/26 Ian Horrocks <ian.horrocks@xxxxxxxxxxxxxxx>
Jeff,
See forwarded message from Bernardo Cuenca Grau giving details of various
modularisation tools, including a Protege plug-in. The implementor of these
tools is Ernesto Jimenez-Ruiz.
Ian
Begin forwarded message:
> From: Bernardo Cuenca Grau <bcuencagrau@xxxxxxxxxxxxxx>
> Date: 25 July 2010 12:41:51 GMT+01:00
> To: Ian Horrocks <ian.horrocks@xxxxxxxxxxxxxxx>
> Subject: Re: owl and scalability
>
> Hi Ian,
>
> Ernesto has a full implementation of the locality-based module
> extractor that can be used both from command line and from Java. There
> is also a Protege plugin.
>
> The plugin that combines safety and module extraction is ProSe. The
> plugin and user manual can be downloaded from:
>
> http://krono.act.uji.es/people/Ernesto/safety-ontology-reuse
>
> Here are the instructions he sent me for using the module extractor
> directly without Protege:
>
> ----
>
> In http://krono.act.uji.es/people/Ernesto/safety-ontology-reuse/localityModuleExtractor.tgz/view
> you can find the locality module extractor (compiled for OWL API 2)
> with some comand line scripts and signature examples to extract from
> GALEN and NCI.
>
> Basically the extractor has the following functionalities:
> - Command line extractor via the "CreatePhysicalOntologyModule"
class
> (see usage in command line)
>
> - Extraction of modules top/bottom modules via the
"ModuleExtractor" class.
> * Constructor ModuleExtractor(OWLOntology ontology, boolean
> dualConcepts, boolean dualRoles,
> boolean considerImportsClosure,
boolean considerEntityAnnotations)
> For bottom modules: dual roles and dual conceps
=false
> For top modules: dual roles and dual conceps
=true
>
> * Method: public OWLOntology
> getLocalityModuleForSignatureGroup(Set<OWLEntity> signature, String
> moduleURIStr)
> Gets the OWLOntology module for a given
signature set
>
> * Method public Set<OWLEntity>
> extractModuleEntitiesForGroupSignature(Set<OWLEntity> signature)
> Gets the set of entities of the module for the
given signature set
>
> * Methdo public Set<OWLEntity>
> extractModuleEntitiesForEntity(OWLEntity entity)
> Gets the set of entities of the module for the
a signature
> with only one entity
> ----
>
>
>
>
> Bernardo
>
>
> On Sun, Jul 25, 2010 at 7:25 AM, Ian Horrocks
> <ian.horrocks@xxxxxxxxxxxxxxx>
wrote:
>> What is the current state of implementation of modularisation -- is
there a Protege plug-in or some such?
>>
>> Ian
>>
>>
>> Begin forwarded message:
>>
>>> From: "Zhuk, Yefim" <Yefim.Zhuk@xxxxxxxxxxxxx>
>>> Date: 24 July 2010 00:16:59 GMT+01:00
>>> To: Peter Yim <peter.yim@xxxxxxxx>,
Ian Horrocks <ian.horrocks@xxxxxxxxxxxxxxx>,
"[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
>>> Subject: RE: owl and scalability
>>>
>>> Ian, Peter,
>>>
>>> I've read the paper on modularization. The safety idea definitely
makes sense to me.
>>>
>>> In your article several screen shots were taken to illustrate the
methods.
>>>
>>> Was it Protégé or some other tools?
>>>
>>> Do they implement to some degree these methods or you have to
manually massage ontology to make the modules?
>>>
>>> I wonder if any tools exist today (or almost ready:-)) to
implement this or similar methods.
>>>
>>> Do you have specific plans on such tools?
>>>
>>> Or maybe you collaborate with some other group, like Stanford U,
to implement these ideas? Open source project?
>>>
>>> Thank you,
>>>
>>> Jeff
>>>
>>> -----Original Message-----
>>> From: peter.yim@xxxxxxxxx
[mailto:peter.yim@xxxxxxxxx] On Behalf
Of Peter Yim
>>> Sent: Friday, July 23, 2010 9:16 AM
>>> To: Ian Horrocks; Zhuk, Yefim; [ontolog-forum]
>>> Subject: Fwd: owl and scalability
>>>
>>> Thank you, Ian. ... Let's put this conversation onto the
discussion
>>> list to share it with the community.
>>>
>>> Jeff, please check out our membership details (see:
>>> http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid1J
) in case
>>> you aren't already an Ontolog member (and is therefore not
subscribed
>>> to the [ontolog-forum] list yet.)
>>>
>>> Regards. =ppy
>>> --
>>>
>>>
>>> ---------- Forwarded message ----------
>>> From: Ian Horrocks <ian.horrocks@xxxxxxxxxxxxxxx>
>>> Date: Fri, Jul 23, 2010 at 2:56 AM
>>> Subject: Re: owl and scalability
>>> To: "Zhuk, Yefim (Jeff)" <Yefim.Zhuk@xxxxxxxxxxxxx>
>>> Cc: Peter Yim <peter.yim@xxxxxxxx>
>>>
>>>
>>> Quick answer -- if you need more please come along next week.
>>>
>>> OWL ontologies can be split into multiple files. From a
>>> formal/semantic POV this makes absolutely no difference. Effects
on
>>> performance will be very much tool dependent. If you can really
>>> identify a subset of the ontology that is (for example) sufficient
to
>>> answer queries at run time, then this may well improve performance
>>> with some tools. Identifying such subsets is highly non-trivial in
>>> general (naive syntactic techniques don't work in general), but
there
>>> are now well understood techniques that can achieve semantic
>>> modularisation, and even some tool support -- see, e.g., [1].
>>>
>>> Regards,
>>> Ian
>>>
>>> [1] http://www.comlab.ox.ac.uk/people/ian.horrocks/Publications/download/2008/CHKS08a.pdf
>>> ---
>>>
>>>
>>> On 23 Jul 2010, at 05:01, Peter Yim wrote:
>>>> Hello Jeff,
>>>>
>>>>
>>>> Thank you for the message.
>>>>
>>>> You are probably aware that Professor Horrocks (who gave
today's talk
>>>> on "Scalable Ontology-Based Information Systems")
will be championing
>>>> two more sessions (on Thu 2010.07.29 & 2010.08.05, i.e. on
the next
>>>> two coming Thursdays) on "OWL 2." The Jul-29 session
will cover the
>>>> OWL 2 standard and specifications, and the Aug-5 sessions will
be on
>>>> Tools and Applications. He has invited a panel of experts to
join him
>>>> at the Aug-5 session too. See:
>>>> http://ontolog.cim3.net/forum/ontolog-forum/2010-07/msg00028.html
>>>>
>>>> I would, therefore, strongly suggest that you come join us at
these
>>>> two sessions. There will be plenty of time for discussion, and
a lot
>>>> of expertise around. You might bring up your questions and
suggested
>>>> approach for discussion then ... your question would be
especially
>>>> appropriate for the Aug-5 session.
>>>>
>>>>
>>>> Regards. =ppy
>>>>
>>>> Peter P. Yim
>>>> --
>>>
>>>
>>>> On Thu, Jul 22, 2010 at 12:11 PM, Zhuk, Yefim <Yefim.Zhuk@xxxxxxxxxxxxx> wrote:
>>>>> Hi Peter!
>>>>>
>>>>>
>>>>>
>>>>> Thank you so much for facilitating this event (7/22,
Scalable Ontology-Based
>>>>> Information Systems).
>>>>>
>>>>>
>>>>>
>>>>> A question: OWL can be split into multiple files. What are
the best
>>>>> practices to use this feature for better performance.
>>>>>
>>>>> For example, I'd think of taking into a separate file a
specific sub-domain
>>>>> that is a focus of run-time query, while keeping the rest
in another file
>>>>> and have some pre-compiled (design-time created) things
that would help at
>>>>> run-time processing. This balance might vary from task to
task.
>>>>>
>>>>>
>>>>>
>>>>> Any practices like this or similar and better?
>>>>>
>>>>>
>>>>>
>>>>> Thank you,
>>>>>
>>>>>
>>>>>
>>>>> Jeff
>>>
>>> This E-Mail has been scanned for viruses.
>>
>>
>
>
>
> --
> Dr. Bernardo Cuenca Grau
> Royal Society University Research Fellow
> Computing Laboratory
> University of Oxford
> Wolfson Building
> Parks Road
> OXFORD
> OX1 3QD
--
Ernesto Jiménez Ruiz
Despacho TI2227DD
Departamento de Lenguajes y Sistemas Informáticos
Universidad Jaume I
12071, Castellón de la Plana (Spain)
Tfno.: +34 964728371
Fax: +34 964728435
e-mail: ejimenez@xxxxxxxxxx
http://krono.act.uji.es/people/Ernesto
http://www.jimenez-ruiz.es
This E-Mail has been scanned for viruses.
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