Re: [ontology-summit] [BigSystems and SystemsEngineering] Relationship b

["Christopher Spottiswoode" <cms@xxxxxxxxxxxxx>]

Bradley, many thanks for your input.

 

The SADI service broking concept certainly has significant overlap with the corresponding function within Ontology Chemistry.  And interestingly, they both explicitly share the market-boot problem, or how to achieve the critical mass of usage for the addressed supply and demand.to be self-generating.

 

But re the Baker paper ("An OWL-DL Ontology for Classification of Lipids") maybe I should point out that when I talk of "Ontology Chemistry" the "chemistry" part of it is purely metaphorical.  So it's not addressing chemical compounds in any way.   Low, Baker et al are indeed trying to build up to the structure/function relationship.  But as the paper says, "lipid definition and classification are required before annotation of chemical functions can be applied."  Or have I misunderstood the relevance you saw there?

 

As you can see on http://ontolog.cim3.net/cgi-bin/wiki.pl?ChristopherSpottiswoode/OntologyChemistry_WorkingDraft (though better wait till I have largely replaced that material, which will hopefully be quite soon), the project seems insanely ambitious, but I do believe it fully embraces the SADI kind of concept, only far better, thanks only partly to its reasoned rejection of the usual set of basic standards and technologies that SADI is based on.  As I am building up to try to show...

 

Thanks, meanwhile, for that reference, and I hope I can look forward to your continued participation in this project, whether still from far, or closer in due course...

 

Christopher

----- Original Message -----

From: Bradley Shoebottom

To: Ontology Summit 2012 discussion

Sent: Tuesday, January 31, 2012 5:15 PM

Subject: Re: [ontology-summit] [BigSystems and SystemsEngineering] Relationship between system function and system structure

See the work of Christopher JO Baker here (http://www.bioontology.org/sites/default/files/OWL-DL%20Ontology.pdf) for a description of an ontology to describe the chemical make-up of lipids (fat) compounds. This ontology is a classification checking ontology. Lots of axioms at play in this ontology.

 

He is also a co-director of the SADI semantic web services infrastructure which is designed in part to get algorithms published to the web so that ontologies can use them to call and process data. Services can be semantically described processing algorithms or queries that can be used in as re-usable over many applications (ie thinking in terms of big systems).

 

http://sadiframework.org/content/

 

 

Bradley Shoebottom 
Information Architect - R&D, Innovatia Inc.
Tel: (506) 674-5439  |  Skype: bradleyshoebottom  | Toll-Free: 1-800-363-3358 begin_of_the_skype_highlighting       
bradley.shoebottom@xxxxxxxxxxxxx | www.innovatia.net | Follow us on Twitter

 

From: ontology-summit-bounces@xxxxxxxxxxxxxxxx [mailto:ontology-summit-bounces@xxxxxxxxxxxxxxxx] On Behalf Of Christopher Spottiswoode
Sent: January-31-12 9:42 AM
To: Ontology Summit 2012 discussion
Subject: [ontology-summit] [BigSystems and SystemsEngineering] Relationship between system function and system structure

 

Joe, thank you for the distinctions you make here.  (And sorry I have only now opened this input from you.)

 

You have prompted me to open a new thread.

 

Whether or not you would approve of the words I use, you at least remind me of a question I have often thought but promptly forgotten to put to formal ontologists:

What work has been done on formal deduction of system function from system structure, or vice versa?

As far as I am aware, at most very little of practical relevance to our Big Systems has been achieved along those lines, but I would be absolutely delighted to be enlightened, and to study the techniques and their limits.

 

Please, some formal ontologist out there, point me in the right direction?!

 

And why might I be so interested?  Hint:  As one talking so much of "Ontology Chemistry" and composition from components, I am intrigued to note a predominance of links in the areas of chemistry and physiology.upon now, for the first time, googling /structure function deduce/.  Adding "ontology" to the search string brings about an enormous reduction in the number found, from 23M to 3M, and many of the 3M are in some biochemical field.

 

Perhaps I should add that I have long already proceeded on the basis of a largely negative answer to my question, and that the way Ontology Chemistry deals with that presumed problem is particularly interesting.  Oh, yes: and it would remain as interesting however much good work I stand to learn of in answer to my question, if anyone can point me to it.  Any of that would be a special bonus for Ontology Chemistry.

 

Hopefully,

Christopher

 

 

----- Original Message -----

From: joseph simpson

To: Ontology Summit 2012 discussion

Sent: Sunday, January 29, 2012 8:59 PM

Subject: Re: [ontology-summit] [BigSystems and SystemsEngineering]Systemofsystems

 

For example three, now consider:

 

--- "system of (X)"

--- "part of  (X)"

Where X can be , laws, games, airplanes, cars, plants.. and so on..

The "system concept" may be viewed as a real world relationship that is used to order or constrain the environment.

Using this basic view, two types of definitions for a system can be constructed as well as two main types of activity for system concepts.

The two definition types are, function (rule) and constructive (rule).

The two main activity types are discovery and design.

The functional rule definition for a system was given previously and is restated here, "A system is a constraint on variety, where the constraint identifies and defines the system of interest."

The construction rule definition for a system is, " A system is a non-empty set of objects and a non-empty set  of relationships mapped over these objects and their attributes."

Humans tend to use the concept of a system for two main activities:

   ---  Discovering, documenting and discussing natural systems (systems not constructed by man).

   ---  Designing, documenting and discussing artificial systems (systems constructed by man).

Johannes Kepler's laws of planetary motion that describe the behavior of solar system under the defining constraints of natural physical forces is one example of using the system concept in the discovery mode.

The Wright brothers are an example of the application of the system concept used in the design mode.

These modes of application have different approaches, methods and techniques.

Mixing these modes may generate a high degree of semantic conflict.

Have fun,

Joe

On Sun, Jan 29, 2012 at 3:36 AM, Christopher Spottiswoode <cms@xxxxxxxxxxxxx> wrote:

Joe, Anatoly,

You both make very useful points.  Here I highlight just 2 of them:

AL:
> This ontologizing-in-the-large lead to your need to define not only
> ontology-as-algorithm but also communication protocol between ontology
> components that reside in different nodes. I doubt that mantra about
> "federation" is helpful here. If you have web programming (that is in
> essence programming-in-the-large) you speak not about "federating" of
> web-server, load balancer, database, web-page generation, ad banner
> importing, etc. but have another engineering approach (while all that
> software developed by different organizations and reside on different
> computers).

As I shall be describing in some detail later, appropriate architecture
leads to good 'Separation of Concerns', hence reliable and flexible
application modularity while also enhancing the various other qualities
usually sought.  That is what a properly ontology-based architecture
should of course produce, and "federation" is a good word to describe
the result at the in-the-large level.

In contrast to what I shall be describing, the conventional web
programming you highlight is complication-inducing rather than
complexity-respecting

JS:

> I suggest that the "binding force" or "binding concept" that forms a
> number of items in to one entity  is a key feature.

Yes!  That is indeed most strongly the case in the architecture I shall
be describing (or trying once again to describe, lessons hopefully
having been learnt...).

All of which recalls that now very mainstream IS programming precept:
Larry Constantine's "high module cohesion with loose module coupling".
We don't have to reinvent that wheel.

> Have fun,
>
> Joe

Yes thanks, Joe, we sure will!

Christopher

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Sent From My DROID!!

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