Re: updated updated bams model

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-50710462ea5aac416fd063dce8621ce0354 
> 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
>
>

Received on Tuesday, 27 March 2007 12:20:35 UTC