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[protege-owl] Protege 4

Girish Joglekar gjogleka at
Fri Nov 11 14:32:05 PST 2011

Hi Timothy,
I appreciate your detailed response. I do understand the need for the 
rigor in developing specifications for a standard like OWL. However, I 
am coming more from the applications stand point and find it frustrating 
to not be able to do simple things like ordered list within the 
framework. Methinks it would be easy to implement such a functionality 
without taking away the rigor, because the property range would be the 
same whether it is an ordered list or not, and as a bonus it will help 
in certain domains. One could extend it easily through list of lists to 
represent an array. To keep it simple, it could just be the order as it 
appears on the screen. I will certainly try to dig up the references you 

What liberties does OWL Full offer which can help me in this regard. 
Also, how do I build mappings? Is that through Protege or external to 
Thanks much.

On 11/11/2011 4:53 PM, Timothy Redmond wrote:
>> I am too much of a novice to understand what you mean by "encode OWL 
>> ...", but I find it difficult to understand why their use is not 
>> recommended. Afterall, OWL is built on RDF. I find rdf:seq very 
>> useful because that is the only class that ensures order in the 
>> associated collections which I can exploit in my application. 
> Technically, using these terms in an OWL file takes the ontology out 
> of OWL DL.  You can see this by comparing the following from section 
> 2.4 of the OWL structural specification:
>     IRIs with prefixes /rdf:/, /rdfs:/, /xsd:/, and /owl:/ constitute
>     the /reserved vocabulary/ of OWL 2. As described in the following
>     sections, the IRIs from the reserved vocabulary that are listed in
>     Table 3 have special treatment in OWL 2.
> with the following from section 3 of the structural specification [2]
>     Each entity in /O/ /must/ have an IRI satisfying the restrictions
>     on the usage of the reserved vocabulary from Sections 5.1
>     <>--5.6
>     <>.
> and such quotes as the following from section 5.1 of the structural 
> specification [3]
>     IRIs from the reserved vocabulary other than /owl:Thing/ and
>     /owl:Nothing/ /must not/ be used to identify classes in an OWL 2
>     DL ontology.
>> Afterall, OWL is built on RDF. 
> This is a surprisingly complicated and controversial statement.  You 
> will note that in [4] the OWL syntax is defined in terms of UML.  
> Other syntaxes such as the rdf and functional syntaxes are just 
> serializations of the OWL language.  This is expressed in some detail 
> in the following quote from the introduction of [1]:
>     This document defines the OWL 2 language. The core part of this
>     specification --- called the /structural specification/ --- is
>     independent of the concrete exchange syntaxes for OWL 2
>     ontologies. The structural specification describes the conceptual
>     structure of OWL 2 ontologies and thus provides a normative
>     abstract representation for all (normative and nonnormative)
>     syntaxes of OWL 2. This allows for a clear separation of the
>     essential features of the language from issues related to any
>     particular syntax. Furthermore, such a structural specification of
>     OWL 2 provides the foundation for the implementation of OWL 2
>     tools such as APIs and reasoners. Each OWL 2 ontology represented
>     as an instance of this conceptual structure can be converted into
>     an RDF graph [OWL 2 RDF Mapping
>     <>];
>     conversely, most OWL 2 ontologies represented as RDF graphs can be
>     converted into the conceptual structure defined in this document
>     [OWL 2 RDF Mapping
>     <>].
> There is another document [5] which describes the mapping of OWL 
> ontologies to and from RDF.  But it should be noticed that this 
> document does not allow for the parsing of arbitrary RDF.  Some care 
> is taken to ensure that the RDF being parsed can be mapped to the OWL 
> structural syntax.
> Finally - and this really confuses the issue - there is a second 
> language, OWL full [6], described in the OWL specifications.  This 
> language is based on RDF/RDFS.  It has a distinct syntax and semantics 
> from OWL DL.  The syntax for OWL 2 Full is the RDF syntax and the 
> semantics is given by [6] instead of by [7].
> The Protege 4 OWL editor is based on the OWL 2 DL language.  In the 
> future there are plans to provide an RDF editor and through this we 
> will have support for OWL 2 Full (the syntax anyway).
>> For example, in our domain which is related to chemical engineering, 
>> we have a concept of "stream" which is a collection of chemical 
>> species and phases, and the composition of stream is defined by mass 
>> fraction of these species and phases. Since the same species and 
>> phases appear in the entire process it is very convenient that the 
>> species names and the associated compositions come out in the same 
>> order. Normally, when the range of a property is "multiple objects of 
>> a class", the order is not guaranteed. I can see a problem with 
>> reasoning but that would not be any different from the current state. 
>> Are you implying that the work around you suggested below will solve 
>> that problem?
> I think that a search of the web will find OWL DL ontologies that 
> handle lists.  I always forget where these are but Nick Drummond had a 
> paper that described on such ontology and there was another one somewhere.
> -Timothy
> [1]
> [2]
> [3]
> [4]
> [5]
> [6]
> [7]
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