Jeff, (01)
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. (02)
Ian (03)
Begin forwarded message: (04)
> 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 (05)
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