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RE: updated updated bams model

From: Eric Neumann <eneumann@teranode.com>
Date: Wed, 28 Mar 2007 20:01:17 -0400
Message-ID: <A3970D83EC72E84B8D2C2400CD6F0B9F025430CA@MI8NYCMAIL16.Mi8.com>
To: "William Bug" <William.Bug@DrexelMed.edu>
cc: jbarkley@nist.gov, "Chris Mungall" <cjm@fruitfly.org>, public-semweb-lifesci@w3.org

Bill,

Could Protege show a simplifed (reduced for non-CS, human understanding) map of no more than 6 or so items? I'm thinking more of a powerpoint graph than an acurrate portrayal...

Eric


-----Original Message-----
From: William Bug [mailto:William.Bug@DrexelMed.edu]
Sent: Wed 3/28/2007 6:56 PM
To: Eric Neumann
Cc: jbarkley@nist.gov; Chris Mungall; public-semweb-lifesci@w3.org
Subject: Re: updated updated bams model
 
Hi Eric,

For any OWL ontology you open in Protege-OWL, you can represent it  
using either OWLViz or Jamabalaya.

There are also many customized GUI graph viewers for the specific  
terminologies/ontologies.

For GO, there is both:
	- EBI QuickGO (see this link for tyrosine 3-monooxygenase activity -  
http://www.ebi.ac.uk/ego/DisplayGoTerm?id=GO:0004511)
	- you can also just open ANY OBO ontology in OBO-Edit and use the  
Graph Viewer Plugin

I find the QuickGO & OWLViz options the easiest to work with.

WIth either OWLViz or Jamabalaya, you can save any sub-graph in a  
standard graphic file format (JPG, PNG, etc.) to attach to a Wiki page.

Cheers,
Bill


On Mar 28, 2007, at 6:20 PM, Eric Neumann wrote:

>
> Looking at this discussion, I was wondering if anyone had some sort  
> of "concept map" visual for these kinds of ontologies, i.e., BAMS,  
> GO, MESH, etc...?
>
> Shouldn't be too complicated, and would be useful as a back drop  
> for the demo, as to how the "data pieces" fit together. Anyone  
> willing to do it?
>
> Eric
>
>
> On Mar 28, 2007, at 5:20 PM, William Bug wrote:
>
>
>         Absolutely, John.  I completely agree.
>
>         Just stash that feedback on the page for now.
>
>         Getting a working OWL version of BAMS that best reflects  
> the suggestions Alan, Kei, Luis, Mihail and others have made - one  
> particularly suited to catalyzing an RDF-driven integration of the  
> various BioRDF data sets is definitely the priority.
>
>         Many thanks for all the work you are doing.  I know this  
> will be an important resource not only for the HCLS demo but also  
> for the community at-large.
>
>         Cheers,
>         Bill
>
>         On Mar 28, 2007, at 12:45 PM, jbarkley@nist.gov wrote:
>
>
>
>                 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
>
>
>
>
>
>
>
>
>
>                 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
>
>
>
>
>
>
>
>

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 Thursday, 29 March 2007 00:03:01 UTC

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