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Re: updated updated bams model

From: <jbarkley@nist.gov>
Date: Wed, 28 Mar 2007 12:45:47 -0400
Message-ID: <1175100346.460a9bbb028e0@webmail.nist.gov>
To: William Bug <William.Bug@DrexelMed.edu>
Cc: Chris Mungall <cjm@fruitfly.org>, public-semweb-lifesci@w3.org, jbarkley@nist.gov


hi bill,

Thanks very much for your suggestions. I'm deep into doing the conversion of 
BAMS. I want to make significant enough progress with this before attempting 
to deal with changing the section. 

jb


Quoting William Bug <William.Bug@DrexelMed.edu>:

> Hi John,
> 
> I agree - I think it's important to keep things simple and clear,  
> though I do also agree I believe Chris's comments are actually very  
> helpful in achieving this goal.
> 
> A few thoughts that came to mind when reading Chris's comments:
> 
> 	1) XML as a database language
> 		Chris is correct.  XML qua XML is primarily a markup language  
> designed for the task of providing an "extensible" data exchange mark  
> up formalism.  When I read what you say on the page, I thought you  
> might have been referring to XML databases - e.g., RDBMS frameworks  
> that actually store XML internally OR use XML-based disk files as  
> their serialization format.  If that is what you meant, it might be  
> useful to state that explicitly.
> 
> 	2) RDBMS syntax & semantics
> 		It is important to be clear RDBMS architectures are based on 
very  
> formal and explicit syntax designed specifically to express a set  
> theoretic view of how data sets inter-relate.  As you say, its best  
> to keep things clear and simple but given the what you are trying to  
> explain, I do agree with Chris it is important to be clear RDBMS  
> systems are based on very formal representations - they just are  
> representations devoid of any explicit semantic entailments beyond  
> the most abstract "set X relates to set Y via relation A".
> 		I believe its also important to the argument you are making to 
be  
> clear we recognize there are long-standing RDBMS approaches that do  
> attempt to take semantics into account - i.e., "Semantic Data  
> Models" (http://portal.acm.org/citation.cfm?id=509264).  These do  
> provide a means of defining a local, application-specific semantic  
> description of the data held in a relational data model, but they do  
> not provide an explicit externalized semantics expressed in a common,  
> standard formalism such as what is provided by RDF & OWL.
> 
> 	3) SQL "standard"
> 		It would be useful to simply list "SQL 92", "SQL 99", "SQL 
2003",  
> if that is what you mean.  You could also mention there is  
> considerable variation in the ways in which a given RDBMS framework -  
> e.g., Oracle, PostgreSQL, Ingres, DB2, etc. - implements the  
> "optional" portions of these specs and extends the available calculus  
> beyond the SQL standard.  This means that in addition to their being  
> not explicit statement of semantic-to-syntactic mapping, there is  
> also considerable variation at the implementation level even in the  
> syntax.
> 		As Chris says, the underlying relational algebra on which all 
of  
> these systems are based does provide a solid, formal basis for each  
> implementation, but in the context of the point you are making on  
> this page, this does not provide an explicit and shared formalism for  
> representing the underlying semantics - AND - the variety in formal  
> syntactic implementations adds to the cost and the ultimate  
> "brittleness" of trying to provide such semantic mapping as an  
> adjunct to the underlying relational syntax.
> 
> 	4) Documentation
> 		I suppose what Chris is asking on this front is simply to be 
clear  
> it's not the fact that "documentation" is required to support the  
> applications one constructs whether you are using XML, an RDBMS, or  
> SemWeb tools to build your application.  The point I believe you are  
> trying to make here is with XML & RDBMS approaches, the documentation  
> describing the semantic "mapping" is an absolute pre-requisite to  
> fully describing the semantic content of the information and this is  
> essentially opaque to the algorithms one creates to parse the  
> information - therefore, the algorithms have no direct access to the  
> semantic assertions and entailments.
> 
> 	5) Qualified Relations
> 		To some extent, what you are trying to express regarding the 
use of  
> Domain & Range when defining RDF predicate relations can be expressed  
> in a RDBMS idiom - especially if one includes Object-Relational  
> systems in this category.  In an ORDBMS, the table "class" containing  
> the PK becomes the domain for a relation, and the set of all tables  
> (and their sub-classes) whose tuples include the corresponding FK is  
> equivalent to the range for the relation.  Of course, the underlying  
> formalism provides no explicit support for algorithmically  
> manipulation or interpretation of semantic entailments of such  
> relation(s).  This is where the model-theoretic underpinnings of OWL  
> certainly provide considerably more support for this activity.  Even  
> outside the ORBMS frameworks, one can provide SQL DDL models where  
> relations are "qualified".  Without such modeling patterns, it would  
> be impossible to represent the full expressiveness of MeSH or UMLS in  
> a RDBMS backend.  These implementations in an RDBMS framework,  
> however, tend to get very complex and brittle and require specialized  
> RDBMS skills to implement effectively.  They can also be MUCH more  
> complicated to access and manipulate when using a particular language  
> to access the data stored in such models.  I do think one can argue  
> the standard tools growing up around RDF & OWL provide a much more  
> powerful, less fragile, and ultimately less complicated (at least  
> measured in lines of code) means to manipulate the semantic  
> assertions & entailments expressed in the underlying data relations.
> 		There is also the issue of "directionality" that you bring 
up,  
> which to my mind is explicitly defined both for XML graphs and  
> relational systems, but I think you mean to capture more than simply  
> the directionality of a semantic entailment in this argument re: use  
> of domain & range.
> 
> 	6) RDFS and/or OWL compared to XML Schema & SQL DDL
> 		Chris is definitely correct here.  Even if you don't go into 
the  
> details, these are the correct, more specific comparisons to be  
> making in terms of the inherent ability of these formalisms to  
> explicit represent semantic assertions and entailments.
> 		It would also be useful to be more explicit regarding both 
the  
> expressivity and computability of semantic assertions encoded using  
> XML Schema, RDBMS formalisms, ORBMS formalisms, and systems that  
> convolve XML & RDBMS together.  When compared with the formalism and  
> tools provided for performing these same tasks with RDF & OWL, one  
> would hope the result of such a comparison would strongly indicate  
> RDF & OWL provide a significant advantage when representing real- 
> world entities in a semantic meaningful way.
> 
> Sorry - I've only had a brief moment to capture some of these  
> thoughts.  The idea is to follow-up on Chris's suggestion there is a  
> need to do more to define "the strength of the OWL/RDF approach  
> (over) a traditional XML or SQL approach".  XML "databases", ORBMS,  
> Semantic Data Models - these are all tools likely to be cited as  
> addressing some of the requirements to handling semantically  
> qualified data, and it's worth placing them in these arguments  
> somewhere.
> 
> Hope this helps a little - and doesn't make things worse.
> 
> Cheers,
> Bill
> 
> 	
> On Mar 27, 2007, at 8:19 AM, John Barkley wrote:
> 
> >
> > chris,
> >
> > I appreciate your comments, and I agree that if the demo is to show  
> > the superiority of the semantic web approach, then that section  
> > should be more carefully worded. I was trying to create something  
> > that would be (reasonably) readable by RDB and XML practitioners  
> > who are likely not to appreciate subtleties of differences. I will  
> > try to redo the section.
> >
> > jb
> >
> >
> > ----- Original Message ----- From: "Chris Mungall" <cjm@fruitfly.org>
> > To: <jbarkley@nist.gov>
> > Cc: <public-semweb-lifesci@w3.org>
> > Sent: Monday, March 26, 2007 11:06 AM
> > Subject: Re: updated updated bams model
> >
> >
> >>
> >>
> >> I have some comments on:
> >> http://esw.w3.org/topic/HCLS/  
> >> HCLSIG_DemoHomePage_HCLSIG_Demo#head-50710462ea5aac416fd063dce8621ce0 
> >> 354 d2d5a
> >>
> >>> Formal Definition of Semantics
> >>>
> >>> OWL and RDF have a formal definition for the semantics of an OWL/  
> >>> RDF knowledge base, i.e., given a knowledge base, associated   
> >>> semantics are primarily provided explicitly within the knowledge   
> >>> base itself. Commonly used database languages, e.g., XML and   
> >>> relational database (RDB), have at most a semi-formal definition.
> >>
> >> XML is a way of standardising syntax, not semantics. XML isn't a   
> >> database language, I'm not sure why it's classified as such here.
> >>
> >> It's not quite correct to state that an RDB (which is not a  
> >> database language either) has only a semi-formal definition. The  
> >> strength of  the relational model is precisely the formal  
> >> definition - either as relational algebra or relational calculus.  
> >> How much more formal do  you want?
> >>
> >> Of course, existing databases use various extensions to the   
> >> relational model, and, regrettably, departures from it. But this  
> >> may  well be the case for practical OWL/RDF implementations. I  
> >> think it's  a fairly minor point, and not something you want to  
> >> base your  argument on.
> >>
> >>> XML is a grammar writing system with no defined relationship   
> >>> between a given schema and its semantic meaning. An XML schema  
> >>> is  simply a grammar. Any semantics represented by that schema  
> >>> and its  associated documents are specified external to those   
> >>> representations, e.g., in documentation.
> >>>
> >>> RDB has more than one semi-formal definition, e.g., the ISO   
> >>> Standard SQL [sql].
> >>
> >> You state there is >1 formal definition, give the SQL standard as  
> >> an example of one - can you give an example of another? Perhaps  
> >> you mean successive iterations of the SQL standard? Again,  
> >> variations from  this are relatively minor. Relational algebra  
> >> precedes the ISO SQL  standard and forms the basis for all  
> >> relational databases.
> >>
> >>> Thus, given an RDB schema and repository, it is not possible to   
> >>> know from those which definition of semantics, if any, was used.  
> >>> In  common use, a given RDB database and repository may make use  
> >>> of no  semi-formal definition of semantics or borrow from  
> >>> several  different ones.
> >>
> >> What is a repository in this context?
> >>
> >>> Like XML, other means, such as, documentation, external to the   
> >>> schema and repository describes the semantics.
> >>
> >> So OWL/RDF dispenses with documentation?
> >>
> >>> For example, consider how a relation between two sets would be  
> >>> represented in OWL/RDF, XML, and RDB. In OWL/RDF, the semantics  
> >>> of  a relation is formally defined similar to the mathematical   
> >>> definition, i.e., as a subset of the cross product of the domain   
> >>> and range. Because the relation is a cross product, it has a   
> >>> direction. An element of the domain is related to an element of  
> >>> the  range, but not necessarily the other way around. In an XML  
> >>> schema,  there are many different ways of representing a relation  
> >>> using  elements, subelements, and attributes. Similarly, in an  
> >>> RDB schema,  depending on which semi-formal definition of RDB  
> >>> semantics is used,  there are multiple ways to represent a  
> >>> relation. How a relation is  represented in an XML or RDB schema/ 
> >>> repository can only be known  external to the schema/repository  
> >>> itself.
> >>
> >> I'm afraid I can't make head nor tail of this.
> >>
> >>   "In OWL/RDF, the semantics of a relation is formally defined   
> >> similar to the mathematical definition, i.e., as a subset of the   
> >> cross product of the domain and range."
> >>
> >> Actually, I think you are talking about mathematical functions,  
> >> not relations. As OWL/RDF is restricted to binary relations the   
> >> terminology of functions makes sense (ie we can call the first   
> >> argument domain the domain, and the second the range)
> >>
> >> So you seem to be stating a strength of OWL/RDF is that you can  
> >> state  the domain and range of a relation? Note that in the  
> >> relational model  you can of course state the domain of every  
> >> argument of the relation.
> >>
> >>   "Because the relation is a cross product, it has a direction. An  
> >> element of the domain is related to an element of the range, but  
> >> not necessarily the other way around"
> >>
> >> Can you elaborate on this? I don't understand this at all.
> >>
> >>   "in an RDB schema, depending on which semi-formal definition of   
> >> RDB semantics is used, there are   multiple ways to represent a   
> >> relation"
> >>
> >> ??
> >>
> >> Are we talking about mathematical relations? As far as I  
> >> understand  this, this is simply false. Using the relational model  
> >> you would  represent a relation using, ummm, a relation. A  
> >> relation is the cross- product of the domains of each argument. It  
> >> would seem that an RDB  relation is much closer to a mathematical  
> >> relation than the OWL/RDF  equivalent. (For one thing, there is no  
> >> restriction to binary  relations forcing use of n-ary patterns).  
> >> This is true for all RDBs,  even ones that fall short of the ideal  
> >> relational model. Can you give  an example of two different  
> >> definitions of RDB semantics that would  give different answers here?
> >>
> >>
> >> If this demo is to convince people of the strength of the OWL/RDF  
> >> approach as opposed to a traditional XML or SQL approach, then  
> >> this section needs some work.
> >>
> >> I would not lump XML in with the relational model - the  
> >> relational  model has more in common with logic-based approaches  
> >> than with XML  (it's unfortunate for both camps they do not yet  
> >> have more in common)
> >>
> >> I think it would be more appropriate to compare and contrast the  
> >> expressivity of, say, XML Schema with OWL than, say, XML with OWL/  
> >> RDF. Make sure you are comparing like with like. Similarly, I  
> >> would  compare the expressivity of standard SQL DDL with OWL,  
> >> perhaps using  an example - e.g. a simple one with class  
> >> subsumption. If you're  going to use the term semantics, give a  
> >> definition. Note that both  relational algebra and OWL's model  
> >> theoretic semantics are rock-solid  and formal (I'll leave others  
> >> to comment on the semantics of OWL  layered on RDF/RDFS).
> >>
> >> I think the point you want to make is that OWL (arguably) provides  
> >> a  more expressive (and perhaps agile?) framework for  
> >> representations of real-world entities. Although you  
> >> simultaneously seem to be making  the case for RDF too, which  
> >> makes your task harder.
> >>
> >> Cheers
> >> Chris
> >>
> >
> >
> >
> 
> Bill Bug
> Senior Research Analyst/Ontological Engineer
> 
> Laboratory for Bioimaging  & Anatomical Informatics
> www.neuroterrain.org
> Department of Neurobiology & Anatomy
> Drexel University College of Medicine
> 2900 Queen Lane
> Philadelphia, PA    19129
> 215 991 8430 (ph)
> 610 457 0443 (mobile)
> 215 843 9367 (fax)
> 
> 
> Please Note: I now have a new email - William.Bug@DrexelMed.edu
> 
> 
> 
> 
> 
Received on Wednesday, 28 March 2007 16:47:27 GMT

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