I want some solid real world examples!

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I want some solid real world examples!

sridevi polavaram
Hello All,
 Please help me find an answer to my questions. I suppose some of you might
also have the same questions. so let's brainstorm. I totally understand what
ontology is theoretically, and how tools like protege helping to build them.
But i still can't get a vision for how and where exactly these ontologies
are used in the real world. Are there any solid examples in any field like
biomedical, engineering, etc. that actually shared ontologies and helped to
setup a knowldge based systems? let's say i have build an ontology for
"desiging a car" now so what? what's next? who is ready to share this
onology with me? people differ in their opinions? how am i exactly
benefiting form this? I want an answer that can justify that my time and
energy spend on this is worthy.
please help me with this, i believe in this philosophy of ontologies but i
am having touble to reason out things to myself...I know about UNSPSC,
SNOMED, etc., but i want to actually test something handson!!
Thanks
Sri


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Re: I want some solid real world examples!

Mícheál Mac_an_Airchinnigh


On 17 Jul 2006, at 16:52, sridevi polavaram wrote:

> Hello All,
>  Please help me find an answer to my questions. I suppose some of  
> you might
> also have the same questions. so let's brainstorm. I totally  
> understand what
> ontology is theoretically, and how tools like protege helping to  
> build them.
> But i still can't get a vision for how and where exactly these  
> ontologies
> are used in the real world. Are there any solid examples in any  
> field like
> biomedical, engineering, etc. that actually shared ontologies and  
> helped to
> setup a knowldge based systems? let's say i have build an ontology for
> "desiging a car" now so what? what's next? who is ready to share this
> onology with me? people differ in their opinions? how am i exactly
> benefiting form this? I want an answer that can justify that my  
> time and
> energy spend on this is worthy.
> please help me with this, i believe in this philosophy of  
> ontologies but i
> am having touble to reason out things to myself...I know about UNSPSC,
> SNOMED, etc., but i want to actually test something handson!!
> Thanks
> Sri
===
In Computing we use "language" such as "car", "design",
and then "colourOf" car, "race of" buyer.
Computer does not understand such stuff.
Humans need to interpret EVERYTHING!

Databases alreay use these same "names/labels".
Humans need to interpret consequences of what they QUERY of DATABASES.

Ontology binds Names/Labels to reality.

What is a Car?
Explain this, if you can, to a computer?

Well, did you do it?

This is exactly what we do with an Ontology.
To tell a computer what exactly it is that a car is!
A database can not ever do this.

But my friend, you are lucky and fortunate,

you have asked the right question,
and there are others more informed that I who shall explain further  
and better.

Mihal Orel

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Re: I want some solid real world examples!

Alan March
In reply to this post by sridevi polavaram

 Hi Sri.

I am presently using an ontology-based approach to reorganize the list of
Diagnostic and Therapeutic Procedures for a major HMO here in Argentina. I
had to resort to ontologies 'cause all available "solutions" failed to
fullfill our requirements, including apparently sophisticated devices such
as SNOMED or UMLS (not to mention CPT or others, which are completely
useless for our requirements.

In that sense, I find that ontologies are "the" techique for design,
development and maintaince of so-called controlled terminologies. OF course,
in the process of using ontologies one quickly realizes the fact that they
could probably be usefull for analysis and design of complex systems, and I
personally feel that they could ultimately replace other tools such as UML
and the like. This, of course (and at least as far as my comprehension
goes), still requires much work regarding methodology and probably software
tools. But I feel that there is more to ontologies than what meets the eye
of the casual user. Example: I've been following developments in HL7 v3 and
am every day more convinced that v3 should be redesigned using readily
available tools such as Protégé (I don't think it shoud be thrown away as
others have suggestes, as the RIM contains a lot of useful domain
information, but the methodolgy user does not seem adequate).

So, I personally feel that ontologies and Protégé-type tools could turn out
to be a small revolution in systems design. Should my idea prove right, we
are now in a sort of pre-paradigmatic situation as far as application of
ontologies is concerened.

Best regards

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf
> Of sridevi polavaram
> Sent: Monday, July 17, 2006 12:52 PM
> To: [hidden email]
> Subject: [protege-discussion] I want some solid real world examples!
>
> Hello All,
>  Please help me find an answer to my questions. I suppose
> some of you might also have the same questions. so let's
> brainstorm. I totally understand what ontology is

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Re: I want some solid real world examples!

Raza-2
In reply to this post by sridevi polavaram
Hi Protege World!

This is  a great question/challenge.  I have been struggling with it for 4 years and successfully sunk a venture called Ontologent, that solved the problem of network management automation.  Subsequently me and my partner were able to deploy ontology/RDF derived content management at 2 mobile operators but really it was an RDF extension and that cannot qualify as a solution to Sridevi's dilema.

My hunch is that beyond the ontologies and RDF framework we need to create 'intelligent objects' (IO) (for sake of a better term) to really put this to practical use.  The IOs can have two classes.  One with independent self governed intelligence. Second with co-opted, interdependent intelligence.  Pratically this will provide an information and control mechanism to put ontologies to practical use.

Example: Human Mind Ontology: Mind, Sub-categories, relationships, mind activities.
Practical Use: Human Consciousness Research.
Ontology Use:  Systems approach to input and output prediction of the human mind in sensory response for unique and aggregated consciousness, including sight, smell, feel but also, emotion and intellect.

While mind research may be a far fetched idea, but the the same applies to creating input-output relationships in other complex systems, including, economics, network management, data storage, content management,  product management.

A good suggestion in my mind will be to look at Ontologies in Sense and Respond models.  I believe Caltech has public code for S&R systems.  


Good luck, and please do keep me posted if you find any success and also if you are available to join an  source practical ontology apps project.  I am trying get this community started.
Best of luck

Haider

sridevi polavaram <[hidden email]> wrote: Hello All,
 Please help me find an answer to my questions. I suppose some of you might
also have the same questions. so let's brainstorm. I totally understand what
ontology is theoretically, and how tools like protege helping to build them.
But i still can't get a vision for how and where exactly these ontologies
are used in the real world. Are there any solid examples in any field like
biomedical, engineering, etc. that actually shared ontologies and helped to
setup a knowldge based systems? let's say i have build an ontology for
"desiging a car" now so what? what's next? who is ready to share this
onology with me? people differ in their opinions? how am i exactly
benefiting form this? I want an answer that can justify that my time and
energy spend on this is worthy.
please help me with this, i believe in this philosophy of ontologies but i
am having touble to reason out things to myself...I know about UNSPSC,
SNOMED, etc., but i want to actually test something handson!!
Thanks
Sri


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Re: I want some solid real world examples!

Safran, Tracy (NIH/NCI) [C]
In reply to this post by sridevi polavaram

Please check out the following sites:
http://ncicb.nci.nih.gov/NCICB/infrastructure/cacore_overview/vocabulary

https://cabig.nci.nih.gov/inventory/Infrastructure/document_view

These describe how the National Cancer Institute is using controlled
vocabulary to build a data exchange network for cancer research.


Tracy M. Safran
Contractor - SAIC Frederick
caLIMS, EVS support
301-402-1537

-----Original Message-----
From: sridevi polavaram [mailto:[hidden email]]
Sent: Monday, July 17, 2006 11:52 AM
To: [hidden email]
Subject: [protege-discussion] I want some solid real world examples!

Hello All,
 Please help me find an answer to my questions. I suppose some of you
might also have the same questions. so let's brainstorm. I totally
understand what ontology is theoretically, and how tools like protege
helping to build them.
But i still can't get a vision for how and where exactly these
ontologies are used in the real world. Are there any solid examples in
any field like biomedical, engineering, etc. that actually shared
ontologies and helped to setup a knowldge based systems? let's say i
have build an ontology for "desiging a car" now so what? what's next?
who is ready to share this onology with me? people differ in their
opinions? how am i exactly benefiting form this? I want an answer that
can justify that my time and energy spend on this is worthy.
please help me with this, i believe in this philosophy of ontologies but
i am having touble to reason out things to myself...I know about UNSPSC,
SNOMED, etc., but i want to actually test something handson!!
Thanks
Sri


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Re: I want some solid real world examples!

sridevi polavaram
In reply to this post by Mícheál Mac_an_Airchinnigh
that's what the object oriented design principle says and that's how we have
been programming in JAva, C++ etc.. ofcourse the databases are intelligently
populated via these OOP methods only. a RDBMS is also by itself represents a
concept. so how different is ontology from this!! once again i insists that
I totally understand the theoritical standpoint of ontologies all i want is
some compelling examples!! if i an ignorant of something please help me
understand!


On 7/17/06, Mícheál Mac_an_Airchinnigh <[hidden email]> wrote:

>
>
>
> On 17 Jul 2006, at 16:52, sridevi polavaram wrote:
>
> > Hello All,
> >  Please help me find an answer to my questions. I suppose some of
> > you might
> > also have the same questions. so let's brainstorm. I totally
> > understand what
> > ontology is theoretically, and how tools like protege helping to
> > build them.
> > But i still can't get a vision for how and where exactly these
> > ontologies
> > are used in the real world. Are there any solid examples in any
> > field like
> > biomedical, engineering, etc. that actually shared ontologies and
> > helped to
> > setup a knowldge based systems? let's say i have build an ontology for
> > "desiging a car" now so what? what's next? who is ready to share this
> > onology with me? people differ in their opinions? how am i exactly
> > benefiting form this? I want an answer that can justify that my
> > time and
> > energy spend on this is worthy.
> > please help me with this, i believe in this philosophy of
> > ontologies but i
> > am having touble to reason out things to myself...I know about UNSPSC,
> > SNOMED, etc., but i want to actually test something handson!!
> > Thanks
> > Sri
> ===
> In Computing we use "language" such as "car", "design",
> and then "colourOf" car, "race of" buyer.
> Computer does not understand such stuff.
> Humans need to interpret EVERYTHING!
>
> Databases alreay use these same "names/labels".
> Humans need to interpret consequences of what they QUERY of DATABASES.
>
> Ontology binds Names/Labels to reality.
>
> What is a Car?
> Explain this, if you can, to a computer?
>
> Well, did you do it?
>
> This is exactly what we do with an Ontology.
> To tell a computer what exactly it is that a car is!
> A database can not ever do this.
>
> But my friend, you are lucky and fortunate,
>
> you have asked the right question,
> and there are others more informed that I who shall explain further
> and better.
>
> Mihal Orel
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

Mícheál Mac_an_Airchinnigh-2


On 17 Jul 2006, at 18:02, sridevi polavaram wrote:

> that's what the object oriented design principle says and that's  
> how we have
> been programming in JAva, C++ etc.. ofcourse the databases are  
> intelligently
> populated via these OOP methods only. a RDBMS is also by itself  
> represents a
> concept. so how different is ontology from this!! once again i  
> insists that
> I totally understand the theoritical standpoint of ontologies all i  
> want is
> some compelling examples!! if i an ignorant of something please  
> help me
> understand!
>
>
===
Hi!

Good question!

You know too much technology :)

You need to strip down to foundations of Ontology.

I use Sowa; I begin with 12 concepts,
(I think Aristotle had fewer)

You can read about my personal struggle at

http://web.mac.com/micheal1/iWeb/Site/Blog/Blog.html

Best wishes and kind regards and thanks for all the questions

Mícheál
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Re: I want some solid real world examples!

sridevi polavaram
In reply to this post by Alan March
On 7/17/06, Alan March <[hidden email]> wrote:

>
>
> Hi Sri.
>
> I am presently using an ontology-based approach to reorganize the list of
> Diagnostic and Therapeutic Procedures for a major HMO here in Argentina. I
> had to resort to ontologies 'cause all available "solutions" failed to
> fullfill our requirements, including apparently sophisticated devices such
> as SNOMED or UMLS (not to mention CPT or others, which are completely
> useless for our requirements.


> Wow SNOMED and UMLS are supposingly success stories for ontology
applications. and they failed to mee your requirements!!
then the whole point of "sharing knowldge" seems skeptical. So are u
designing ontologies from scratch for your HMO application! everyone is
apparently having there own ontology

In that sense, I find that ontologies are "the" techique for design,
> development and maintaince of so-called controlled terminologies.


> yes, i would say, that even i am convinced that at the level of
vocabularies. like a dictionary sort of thing. the wikipedia for
encyclopedia also uses ontologies!!
Thanks a lot for giving me some idea about the real workd scenario.
Best,
-Sri

OF course,

> in the process of using ontologies one quickly realizes the fact that they
> could probably be usefull for analysis and design of complex systems, and
> I
> personally feel that they could ultimately replace other tools such as UML
> and the like. This, of course (and at least as far as my comprehension
> goes), still requires much work regarding methodology and probably
> software
> tools. But I feel that there is more to ontologies than what meets the eye
> of the casual user. Example: I've been following developments in HL7 v3
> and
> am every day more convinced that v3 should be redesigned using readily
> available tools such as Protégé (I don't think it shoud be thrown away as
> others have suggestes, as the RIM contains a lot of useful domain
> information, but the methodolgy user does not seem adequate).
>
> So, I personally feel that ontologies and Protégé-type tools could turn
> out
> to be a small revolution in systems design. Should my idea prove right, we
> are now in a sort of pre-paradigmatic situation as far as application of
> ontologies is concerened.
>
> Best regards
>
> > -----Original Message-----
> > From: [hidden email]
> > [mailto:[hidden email]] On Behalf
> > Of sridevi polavaram
> > Sent: Monday, July 17, 2006 12:52 PM
> > To: [hidden email]
> > Subject: [protege-discussion] I want some solid real world examples!
> >
> > Hello All,
> >  Please help me find an answer to my questions. I suppose
> > some of you might also have the same questions. so let's
> > brainstorm. I totally understand what ontology is
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

sridevi polavaram
In reply to this post by Mícheál Mac_an_Airchinnigh-2
Thanks for the blog...for the first glance everything went right above my
head.

On 7/17/06, Mícheál Mac_an_Airchinnigh <[hidden email]> wrote:

>
>
>
> On 17 Jul 2006, at 18:02, sridevi polavaram wrote:
>
> > that's what the object oriented design principle says and that's
> > how we have
> > been programming in JAva, C++ etc.. ofcourse the databases are
> > intelligently
> > populated via these OOP methods only. a RDBMS is also by itself
> > represents a
> > concept. so how different is ontology from this!! once again i
> > insists that
> > I totally understand the theoritical standpoint of ontologies all i
> > want is
> > some compelling examples!! if i an ignorant of something please
> > help me
> > understand!
> >
> >
> ===
> Hi!
>
> Good question!
>
> You know too much technology :)
>
> You need to strip down to foundations of Ontology.
>
> I use Sowa; I begin with 12 concepts,
> (I think Aristotle had fewer)
>
> You can read about my personal struggle at
>
> http://web.mac.com/micheal1/iWeb/Site/Blog/Blog.html
>
> Best wishes and kind regards and thanks for all the questions
>
> Mícheál
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

Alan March
In reply to this post by sridevi polavaram

> > Wow SNOMED and UMLS are supposingly success stories for ontology
> applications. and they failed to mee your requirements!!
> then the whole point of "sharing knowldge" seems skeptical.
> So are u designing ontologies from scratch for your HMO
> application! everyone is apparently having there own ontology

The trouble we faced with SNOMED and UMLS is they appeared to us as
incomplete as far as attributes (relations) are concerned: too few, failing
to capture the richness of possible relations. And then of course, the
mistakes found in them, which Barry Smith and others have mentioned in their
papers. Also, much of the terms we had to use were highly local and neither
SNOMED nor UMLS offered a clear method for extensions. Although SNOMED has
something on those lines, the problem of its "ontological incompleteness"
and licensing questions represented a drawback for us. But then again: both
SNOMED and UMLS have been extremely usefull to us as a sort of knowledge
repositories, but we just could not use them "out-of-the-box".

Actually, we didn't start from scratch: we reutilized much of the publically
available Galen files, and modelled our ontology following an upper level
ontology. For anatomy we used Digital Anatomist as published in UMLS. We
tried to use as much as possible from several ontologies we found to be
suitable to our purposes. But yes, we had to reinvent the wheel in some
circumstances. In any case, I am not quite sure if we will ever manage to
arrive at a universally accepted ontology. Probably at the upper and middle
levels this will be achieved, but I doubt it will work for "bottom" levels.

Regarding success stories: well, I guess SNOMED is a success story in a
certain sense, but I am not quite sure if it can be called that way as far
as ontological principles are concerned. Not to deny its value: it is rich
in content. Worth mentioning is the fact that we didn't want to consider
terminologies which weren't in the public domain or commercial in nature. I
personally feel that medical terminologies such be built in a collaborative
manner, probable on the same lines as Linux was made (by having different
groups managing different parts of the domain). In that sense, I feel that
Rector's advice regarding the way ontologies should be built (by
"untangling") allows for this. I am relly sorry that the Galen project
didn't continue. Looking back on it, I think it is still the best thing we
have seen in all these decades of discussion on terminologies and how they
should be built and maintained.

>
> In that sense, I find that ontologies are "the" techique for design,
> > development and maintaince of so-called controlled terminologies.
>
>
> > yes, i would say, that even i am convinced that at the level of
> vocabularies. like a dictionary sort of thing. the wikipedia
> for encyclopedia also uses ontologies!!
> Thanks a lot for giving me some idea about the real workd scenario.
> Best,
> -Sri
>
> OF course,
> > in the process of using ontologies one quickly realizes the
> fact that
> > they could probably be usefull for analysis and design of complex
> > systems, and I personally feel that they could ultimately replace
> > other tools such as UML and the like. This, of course (and
> at least as
> > far as my comprehension goes), still requires much work regarding
> > methodology and probably software tools. But I feel that
> there is more
> > to ontologies than what meets the eye of the casual user. Example:
> > I've been following developments in HL7 v3 and am every day more
> > convinced that v3 should be redesigned using readily
> available tools
> > such as Protégé (I don't think it shoud be thrown away as
> others have
> > suggestes, as the RIM contains a lot of useful domain
> information, but
> > the methodolgy user does not seem adequate).
> >
> > So, I personally feel that ontologies and Protégé-type tools could
> > turn out to be a small revolution in systems design. Should my idea
> > prove right, we are now in a sort of pre-paradigmatic
> situation as far
> > as application of ontologies is concerened.
> >
> > Best regards
> >
> > > -----Original Message-----
> > > From: [hidden email]
> > > [mailto:[hidden email]] On Behalf Of
> > > sridevi polavaram
> > > Sent: Monday, July 17, 2006 12:52 PM
> > > To: [hidden email]
> > > Subject: [protege-discussion] I want some solid real
> world examples!
> > >
> > > Hello All,
> > >  Please help me find an answer to my questions. I suppose some of
> > > you might also have the same questions. so let's brainstorm. I
> > > totally understand what ontology is
> >
> >
> ----------------------------------------------------------------------
> > --- To unsubscribe go to
> > http://protege.stanford.edu/community/subscribe.html
> >
> >
>
> --------------------------------------------------------------
> -----------
> To unsubscribe go to
> http://protege.stanford.edu/community/subscribe.html
>

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Re: I want some solid real world examples!

Jennifer Vendetti-2
In reply to this post by sridevi polavaram

We have a section in the Protege Wiki entitled "Projects That Use Protege":

http://protege.cim3.net/cgi-bin/wiki.pl?ProjectsThatUseProtege

There is a lot of content there, but if you have some time to look
through it, you may find some useful examples.

Jennifer

sridevi polavaram wrote:

>Hello All,
> Please help me find an answer to my questions. I suppose some of you might
>also have the same questions. so let's brainstorm. I totally understand what
>ontology is theoretically, and how tools like protege helping to build them.
>But i still can't get a vision for how and where exactly these ontologies
>are used in the real world. Are there any solid examples in any field like
>biomedical, engineering, etc. that actually shared ontologies and helped to
>setup a knowldge based systems? let's say i have build an ontology for
>"desiging a car" now so what? what's next? who is ready to share this
>onology with me? people differ in their opinions? how am i exactly
>benefiting form this? I want an answer that can justify that my time and
>energy spend on this is worthy.
>please help me with this, i believe in this philosophy of ontologies but i
>am having touble to reason out things to myself...I know about UNSPSC,
>SNOMED, etc., but i want to actually test something handson!!
>Thanks
>Sri
>
>
>-------------------------------------------------------------------------
>To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>  
>
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Re: I want some solid real world examples!

Biswanath Dutta
In reply to this post by sridevi polavaram
Hi,
   In short I can tell you, please go through the articles written on
Semantic Web Services. The moto is to convert the already exting web
services to Semantic Web based information services. But for that again you
have to create service ontology using some services ontology language (e.g.
OWL-S). Basically, for example using OWL we use to describe our domain
knowledge. So now we need also to describe our services using some ontology
language, like OWL-S. Once you have both the ontology you will be able to
generate Semantic Web services using some tool.

/Biswanath




On 7/17/06, sridevi polavaram <[hidden email]> wrote:

>
> Hello All,
> Please help me find an answer to my questions. I suppose some of you might
> also have the same questions. so let's brainstorm. I totally understand
> what
> ontology is theoretically, and how tools like protege helping to build
> them.
> But i still can't get a vision for how and where exactly these ontologies
> are used in the real world. Are there any solid examples in any field like
> biomedical, engineering, etc. that actually shared ontologies and helped
> to
> setup a knowldge based systems? let's say i have build an ontology for
> "desiging a car" now so what? what's next? who is ready to share this
> onology with me? people differ in their opinions? how am i exactly
> benefiting form this? I want an answer that can justify that my time and
> energy spend on this is worthy.
> please help me with this, i believe in this philosophy of ontologies but i
> am having touble to reason out things to myself...I know about UNSPSC,
> SNOMED, etc., but i want to actually test something handson!!
> Thanks
> Sri
>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>


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How to write a tab widget plug-in?

baishali chanda
 
  I am facing some difficulty to follow the example  to create a sample plugin.
 
http://protege.stanford.edu/doc/pdk/plugins/tab_widget.html
   
  1.Download the source code: I have downloaded FrameCounter.java. There are several other source files. Do I need to download all of them to create the tabwidget plugin?
   
  2. I have compiled the code using following batch file
   
  javac -classpath C:\myWork\protege\protege.jar;C:\myWork\protege\looks.jar;C:\myWork\protege\unicode_panel.jar;. FrameCounter.java
   
  What I do not understand from the Stanford website why do I need to define a
  Dprotege.dir=<protege_install_dir>. if I plan to compile the code using the above syntax.
   
  3. Okay for me.
   
  4. "Run the example from your development environment, specifying edu.stanford.smi.protege.Application as the main class.
  How the Application is created here?
   
   

 
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Re: I want some solid real world examples!

Dimitra Alexopoulou
In reply to this post by sridevi polavaram

> Hello All,
>  Please help me find an answer to my questions. I suppose some of you
> might
> also have the same questions. so let's brainstorm. I totally understand
> what
> ontology is theoretically, and how tools like protege helping to build
> them.
> But i still can't get a vision for how and where exactly these ontologies
> are used in the real world. Are there any solid examples in any field like
> biomedical, engineering, etc. that actually shared ontologies and helped
> to
> setup a knowldge based systems? let's say i have build an ontology for
> "desiging a car" now so what? what's next? who is ready to share this
> onology with me? people differ in their opinions? how am i exactly
> benefiting form this? I want an answer that can justify that my time and
> energy spend on this is worthy.
> please help me with this, i believe in this philosophy of ontologies but i
> am having touble to reason out things to myself...I know about UNSPSC,
> SNOMED, etc., but i want to actually test something handson!!
> Thanks
> Sri

>
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

Hello Sri,

You might want to try GoPubMed:

http://gopubmed.org/

It uses the Gene Ontology to search for biomedical literature in PubMed.
Your query is submitted to PubMed and the resulting abstracts are
classified using Gene Ontology terms.

regards,
Dimitra

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Re: How to write a tab widget plug-in?

John Paulett
In reply to this post by baishali chanda

I recently just made a tab plugin, I found the most important (and
easiest to mess up) part was getting the directory structure correct.  I
used Eclipse to compile everything, but you should be ok just using
javac.  See below for individual answers

baishali chanda wrote:
>
> I am facing some difficulty to follow the example  to create a sample
> plugin.
>
> http://protege.stanford.edu/doc/pdk/plugins/tab_widget.html
>
> 1.Download the source code: I have downloaded FrameCounter.java.
> There are several other source files. Do I need to download all of
> them to create the tabwidget plugin?
Those other files are other examples for other types of plugins.  You
don't need to worry about them.  If you do don't compile those other
examples, I would delete their entry from the manifest.mf file (make
sure this file still has the correct whitespace..there should be a few
lines at the end of just linefeeds)

> 2. I have compiled the code using following batch file
>
> javac -classpath
> C:\myWork\protege\protege.jar;C:\myWork\protege\looks.jar;C:\myWork\protege\unicode_panel.jar;.
> FrameCounter.java
Now make sure that the class files are in the plugin directory
<protege_install_dir>
  plugins
     examples
        tabwidget
          <class files>
     meta-inf
        manifest.mf
Also make sure the meta-inf dir is in the plugin dir--with the
manifest.mf file

> What I do not understand from the Stanford website why do I need to
> define a Dprotege.dir=<protege_install_dir>. if I plan to compile the
> code using the above syntax.
I didn't bother doing this, and didn't have any problems.

> 3. Okay for me.


> 4. "Run the example from your development environment, specifying
> edu.stanford.smi.protege.Application as the main class. How the
> Application is created here?
This should just launch Protege.  However, you do not need to worry
about this if you just launch Protege as you normally do.  Once you open
protege go to Project->Configure and select your plugin.  If you don't
see it in the list, I would check your directory structure and your
manifest.mf.

>
>
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Re: I want some solid real world examples!

sridevi polavaram
In reply to this post by Alan March
Alan,
 Thankyou very much for explaining things so patiently. So, how exactly are
you using the ontology that you have tailored for your purpose at the
application level? are you mapping the ontology properties as attributes at
the database-level? if so, what are the other kinds of mapping that u do?
are u using any logic based programming languages? How is the rich
annotation that's inherent in ontologies is helping you at the application
level, apart from the fact that it serves as a reinforcement knowldge base
for humans. how are you extracting and storing information using
ontologies?  can you say that ontology is crucial for your application and
that it's not replacable by any other design methodologies.
I am sorry but my mind is full of questions...just can't stop the flow..i am
reading all the related literature that's available (white papers, tools,
theroies, real examples, technology etc.,) but none of them help me converge
my understanding.
-regards,
Sri

On 7/17/06, Alan March <[hidden email]> wrote:

>
>
> > > Wow SNOMED and UMLS are supposingly success stories for ontology
> > applications. and they failed to mee your requirements!!
> > then the whole point of "sharing knowldge" seems skeptical.
> > So are u designing ontologies from scratch for your HMO
> > application! everyone is apparently having there own ontology
>
> The trouble we faced with SNOMED and UMLS is they appeared to us as
> incomplete as far as attributes (relations) are concerned: too few,
> failing
> to capture the richness of possible relations. And then of course, the
> mistakes found in them, which Barry Smith and others have mentioned in
> their
> papers. Also, much of the terms we had to use were highly local and
> neither
> SNOMED nor UMLS offered a clear method for extensions. Although SNOMED has
> something on those lines, the problem of its "ontological incompleteness"
> and licensing questions represented a drawback for us. But then again:
> both
> SNOMED and UMLS have been extremely usefull to us as a sort of knowledge
> repositories, but we just could not use them "out-of-the-box".
>
> Actually, we didn't start from scratch: we reutilized much of the
> publically
> available Galen files, and modelled our ontology following an upper level
> ontology. For anatomy we used Digital Anatomist as published in UMLS. We
> tried to use as much as possible from several ontologies we found to be
> suitable to our purposes. But yes, we had to reinvent the wheel in some
> circumstances. In any case, I am not quite sure if we will ever manage to
> arrive at a universally accepted ontology. Probably at the upper and
> middle
> levels this will be achieved, but I doubt it will work for "bottom"
> levels.
>
> Regarding success stories: well, I guess SNOMED is a success story in a
> certain sense, but I am not quite sure if it can be called that way as far
> as ontological principles are concerned. Not to deny its value: it is rich
> in content. Worth mentioning is the fact that we didn't want to consider
> terminologies which weren't in the public domain or commercial in nature.
> I
> personally feel that medical terminologies such be built in a
> collaborative
> manner, probable on the same lines as Linux was made (by having different
> groups managing different parts of the domain). In that sense, I feel that
> Rector's advice regarding the way ontologies should be built (by
> "untangling") allows for this. I am relly sorry that the Galen project
> didn't continue. Looking back on it, I think it is still the best thing we
> have seen in all these decades of discussion on terminologies and how they
> should be built and maintained.
>
> >
> > In that sense, I find that ontologies are "the" techique for design,
> > > development and maintaince of so-called controlled terminologies.
> >
> >
> > > yes, i would say, that even i am convinced that at the level of
> > vocabularies. like a dictionary sort of thing. the wikipedia
> > for encyclopedia also uses ontologies!!
> > Thanks a lot for giving me some idea about the real workd scenario.
> > Best,
> > -Sri
> >
> > OF course,
> > > in the process of using ontologies one quickly realizes the
> > fact that
> > > they could probably be usefull for analysis and design of complex
> > > systems, and I personally feel that they could ultimately replace
> > > other tools such as UML and the like. This, of course (and
> > at least as
> > > far as my comprehension goes), still requires much work regarding
> > > methodology and probably software tools. But I feel that
> > there is more
> > > to ontologies than what meets the eye of the casual user. Example:
> > > I've been following developments in HL7 v3 and am every day more
> > > convinced that v3 should be redesigned using readily
> > available tools
> > > such as Protégé (I don't think it shoud be thrown away as
> > others have
> > > suggestes, as the RIM contains a lot of useful domain
> > information, but
> > > the methodolgy user does not seem adequate).
> > >
> > > So, I personally feel that ontologies and Protégé-type tools could
> > > turn out to be a small revolution in systems design. Should my idea
> > > prove right, we are now in a sort of pre-paradigmatic
> > situation as far
> > > as application of ontologies is concerened.
> > >
> > > Best regards
> > >
> > > > -----Original Message-----
> > > > From: [hidden email]
> > > > [mailto:[hidden email]] On Behalf Of
> > > > sridevi polavaram
> > > > Sent: Monday, July 17, 2006 12:52 PM
> > > > To: [hidden email]
> > > > Subject: [protege-discussion] I want some solid real
> > world examples!
> > > >
> > > > Hello All,
> > > >  Please help me find an answer to my questions. I suppose some of
> > > > you might also have the same questions. so let's brainstorm. I
> > > > totally understand what ontology is
> > >
> > >
> > ----------------------------------------------------------------------
> > > --- To unsubscribe go to
> > > http://protege.stanford.edu/community/subscribe.html
> > >
> > >
> >
> > --------------------------------------------------------------
> > -----------
> > To unsubscribe go to
> > http://protege.stanford.edu/community/subscribe.html
> >
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

Alan March

Well, one of the first problems we run into is OWL itself. Although it is
very powefull in expressivity, we believe it is not efficient as a storage
and retrieval repository (indeed, it was probably not designed with
efficiency in mind, and in that sense it reminds me of my old Prolog days).
So we used the JDBC database backend. The database backend is not that
efficient in itself (and, again, its creators mention in the documentation
that efficiency was not one of their requirements) but it is extremely
elastic. Stated simply, the DB backend is a (sort of) adjacency list with
the particularly interesting characteristic that the list is double linked.
From what I gather, one important difference with the pure RDF approach is
that nodes are loaded on demand, and there is a slight performance issue
there, but then, it allows for managing large ontologies. So all design is
managed using Protégé as the front-end.

The advantage of the database backend is that it makes all the elements of
the ontology easily accesible for other applications when these applications
aren't involved with the design task itself. Example: the multiple
classifications built by reasoners such as Fact++ may be accessed from web
pages and applications using simple approaches such as treeviews and the
like, according to user's different classification requirements (a CFO is
interested if a cost based classification of procedures, whilst a chief
medical officer is interested in a body systems classification of
procedures). Another example: extracting dimensions for a warehouse. And of
course there are more.

Most of these tasks are carried out by writing queries to the database. We
use stored procedures, which are included in the same database  that
contains the main "RDF" table. The pattern generally used is a self linked
table for accessing the adjacency list schema

Don't know how much "state of the art" this is, but it works for us.

Regards,

AM

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf
> Of sridevi polavaram
> Sent: Tuesday, July 18, 2006 9:35 AM
> To: [hidden email]
> Subject: [protege-discussion] Re: I want some solid real
> world examples!
>
> Alan,
>  Thankyou very much for explaining things so patiently. So,
> how exactly are you using the ontology that you have tailored
> for your purpose at the application level? are you mapping
> the ontology properties as attributes at the database-level?
> if so, what are the other kinds of mapping that u do?
> are u using any logic based programming languages? How is the
> rich annotation that's inherent in ontologies is helping you
> at the application level, apart from the fact that it serves
> as a reinforcement knowldge base for humans. how are you
> extracting and storing information using ontologies?  can you
> say that ontology is crucial for your application and that
> it's not replacable by any other design methodologies.
> I am sorry but my mind is full of questions...just can't stop
> the flow..i am reading all the related literature that's
> available (white papers, tools, theroies, real examples,
> technology etc.,) but none of them help me converge my understanding.
> -regards,
> Sri
>
> On 7/17/06, Alan March <[hidden email]> wrote:
> >
> >
> > > > Wow SNOMED and UMLS are supposingly success stories for ontology
> > > applications. and they failed to mee your requirements!!
> > > then the whole point of "sharing knowldge" seems skeptical.
> > > So are u designing ontologies from scratch for your HMO
> application!
> > > everyone is apparently having there own ontology
> >
> > The trouble we faced with SNOMED and UMLS is they appeared to us as
> > incomplete as far as attributes (relations) are concerned: too few,
> > failing to capture the richness of possible relations. And then of
> > course, the mistakes found in them, which Barry Smith and
> others have
> > mentioned in their papers. Also, much of the terms we had
> to use were
> > highly local and neither SNOMED nor UMLS offered a clear method for
> > extensions. Although SNOMED has something on those lines,
> the problem
> > of its "ontological incompleteness"
> > and licensing questions represented a drawback for us. But
> then again:
> > both
> > SNOMED and UMLS have been extremely usefull to us as a sort of
> > knowledge repositories, but we just could not use them
> "out-of-the-box".
> >
> > Actually, we didn't start from scratch: we reutilized much of the
> > publically available Galen files, and modelled our ontology
> following
> > an upper level ontology. For anatomy we used Digital Anatomist as
> > published in UMLS. We tried to use as much as possible from several
> > ontologies we found to be suitable to our purposes. But
> yes, we had to
> > reinvent the wheel in some circumstances. In any case, I am
> not quite
> > sure if we will ever manage to arrive at a universally accepted
> > ontology. Probably at the upper and middle levels this will be
> > achieved, but I doubt it will work for "bottom"
> > levels.
> >
> > Regarding success stories: well, I guess SNOMED is a
> success story in
> > a certain sense, but I am not quite sure if it can be
> called that way
> > as far as ontological principles are concerned. Not to deny
> its value:
> > it is rich in content. Worth mentioning is the fact that we didn't
> > want to consider terminologies which weren't in the public
> domain or commercial in nature.
> > I
> > personally feel that medical terminologies such be built in a
> > collaborative manner, probable on the same lines as Linux
> was made (by
> > having different groups managing different parts of the domain). In
> > that sense, I feel that Rector's advice regarding the way
> ontologies
> > should be built (by
> > "untangling") allows for this. I am relly sorry that the
> Galen project
> > didn't continue. Looking back on it, I think it is still the best
> > thing we have seen in all these decades of discussion on
> terminologies
> > and how they should be built and maintained.
> >
> > >
> > > In that sense, I find that ontologies are "the" techique
> for design,
> > > > development and maintaince of so-called controlled
> terminologies.
> > >
> > >
> > > > yes, i would say, that even i am convinced that at the level of
> > > vocabularies. like a dictionary sort of thing. the wikipedia for
> > > encyclopedia also uses ontologies!!
> > > Thanks a lot for giving me some idea about the real workd
> scenario.
> > > Best,
> > > -Sri
> > >
> > > OF course,
> > > > in the process of using ontologies one quickly realizes the
> > > fact that
> > > > they could probably be usefull for analysis and design
> of complex
> > > > systems, and I personally feel that they could
> ultimately replace
> > > > other tools such as UML and the like. This, of course (and
> > > at least as
> > > > far as my comprehension goes), still requires much work
> regarding
> > > > methodology and probably software tools. But I feel that
> > > there is more
> > > > to ontologies than what meets the eye of the casual
> user. Example:
> > > > I've been following developments in HL7 v3 and am every
> day more
> > > > convinced that v3 should be redesigned using readily
> > > available tools
> > > > such as Protégé (I don't think it shoud be thrown away as
> > > others have
> > > > suggestes, as the RIM contains a lot of useful domain
> > > information, but
> > > > the methodolgy user does not seem adequate).
> > > >
> > > > So, I personally feel that ontologies and Protégé-type
> tools could
> > > > turn out to be a small revolution in systems design. Should my
> > > > idea prove right, we are now in a sort of pre-paradigmatic
> > > situation as far
> > > > as application of ontologies is concerened.
> > > >
> > > > Best regards
> > > >
> > > > > -----Original Message-----
> > > > > From: [hidden email]
> > > > > [mailto:[hidden email]]
> On Behalf Of
> > > > > sridevi polavaram
> > > > > Sent: Monday, July 17, 2006 12:52 PM
> > > > > To: [hidden email]
> > > > > Subject: [protege-discussion] I want some solid real
> > > world examples!
> > > > >
> > > > > Hello All,
> > > > >  Please help me find an answer to my questions. I
> suppose some
> > > > > of you might also have the same questions. so let's
> brainstorm.
> > > > > I totally understand what ontology is
> > > >
> > > >
> > >
> --------------------------------------------------------------------
> > > --
> > > > --- To unsubscribe go to
> > > > http://protege.stanford.edu/community/subscribe.html
> > > >
> > > >
> > >
> > > --------------------------------------------------------------
> > > -----------
> > > To unsubscribe go to
> > > http://protege.stanford.edu/community/subscribe.html
> > >
> >
> >
> ----------------------------------------------------------------------
> > --- To unsubscribe go to
> > http://protege.stanford.edu/community/subscribe.html
> >
> >
>
> --------------------------------------------------------------
> -----------
> To unsubscribe go to
> http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

sridevi polavaram
Alan,
when you say database backend, i am assuming it is some RDBMS like mysql,
oracle etc.,
but you are referring it as RDF table and a list structure! so what kind of
DB is this! can u maintain owl or RDF DBs!
what is the size limit of these DBs? and how exactly are you achieving data
storage and retrieval methods!
-regards,
Sri.

On 7/18/06, Alan March <[hidden email]> wrote:

>
>
> Well, one of the first problems we run into is OWL itself. Although it is
> very powefull in expressivity, we believe it is not efficient as a storage
> and retrieval repository (indeed, it was probably not designed with
> efficiency in mind, and in that sense it reminds me of my old Prolog
> days).
> So we used the JDBC database backend. The database backend is not that
> efficient in itself (and, again, its creators mention in the documentation
> that efficiency was not one of their requirements) but it is extremely
> elastic. Stated simply, the DB backend is a (sort of) adjacency list with
> the particularly interesting characteristic that the list is double
> linked.
> From what I gather, one important difference with the pure RDF approach is
> that nodes are loaded on demand, and there is a slight performance issue
> there, but then, it allows for managing large ontologies. So all design is
> managed using Protégé as the front-end.
>
> The advantage of the database backend is that it makes all the elements of
> the ontology easily accesible for other applications when these
> applications
> aren't involved with the design task itself. Example: the multiple
> classifications built by reasoners such as Fact++ may be accessed from web
> pages and applications using simple approaches such as treeviews and the
> like, according to user's different classification requirements (a CFO is
> interested if a cost based classification of procedures, whilst a chief
> medical officer is interested in a body systems classification of
> procedures). Another example: extracting dimensions for a warehouse. And
> of
> course there are more.
>
> Most of these tasks are carried out by writing queries to the database. We
> use stored procedures, which are included in the same database  that
> contains the main "RDF" table. The pattern generally used is a self linked
> table for accessing the adjacency list schema
>
> Don't know how much "state of the art" this is, but it works for us.
>
> Regards,
>
> AM
>
> > -----Original Message-----
> > From: [hidden email]
> > [mailto:[hidden email]] On Behalf
> > Of sridevi polavaram
> > Sent: Tuesday, July 18, 2006 9:35 AM
> > To: [hidden email]
> > Subject: [protege-discussion] Re: I want some solid real
> > world examples!
> >
> > Alan,
> >  Thankyou very much for explaining things so patiently. So,
> > how exactly are you using the ontology that you have tailored
> > for your purpose at the application level? are you mapping
> > the ontology properties as attributes at the database-level?
> > if so, what are the other kinds of mapping that u do?
> > are u using any logic based programming languages? How is the
> > rich annotation that's inherent in ontologies is helping you
> > at the application level, apart from the fact that it serves
> > as a reinforcement knowldge base for humans. how are you
> > extracting and storing information using ontologies?  can you
> > say that ontology is crucial for your application and that
> > it's not replacable by any other design methodologies.
> > I am sorry but my mind is full of questions...just can't stop
> > the flow..i am reading all the related literature that's
> > available (white papers, tools, theroies, real examples,
> > technology etc.,) but none of them help me converge my understanding.
> > -regards,
> > Sri
> >
> > On 7/17/06, Alan March <[hidden email]> wrote:
> > >
> > >
> > > > > Wow SNOMED and UMLS are supposingly success stories for ontology
> > > > applications. and they failed to mee your requirements!!
> > > > then the whole point of "sharing knowldge" seems skeptical.
> > > > So are u designing ontologies from scratch for your HMO
> > application!
> > > > everyone is apparently having there own ontology
> > >
> > > The trouble we faced with SNOMED and UMLS is they appeared to us as
> > > incomplete as far as attributes (relations) are concerned: too few,
> > > failing to capture the richness of possible relations. And then of
> > > course, the mistakes found in them, which Barry Smith and
> > others have
> > > mentioned in their papers. Also, much of the terms we had
> > to use were
> > > highly local and neither SNOMED nor UMLS offered a clear method for
> > > extensions. Although SNOMED has something on those lines,
> > the problem
> > > of its "ontological incompleteness"
> > > and licensing questions represented a drawback for us. But
> > then again:
> > > both
> > > SNOMED and UMLS have been extremely usefull to us as a sort of
> > > knowledge repositories, but we just could not use them
> > "out-of-the-box".
> > >
> > > Actually, we didn't start from scratch: we reutilized much of the
> > > publically available Galen files, and modelled our ontology
> > following
> > > an upper level ontology. For anatomy we used Digital Anatomist as
> > > published in UMLS. We tried to use as much as possible from several
> > > ontologies we found to be suitable to our purposes. But
> > yes, we had to
> > > reinvent the wheel in some circumstances. In any case, I am
> > not quite
> > > sure if we will ever manage to arrive at a universally accepted
> > > ontology. Probably at the upper and middle levels this will be
> > > achieved, but I doubt it will work for "bottom"
> > > levels.
> > >
> > > Regarding success stories: well, I guess SNOMED is a
> > success story in
> > > a certain sense, but I am not quite sure if it can be
> > called that way
> > > as far as ontological principles are concerned. Not to deny
> > its value:
> > > it is rich in content. Worth mentioning is the fact that we didn't
> > > want to consider terminologies which weren't in the public
> > domain or commercial in nature.
> > > I
> > > personally feel that medical terminologies such be built in a
> > > collaborative manner, probable on the same lines as Linux
> > was made (by
> > > having different groups managing different parts of the domain). In
> > > that sense, I feel that Rector's advice regarding the way
> > ontologies
> > > should be built (by
> > > "untangling") allows for this. I am relly sorry that the
> > Galen project
> > > didn't continue. Looking back on it, I think it is still the best
> > > thing we have seen in all these decades of discussion on
> > terminologies
> > > and how they should be built and maintained.
> > >
> > > >
> > > > In that sense, I find that ontologies are "the" techique
> > for design,
> > > > > development and maintaince of so-called controlled
> > terminologies.
> > > >
> > > >
> > > > > yes, i would say, that even i am convinced that at the level of
> > > > vocabularies. like a dictionary sort of thing. the wikipedia for
> > > > encyclopedia also uses ontologies!!
> > > > Thanks a lot for giving me some idea about the real workd
> > scenario.
> > > > Best,
> > > > -Sri
> > > >
> > > > OF course,
> > > > > in the process of using ontologies one quickly realizes the
> > > > fact that
> > > > > they could probably be usefull for analysis and design
> > of complex
> > > > > systems, and I personally feel that they could
> > ultimately replace
> > > > > other tools such as UML and the like. This, of course (and
> > > > at least as
> > > > > far as my comprehension goes), still requires much work
> > regarding
> > > > > methodology and probably software tools. But I feel that
> > > > there is more
> > > > > to ontologies than what meets the eye of the casual
> > user. Example:
> > > > > I've been following developments in HL7 v3 and am every
> > day more
> > > > > convinced that v3 should be redesigned using readily
> > > > available tools
> > > > > such as Protégé (I don't think it shoud be thrown away as
> > > > others have
> > > > > suggestes, as the RIM contains a lot of useful domain
> > > > information, but
> > > > > the methodolgy user does not seem adequate).
> > > > >
> > > > > So, I personally feel that ontologies and Protégé-type
> > tools could
> > > > > turn out to be a small revolution in systems design. Should my
> > > > > idea prove right, we are now in a sort of pre-paradigmatic
> > > > situation as far
> > > > > as application of ontologies is concerened.
> > > > >
> > > > > Best regards
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: [hidden email]
> > > > > > [mailto:[hidden email]]
> > On Behalf Of
> > > > > > sridevi polavaram
> > > > > > Sent: Monday, July 17, 2006 12:52 PM
> > > > > > To: [hidden email]
> > > > > > Subject: [protege-discussion] I want some solid real
> > > > world examples!
> > > > > >
> > > > > > Hello All,
> > > > > >  Please help me find an answer to my questions. I
> > suppose some
> > > > > > of you might also have the same questions. so let's
> > brainstorm.
> > > > > > I totally understand what ontology is
> > > > >
> > > > >
> > > >
> > --------------------------------------------------------------------
> > > > --
> > > > > --- To unsubscribe go to
> > > > > http://protege.stanford.edu/community/subscribe.html
> > > > >
> > > > >
> > > >
> > > > --------------------------------------------------------------
> > > > -----------
> > > > To unsubscribe go to
> > > > http://protege.stanford.edu/community/subscribe.html
> > > >
> > >
> > >
> > ----------------------------------------------------------------------
> > > --- To unsubscribe go to
> > > http://protege.stanford.edu/community/subscribe.html
> > >
> > >
> >
> > --------------------------------------------------------------
> > -----------
> > To unsubscribe go to
> > http://protege.stanford.edu/community/subscribe.html
> >
> >
>
> -------------------------------------------------------------------------
> To unsubscribe go to http://protege.stanford.edu/community/subscribe.html
>
>

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Re: I want some solid real world examples!

Alan March

Yep. In our case its SQL Server. What I meant by "RDF" is that we use a
table which contains the info that would otherwise be contained in the
RDF/OWL File. Sorry, I loosely called it "RDF table" but that's just a local
designation we use to refer to that table (the "rdf" table"...granted: it
does no service to proper understanding of the concept...true reification in
the literal sense of the term). You can actually call it any name in the
JDBC implementation of Protégé.

Regarding the use of "list": An adjacency list is a manner in which to
represent a graph structure and it can be implemented in a database table.
It's a classical implmentation of graph structures. Joe Celko has written
extensively on that, using ANSI-SQL.

Finally, there is a lot of literature on how to map (that is, represent) RDF
structures to a RDBMS. The authors of the JDBC backend made it simple and I
actually think they did it very well. Its supposed inefficiency can be dealt

A word of advice: if you use SQL server as a backend, don't use Microsoft
JDBC driver. I think there's an issue regarding the Java runtime, but it
simply hangs when you try to use a reasoner, with a message regarding
"column 6" which I frankly did not research into. I just dumped the driver.

Regards,

Alan

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf
> Of sridevi polavaram
> Sent: Tuesday, July 18, 2006 3:23 PM
> To: [hidden email]
> Subject: [protege-discussion] Re: I want some solid real
> world examples!
>
> Alan,
> when you say database backend, i am assuming it is some RDBMS
> like mysql, oracle etc., but you are referring it as RDF
> table and a list structure! so what kind of DB is this! can u
> maintain owl or RDF DBs!
> what is the size limit of these DBs? and how exactly are you
> achieving data storage and retrieval methods!
> -regards,
> Sri.
>
> On 7/18/06, Alan March <[hidden email]> wrote:
> >
> >
> > Well, one of the first problems we run into is OWL itself.
> Although it
> > is very powefull in expressivity, we believe it is not
> efficient as a
> > storage and retrieval repository (indeed, it was probably
> not designed
> > with efficiency in mind, and in that sense it reminds me of my old
> > Prolog days).
> > So we used the JDBC database backend. The database backend
> is not that
> > efficient in itself (and, again, its creators mention in the
> > documentation that efficiency was not one of their
> requirements) but
> > it is extremely elastic. Stated simply, the DB backend is a
> (sort of)
> > adjacency list with the particularly interesting
> characteristic that
> > the list is double linked.
> > From what I gather, one important difference with the pure RDF
> > approach is that nodes are loaded on demand, and there is a slight
> > performance issue there, but then, it allows for managing large
> > ontologies. So all design is managed using Protégé as the front-end.
> >
> > The advantage of the database backend is that it makes all the
> > elements of the ontology easily accesible for other
> applications when
> > these applications aren't involved with the design task itself.
> > Example: the multiple classifications built by reasoners such as
> > Fact++ may be accessed from web pages and applications using simple
> > approaches such as treeviews and the like, according to user's
> > different classification requirements (a CFO is interested
> if a cost
> > based classification of procedures, whilst a chief medical
> officer is
> > interested in a body systems classification of procedures). Another
> > example: extracting dimensions for a warehouse. And of course there
> > are more.
> >
> > Most of these tasks are carried out by writing queries to the
> > database. We use stored procedures, which are included in the same
> > database  that contains the main "RDF" table. The pattern generally
> > used is a self linked table for accessing the adjacency list schema
> >
> > Don't know how much "state of the art" this is, but it works for us.
> >
> > Regards,
> >
> > AM
> >
> > > -----Original Message-----
> > > From: [hidden email]
> > > [mailto:[hidden email]] On Behalf Of
> > > sridevi polavaram
> > > Sent: Tuesday, July 18, 2006 9:35 AM
> > > To: [hidden email]
> > > Subject: [protege-discussion] Re: I want some solid real world
> > > examples!
> > >
> > > Alan,
> > >  Thankyou very much for explaining things so patiently. So, how
> > > exactly are you using the ontology that you have tailored
> for your
> > > purpose at the application level? are you mapping the ontology
> > > properties as attributes at the database-level?
> > > if so, what are the other kinds of mapping that u do?
> > > are u using any logic based programming languages? How is
> the rich
> > > annotation that's inherent in ontologies is helping you at the
> > > application level, apart from the fact that it serves as a
> > > reinforcement knowldge base for humans. how are you
> extracting and
> > > storing information using ontologies?  can you say that
> ontology is
> > > crucial for your application and that it's not replacable by any
> > > other design methodologies.
> > > I am sorry but my mind is full of questions...just can't stop the
> > > flow..i am reading all the related literature that's available
> > > (white papers, tools, theroies, real examples, technology
> etc.,) but
> > > none of them help me converge my understanding.
> > > -regards,
> > > Sri
> > >
> > > On 7/17/06, Alan March <[hidden email]> wrote:
> > > >
> > > >
> > > > > > Wow SNOMED and UMLS are supposingly success stories for
> > > > > > ontology
> > > > > applications. and they failed to mee your requirements!!
> > > > > then the whole point of "sharing knowldge" seems skeptical.
> > > > > So are u designing ontologies from scratch for your HMO
> > > application!
> > > > > everyone is apparently having there own ontology
> > > >
> > > > The trouble we faced with SNOMED and UMLS is they
> appeared to us
> > > > as incomplete as far as attributes (relations) are
> concerned: too
> > > > few, failing to capture the richness of possible relations. And
> > > > then of course, the mistakes found in them, which Barry
> Smith and
> > > others have
> > > > mentioned in their papers. Also, much of the terms we had
> > > to use were
> > > > highly local and neither SNOMED nor UMLS offered a clear method
> > > > for extensions. Although SNOMED has something on those lines,
> > > the problem
> > > > of its "ontological incompleteness"
> > > > and licensing questions represented a drawback for us. But
> > > then again:
> > > > both
> > > > SNOMED and UMLS have been extremely usefull to us as a sort of
> > > > knowledge repositories, but we just could not use them
> > > "out-of-the-box".
> > > >
> > > > Actually, we didn't start from scratch: we reutilized
> much of the
> > > > publically available Galen files, and modelled our ontology
> > > following
> > > > an upper level ontology. For anatomy we used Digital
> Anatomist as
> > > > published in UMLS. We tried to use as much as possible from
> > > > several ontologies we found to be suitable to our purposes. But
> > > yes, we had to
> > > > reinvent the wheel in some circumstances. In any case, I am
> > > not quite
> > > > sure if we will ever manage to arrive at a universally accepted
> > > > ontology. Probably at the upper and middle levels this will be
> > > > achieved, but I doubt it will work for "bottom"
> > > > levels.
> > > >
> > > > Regarding success stories: well, I guess SNOMED is a
> > > success story in
> > > > a certain sense, but I am not quite sure if it can be
> > > called that way
> > > > as far as ontological principles are concerned. Not to deny
> > > its value:
> > > > it is rich in content. Worth mentioning is the fact
> that we didn't
> > > > want to consider terminologies which weren't in the public
> > > domain or commercial in nature.
> > > > I
> > > > personally feel that medical terminologies such be built in a
> > > > collaborative manner, probable on the same lines as Linux
> > > was made (by
> > > > having different groups managing different parts of the
> domain).
> > > > In that sense, I feel that Rector's advice regarding the way
> > > ontologies
> > > > should be built (by
> > > > "untangling") allows for this. I am relly sorry that the
> > > Galen project
> > > > didn't continue. Looking back on it, I think it is
> still the best
> > > > thing we have seen in all these decades of discussion on
> > > terminologies
> > > > and how they should be built and maintained.
> > > >
> > > > >
> > > > > In that sense, I find that ontologies are "the" techique
> > > for design,
> > > > > > development and maintaince of so-called controlled
> > > terminologies.
> > > > >
> > > > >
> > > > > > yes, i would say, that even i am convinced that at
> the level
> > > > > > of
> > > > > vocabularies. like a dictionary sort of thing. the
> wikipedia for
> > > > > encyclopedia also uses ontologies!!
> > > > > Thanks a lot for giving me some idea about the real workd
> > > scenario.
> > > > > Best,
> > > > > -Sri
> > > > >
> > > > > OF course,
> > > > > > in the process of using ontologies one quickly realizes the
> > > > > fact that
> > > > > > they could probably be usefull for analysis and design
> > > of complex
> > > > > > systems, and I personally feel that they could
> > > ultimately replace
> > > > > > other tools such as UML and the like. This, of course (and
> > > > > at least as
> > > > > > far as my comprehension goes), still requires much work
> > > regarding
> > > > > > methodology and probably software tools. But I feel that
> > > > > there is more
> > > > > > to ontologies than what meets the eye of the casual
> > > user. Example:
> > > > > > I've been following developments in HL7 v3 and am every
> > > day more
> > > > > > convinced that v3 should be redesigned using readily
> > > > > available tools
> > > > > > such as Protégé (I don't think it shoud be thrown away as
> > > > > others have
> > > > > > suggestes, as the RIM contains a lot of useful domain
> > > > > information, but
> > > > > > the methodolgy user does not seem adequate).
> > > > > >
> > > > > > So, I personally feel that ontologies and Protégé-type
> > > tools could
> > > > > > turn out to be a small revolution in systems
> design. Should my
> > > > > > idea prove right, we are now in a sort of pre-paradigmatic
> > > > > situation as far
> > > > > > as application of ontologies is concerened.
> > > > > >
> > > > > > Best regards
> > > > > >
> > > > > > > -----Original Message-----
> > > > > > > From: [hidden email]
> > > > > > > [mailto:[hidden email]]
> > > On Behalf Of
> > > > > > > sridevi polavaram
> > > > > > > Sent: Monday, July 17, 2006 12:52 PM
> > > > > > > To: [hidden email]
> > > > > > > Subject: [protege-discussion] I want some solid real
> > > > > world examples!
> > > > > > >
> > > > > > > Hello All,
> > > > > > >  Please help me find an answer to my questions. I
> > > suppose some
> > > > > > > of you might also have the same questions. so let's
> > > brainstorm.
> > > > > > > I totally understand what ontology is
> > > > > >
> > > > > >
> > > > >
> > >
> --------------------------------------------------------------------
> > > > > --
> > > > > > --- To unsubscribe go to
> > > > > > http://protege.stanford.edu/community/subscribe.html
> > > > > >
> > > > > >
> > > > >
> > > > > --------------------------------------------------------------
> > > > > -----------
> > > > > To unsubscribe go to
> > > > > http://protege.stanford.edu/community/subscribe.html
> > > > >
> > > >
> > > >
> > >
> --------------------------------------------------------------------
> > > --
> > > > --- To unsubscribe go to
> > > > http://protege.stanford.edu/community/subscribe.html
> > > >
> > > >
> > >
> > > --------------------------------------------------------------
> > > -----------
> > > To unsubscribe go to
> > > http://protege.stanford.edu/community/subscribe.html
> > >
> > >
> >
> >
> ----------------------------------------------------------------------
> > --- To unsubscribe go to
> > http://protege.stanford.edu/community/subscribe.html
> >
> >
>
> --------------------------------------------------------------
> -----------
> To unsubscribe go to
> http://protege.stanford.edu/community/subscribe.html
>

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Re: I want some solid real world examples!

sridevi polavaram
Alan,
 Let's say that i have an owl description of the ontology for Neuron (cell
structures in brain that processes information).
Now what? how does this owl file help me? according to my understanding, i
know that having an owl file is like specifying the semantics of Neuron
concept.
Tell me what's the first use that comes to your mind seeing an owl file. you
can probably use ur own example.
-Thanks
Sri

On 7/18/06, Alan March <[hidden email]> wrote:

>
>
> Yep. In our case its SQL Server. What I meant by "RDF" is that we use a
> table which contains the info that would otherwise be contained in the
> RDF/OWL File. Sorry, I loosely called it "RDF table" but that's just a
> local
> designation we use to refer to that table (the "rdf" table"...granted: it
> does no service to proper understanding of the concept...true reification
> in
> the literal sense of the term). You can actually call it any name in the
> JDBC implementation of Protégé.
>
> Regarding the use of "list": An adjacency list is a manner in which to
> represent a graph structure and it can be implemented in a database table.
> It's a classical implmentation of graph structures. Joe Celko has written
> extensively on that, using ANSI-SQL.
>
> Finally, there is a lot of literature on how to map (that is, represent)
> RDF
> structures to a RDBMS. The authors of the JDBC backend made it simple and
> I
> actually think they did it very well. Its supposed inefficiency can be
> dealt
>
> A word of advice: if you use SQL server as a backend, don't use Microsoft
> JDBC driver. I think there's an issue regarding the Java runtime, but it
> simply hangs when you try to use a reasoner, with a message regarding
> "column 6" which I frankly did not research into. I just dumped the
> driver.
>
> Regards,
>
> Alan
>
> > -----Original Message-----
> > From: [hidden email]
> > [mailto:[hidden email]] On Behalf
> > Of sridevi polavaram
> > Sent: Tuesday, July 18, 2006 3:23 PM
> > To: [hidden email]
> > Subject: [protege-discussion] Re: I want some solid real
> > world examples!
> >
> > Alan,
> > when you say database backend, i am assuming it is some RDBMS
> > like mysql, oracle etc., but you are referring it as RDF
> > table and a list structure! so what kind of DB is this! can u
> > maintain owl or RDF DBs!
> > what is the size limit of these DBs? and how exactly are you
> > achieving data storage and retrieval methods!
> > -regards,
> > Sri.
> >
> > On 7/18/06, Alan March <[hidden email]> wrote:
> > >
> > >
> > > Well, one of the first problems we run into is OWL itself.
> > Although it
> > > is very powefull in expressivity, we believe it is not
> > efficient as a
> > > storage and retrieval repository (indeed, it was probably
> > not designed
> > > with efficiency in mind, and in that sense it reminds me of my old
> > > Prolog days).
> > > So we used the JDBC database backend. The database backend
> > is not that
> > > efficient in itself (and, again, its creators mention in the
> > > documentation that efficiency was not one of their
> > requirements) but
> > > it is extremely elastic. Stated simply, the DB backend is a
> > (sort of)
> > > adjacency list with the particularly interesting
> > characteristic that
> > > the list is double linked.
> > > From what I gather, one important difference with the pure RDF
> > > approach is that nodes are loaded on demand, and there is a slight
> > > performance issue there, but then, it allows for managing large
> > > ontologies. So all design is managed using Protégé as the front-end.
> > >
> > > The advantage of the database backend is that it makes all the
> > > elements of the ontology easily accesible for other
> > applications when
> > > these applications aren't involved with the design task itself.
> > > Example: the multiple classifications built by reasoners such as
> > > Fact++ may be accessed from web pages and applications using simple
> > > approaches such as treeviews and the like, according to user's
> > > different classification requirements (a CFO is interested
> > if a cost
> > > based classification of procedures, whilst a chief medical
> > officer is
> > > interested in a body systems classification of procedures). Another
> > > example: extracting dimensions for a warehouse. And of course there
> > > are more.
> > >
> > > Most of these tasks are carried out by writing queries to the
> > > database. We use stored procedures, which are included in the same
> > > database  that contains the main "RDF" table. The pattern generally
> > > used is a self linked table for accessing the adjacency list schema
> > >
> > > Don't know how much "state of the art" this is, but it works for us.
> > >
> > > Regards,
> > >
> > > AM
> > >
> > > > -----Original Message-----
> > > > From: [hidden email]
> > > > [mailto:[hidden email]] On Behalf Of
> > > > sridevi polavaram
> > > > Sent: Tuesday, July 18, 2006 9:35 AM
> > > > To: [hidden email]
> > > > Subject: [protege-discussion] Re: I want some solid real world
> > > > examples!
> > > >
> > > > Alan,
> > > >  Thankyou very much for explaining things so patiently. So, how
> > > > exactly are you using the ontology that you have tailored
> > for your
> > > > purpose at the application level? are you mapping the ontology
> > > > properties as attributes at the database-level?
> > > > if so, what are the other kinds of mapping that u do?
> > > > are u using any logic based programming languages? How is
> > the rich
> > > > annotation that's inherent in ontologies is helping you at the
> > > > application level, apart from the fact that it serves as a
> > > > reinforcement knowldge base for humans. how are you
> > extracting and
> > > > storing information using ontologies?  can you say that
> > ontology is
> > > > crucial for your application and that it's not replacable by any
> > > > other design methodologies.
> > > > I am sorry but my mind is full of questions...just can't stop the
> > > > flow..i am reading all the related literature that's available
> > > > (white papers, tools, theroies, real examples, technology
> > etc.,) but
> > > > none of them help me converge my understanding.
> > > > -regards,
> > > > Sri
> > > >
> > > > On 7/17/06, Alan March <[hidden email]> wrote:
> > > > >
> > > > >
> > > > > > > Wow SNOMED and UMLS are supposingly success stories for
> > > > > > > ontology
> > > > > > applications. and they failed to mee your requirements!!
> > > > > > then the whole point of "sharing knowldge" seems skeptical.
> > > > > > So are u designing ontologies from scratch for your HMO
> > > > application!
> > > > > > everyone is apparently having there own ontology
> > > > >
> > > > > The trouble we faced with SNOMED and UMLS is they
> > appeared to us
> > > > > as incomplete as far as attributes (relations) are
> > concerned: too
> > > > > few, failing to capture the richness of possible relations. And
> > > > > then of course, the mistakes found in them, which Barry
> > Smith and
> > > > others have
> > > > > mentioned in their papers. Also, much of the terms we had
> > > > to use were
> > > > > highly local and neither SNOMED nor UMLS offered a clear method
> > > > > for extensions. Although SNOMED has something on those lines,
> > > > the problem
> > > > > of its "ontological incompleteness"
> > > > > and licensing questions represented a drawback for us. But
> > > > then again:
> > > > > both
> > > > > SNOMED and UMLS have been extremely usefull to us as a sort of
> > > > > knowledge repositories, but we just could not use them
> > > > "out-of-the-box".
> > > > >
> > > > > Actually, we didn't start from scratch: we reutilized
> > much of the
> > > > > publically available Galen files, and modelled our ontology
> > > > following
> > > > > an upper level ontology. For anatomy we used Digital
> > Anatomist as
> > > > > published in UMLS. We tried to use as much as possible from
> > > > > several ontologies we found to be suitable to our purposes. But
> > > > yes, we had to
> > > > > reinvent the wheel in some circumstances. In any case, I am
> > > > not quite
> > > > > sure if we will ever manage to arrive at a universally accepted
> > > > > ontology. Probably at the upper and middle levels this will be
> > > > > achieved, but I doubt it will work for "bottom"
> > > > > levels.
> > > > >
> > > > > Regarding success stories: well, I guess SNOMED is a
> > > > success story in
> > > > > a certain sense, but I am not quite sure if it can be
> > > > called that way
> > > > > as far as ontological principles are concerned. Not to deny
> > > > its value:
> > > > > it is rich in content. Worth mentioning is the fact
> > that we didn't
> > > > > want to consider terminologies which weren't in the public
> > > > domain or commercial in nature.
> > > > > I
> > > > > personally feel that medical terminologies such be built in a
> > > > > collaborative manner, probable on the same lines as Linux
> > > > was made (by
> > > > > having different groups managing different parts of the
> > domain).
> > > > > In that sense, I feel that Rector's advice regarding the way
> > > > ontologies
> > > > > should be built (by
> > > > > "untangling") allows for this. I am relly sorry that the
> > > > Galen project
> > > > > didn't continue. Looking back on it, I think it is
> > still the best
> > > > > thing we have seen in all these decades of discussion on
> > > > terminologies
> > > > > and how they should be built and maintained.
> > > > >
> > > > > >
> > > > > > In that sense, I find that ontologies are "the" techique
> > > > for design,
> > > > > > > development and maintaince of so-called controlled
> > > > terminologies.
> > > > > >
> > > > > >
> > > > > > > yes, i would say, that even i am convinced that at
> > the level
> > > > > > > of
> > > > > > vocabularies. like a dictionary sort of thing. the
> > wikipedia for
> > > > > > encyclopedia also uses ontologies!!
> > > > > > Thanks a lot for giving me some idea about the real workd
> > > > scenario.
> > > > > > Best,
> > > > > > -Sri
> > > > > >
> > > > > > OF course,
> > > > > > > in the process of using ontologies one quickly realizes the
> > > > > > fact that
> > > > > > > they could probably be usefull for analysis and design
> > > > of complex
> > > > > > > systems, and I personally feel that they could
> > > > ultimately replace
> > > > > > > other tools such as UML and the like. This, of course (and
> > > > > > at least as
> > > > > > > far as my comprehension goes), still requires much work
> > > > regarding
> > > > > > > methodology and probably software tools. But I feel that
> > > > > > there is more
> > > > > > > to ontologies than what meets the eye of the casual
> > > > user. Example:
> > > > > > > I've been following developments in HL7 v3 and am every
> > > > day more
> > > > > > > convinced that v3 should be redesigned using readily
> > > > > > available tools
> > > > > > > such as Protégé (I don't think it shoud be thrown away as
> > > > > > others have
> > > > > > > suggestes, as the RIM contains a lot of useful domain
> > > > > > information, but
> > > > > > > the methodolgy user does not seem adequate).
> > > > > > >
> > > > > > > So, I personally feel that ontologies and Protégé-type
> > > > tools could
> > > > > > > turn out to be a small revolution in systems
> > design. Should my
> > > > > > > idea prove right, we are now in a sort of pre-paradigmatic
> > > > > > situation as far
> > > > > > > as application of ontologies is concerened.
> > > > > > >
> > > > > > > Best regards
> > > > > > >
> > > > > > > > -----Original Message-----
> > > > > > > > From: [hidden email]
> > > > > > > > [mailto:[hidden email]]
> > > > On Behalf Of
> > > > > > > > sridevi polavaram
> > > > > > > > Sent: Monday, July 17, 2006 12:52 PM
> > > > > > > > To: [hidden email]
> > > > > > > > Subject: [protege-discussion] I want some solid real
> > > > > > world examples!
> > > > > > > >
> > > > > > > > Hello All,
> > > > > > > >  Please help me find an answer to my questions. I
> > > > suppose some
> > > > > > > > of you might also have the same questions. so let's
> > > > brainstorm.
> > > > > > > > I totally understand what ontology is
> > > > > > >
> > > > > > >
> > > > > >
> > > >
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