Re: URI thoughts

Perhaps a concrete example could enlighten my difficulty in understanding 
the value in:

1) 'forcefully' attempting to dereference all URI terms in an instance 
graph (which is what is described as a 'full' or unrestricted Web 
Closure in http://esw.w3.org/topic/WebClosure)

2) In using data record URLs (which dereference to informational 
resources, not concepts or signs) primarily instead of concept URIs 
(associated with a defining ontology).


It seems more pragmatic to me to follow a social contract to achieve 
'controlled' ontological closure 
(http://esw.w3.org/topic/OntologicalClosure) by establishing 
rdfs:isDefinedBy as a 'best practice' for leaving a trail to the formal 
semantics for the terms used.

On Tue, 20 Jun 2006, Eric Neumann wrote:

> 3) Signifiers: Life science data records of bio or chem entities (genes, 
> snps, protein, chemicals, agents, diseases, pathways, anatomical parts) 
> should always reference a community agreed upon conceptualized 
> bio/chem-entity, i.e., to what the scientist in his or her mind commonly and 
> collectively regard when hearing "human GSK3 beta". These could have 
> ontologies layered on them when they become available. These entities 
> represent the 'signifiers or signs' for the 'signified or real-world objects' 
> such as "Hu GSK3b" or " Mus MAP12" (for the curious, see 
> http://en.wikipedia.org/wiki/Sign_(semiotics), btw the full RDF graph around 
> an entity would be equivalent to Peirce's 'interpretant'). They would exist 
> as non-data objects, more like scientific placeholders, but can use 
> rdfs:seeAlso to point to real data records of them. Data records by 
> themselves WOULD NOT be of this special meta-class. If this sounds fuzzy to 
> you, consider what it took to align most of the gene synonym names to one 
> agreed symbol; sociologically this is no different.

Yes, this distinction is very important and I agree with Xiaoshu's 
characterization of using Wiki Article URIs as a bad modeling practice.

It's worth noting that  Semantic MediaWiki 
(http://wiki.ontoworld.org/index.php/Semantic_MediaWiki) follows a 
convention that maintains this distinction:

- http://wiki.ontoworld.org/index.php/Semantic_MediaWiki (Article)

versus

- http://wiki.ontoworld.org/index.php/_Semantic_MediaWiki (Concept)

The latter is used in assertions about the concept in an RDF export of the 
article: 
http://wiki.ontoworld.org/index.php/Special:ExportRDF/Semantic_MediaWiki

The smw:hasArticle property is used to relate the concept to the 
'database record'

>
> 4)  Covering Mapping: Propose an initial set of properties to support the 
> above model. As a starter, define an equivalent of rdfs:isDefinedBy for life 
> science that would specifically map an instance graph of the data record to 
> the singular conceptualized bio/chem-entity, using something on the order of 
> hcls:isDefinedAs :
>
> <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
> db=gene&cmd=Retrieve&list_uids=2932>  <hcls:isDefinedAs> 
> <http://purl.org/hcls/bioentity/hu_gsk3b>
>
> In line with what Chimezie proposed, rdfs:seeAlso could be used to declare 
> the inverse relation for a select set of data records; not sure if any new 
> relation is needed here.
>

This is perhaps just a nitpick or some impedance in differing domains, but 
it seems to me that the more common convention is to use concept URIs for 
terms in instance graphs primarily and associate an informational resource 
with the concept where it makes sense to have such an annotation using 
rdfs:seeAlso (as in the Semantic MediaWiki case - where the informational resource is really 
what the 'human' consumer is after wherease the concept URI is what an 
intelligent agent will need to extract explicit semantics).  I.e., it 
would seem to make more sense to coin a vocabulary term that goes from 
concept to informational resource / database record (with stronger 
semantics than rdfs:seeAlso - which is very much overloaded) than it's 
inverse property.  Unless there is a usecase in our context that I'm 
unaware of.

> In the absence of any formal ontology that could cover all life sciences data 
> records (e.g., Genes), a relational instance model might be more practical 
> and appealing; A transitive rule could be proposed that states all data 
> records referencing the same bio/chem-entity would be viewed as "bio/chem 
> entity" equivalent, regardless of what ontology/rdfschema were used to define 
> each of them:
> (?data1 hcls:isDefinedAs ?ent) AND (?data2 hcls:isDefinedAs ?ent) -> (?data1 
> hcls:sameEntityAs ?data2 )

Again, wouldn't it make sense for such strong semantics (logical implication in this case) 
to be applied to the concepts / signs than the database records?

Chimezie Ogbuji
Lead Systems Analyst
Thoracic and Cardiovascular Surgery
Cleveland Clinic Foundation
9500 Euclid Avenue/ W26
Cleveland, Ohio 44195
Office: (216)444-8593
ogbujic@ccf.org

Received on Tuesday, 20 June 2006 16:36:47 UTC