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Re: Is the ontology structure stored seamlessly with its data?

From: Tim Berners-Lee <timbl@w3.org>
Date: Mon, 1 Oct 2007 13:55:31 -0400
Message-Id: <D02FDE12-3EF0-4E80-B162-6CF88B89E7DF@w3.org>
Cc: Michael Schneider <schneid@fzi.de>, Emanuele D'Arrigo <manu3d@gmail.com>, Semantic Web Interest Group <semantic-web@w3.org>, "public-owl-dev-request@w3.org" <public-owl-dev@w3.org>
To: "Luciano, Joanne S." <jluciano@mitre.org>

Python: You can with cwm do the same thing, store data and ontology  
ion the same store.
You can also put it into a mode in which it will suck in the  
ontologies automatically

Javascript: The tabulator RDF library pulls ontologies into the store  
and does limited inference automatically.

Tim BL

$ cwm --help
Command line RDF/N3 tool

<command> <options> <steps> [--with <more args> ]

--pipe        Don't store, just pipe out *

steps, in order left to right:

--rdf         Input & Output ** in RDF/XML insead of n3 from now on
--n3          Input & Output in N3 from now on. (Default)
--rdf=flags   Input & Output ** in RDF and set given RDF flags
--n3=flags    Input & Output in N3 and set N3 flags
--ntriples    Input & Output in NTriples (equiv --n3=usbpartane - 
bySubject -quiet)
--language=x  Input & Output in "x" (rdf, n3, etc)  --rdf same as: -- 
--languageOptions=y     --n3=sp same as:  --language=n3 -- 
--ugly        Store input and regurgitate, data only, fastest *
--bySubject   Store input and regurgitate in subject order *
--no          No output *
               (default is to store and pretty print with anonymous  
nodes) *
--base=<uri>  Set the base URI. Input or output is done as though  
theis were the document URI.
--closure=flags  Control automatic lookup of identifiers (see below)
<uri>         Load document. URI may be relative to current directory.

--apply=foo   Read rules from foo, apply to store, adding conclusions  
to store
--patch=foo   Read patches from foo, applying insertions and  
deletions to store
--filter=foo  Read rules from foo, apply to store, REPLACING store  
with conclusions
--query=foo   Read a N3QL query from foo, apply it to the store, and  
replace the store with its conclusions
--sparql=foo   Read a SPARQL query from foo, apply it to the store,  
and replace the store with its conclusions
--rules       Apply rules in store to store, adding conclusions to store
--think       as -rules but continue until no more rule matches (or  
--engine=otter use otter (in your $PATH) instead of llyn for linking,  
--why         Replace the store with an explanation of its contents
--why=u       proof tries to be shorter
--mode=flags  Set modus operandi for inference (see below)
--reify       Replace the statements in the store with statements  
describing them.
--dereify     Undo the effects of --reify
--flatten     Reify only nested subexpressions (not top level) so  
that no {} remain.
--unflatten   Undo the effects of --flatten
--think=foo   as -apply=foo but continue until no more rule matches  
(or forever!)
--purge       Remove from store any triple involving anything in  
class log:Chaff
--data              Remove all except plain RDF triples (formulae,  
forAll, etc)
--strings     Dump :s to stdout ordered by :k whereever { :k  
log:outputString :s }
--crypto      Enable processing of crypto builtin functions. Requires  
python crypto.
--help        print this message
--revision    print CVS revision numbers of major modules
--chatty=50   Verbose debugging output of questionable use, range 0-99
--sparqlServer instead of outputting, start a SPARQL server on port  
8000 of the store


--with        Pass any further arguments to the N3 store as os:argv  

             * mutually exclusive
             ** doesn't work for complex cases :-/
   cwm --rdf foo.rdf --n3 --pipe     Convert from rdf/xml to rdf/n3
   cwm foo.n3 bar.n3 --think         Combine data and find all  
   cwm foo.n3 --flat --n3=spart

Mode flags affect inference extedning to the web:
r   Needed to enable any remote stuff.
a   When reading schema, also load rules pointed to by schema  
(requires r, s)
E   Errors loading schemas of definitive documents are ignored
m   Schemas and definitive documents laoded are merged into the meta  
      (otherwise they are consulted independently)
s   Read the schema for any predicate in a query.
u   Generate unique ids using a run-specific

Closure flags are set to cause the working formula to be  
automatically exapnded to
the closure under the operation of looking up:

s   the subject of a statement added
p   the predicate of a statement added
o   the object of a statement added
t   the object of an rdf:type statement added
i   any owl:imports documents
r   any doc:rules documents
E   errors are ignored --- This is independant of --mode=E

n   Normalize IRIs to URIs
e   Smush together any nodes which are = (owl:sameAs)

See http://www.w3.org/2000/10/swap/doc/cwm  for more documentation.

Setting the environment variable CWM_RDFLIB to 1 maked Cwm use rdflib  
to parse
rdf/xml files. Note that this requires rdflib.

Flags for N3 output are as follows:-

a   Anonymous nodes should be output using the _: convention (p flag  
or not).
d   Don't use default namespace (empty prefix)
e   escape literals --- use \u notation
i   Use identifiers from store - don't regen on output
l   List syntax suppression. Don't use (..)
n   No numeric syntax - use strings typed with ^^ syntax
p   Prefix suppression - don't use them, always URIs in <> instead of  
q   Quiet - don't output comments about version and base URI used.
r   Relative URI suppression. Always use absolute URIs.
s   Subject must be explicit for every statement. Don't use ";"  
t   "this" and "()" special syntax should be suppresed.
u   Use \u for unicode escaping in URIs instead of utf-8 %XX
v   Use  "this log:forAll" for @forAll, and "this log:forAll" for  
/   If namespace has no # in it, assume it ends at the last slash if  

Flags for N3 input:

B   Turn any blank node into a existentially qualified explicitly  
named node.

Flags to control RDF/XML output (after --rdf=) areas follows:

b  - Don't use nodeIDs for Bnodes
c  - Don't use elements as class names
d  - Default namespace supressed.
l  - Don't use RDF collection syntax for lists
r  - Relative URI suppression. Always use absolute URIs.
z  - Allow relative URIs for namespaces

     Flags to control RDF/XML INPUT (after --rdf=) follow:
         S  - Strict spec. Unknown parse type treated as Literal  
instead of error.
         T  - take foreign XML as transparent and parse any RDF in it
              (default it is to ignore unless rdf:RDF at top level)
         L  - If non-rdf attributes have no namespace prefix, assume  
in local <#> namespace
         D  - Assume default namespace decalred as local document is  
assume xmlns=""

     Note: The parser (sax2rdf) does not support reification, bagIds,  
or parseType=Literal.
           It does support the rest of RDF inc. datatypes, xml:lang,  
and nodeIds.


On 2007-10 -01, at 12:54, Luciano, Joanne S. wrote:

> Can anyone suggest a non-Jena / non-Java alternative?
> And for RDF (without OWL) also?
> Thanks,
> Joanne
>> -----Original Message-----
>> From: public-owl-dev-request@w3.org
>> [mailto:public-owl-dev-request@w3.org] On Behalf Of Michael Schneider
>> Sent: Wednesday, September 26, 2007 1:37 PM
>> To: Emanuele D'Arrigo
>> Cc: Semantic Web Interest Group; public-owl-dev-request@w3.org
>> Subject: RE: Is the ontology structure stored seamlessly with its
> data?
>> Hi, Emanuele!
>> Emanuele D'Arrigo wrote at September 26, 2007:
>>> Another thing that is not quite clear in my mind right now is this:
>>> are the sets of triplets describing the class and property
> hierarchies
>>> of an ontology normally stored seamlessly alongside the data that
>>> is classified and characterized by those classes and properties?
>> With OWL, for which an RDF mapping exists, this is technically
> possible
>> without a problem. And when you, for instance, use JENA [1], a
>> well known
>> RDF framework for Java, you generally /work/ with ontology
>> based knowledge
>> bases in such a way (at least in principle).
>> With JENA, you typically build a view to your knowledge base in the
>> following way:
>>  1) Create a so called "Model", which is empty at the beginning
>>  2) Read into this Model the RDF statements representing the
>> axioms of your
>> OWL ontology
>>  3) Read into this Model the RDF statements of your knowledge base
>> A "Model" in Jena represents an RDF graph, i.e. a set of RDF
>> triples. Now,
>> as long as you use a pure "Model", this only gives you a view to the
>> combined set of RDF triples, which come from both your OWL
>> ontology and your
>> knowledge base. But if you instead use an "OntModel" (which stands  
>> for
>> "Ontology Model"), you get an extended view to your RDF graph:
>> Suddenly, you
>> have additional API functionality to access all your OWL classes and
>> properties, and the (explicit) sub-relationships between them (and
> many
>> other ontology specific features). The magic behind this is that the
>> OntModel internally separates out all those triple subsets within the
>> combind RDF graph, which are RDF mappings for OWL axioms.
>> So this is the situation (or at least a possible and perfectly  
>> working
>> situation), when you /work/ with knowledge data. This does
>> not, however,
>> mean that you should also /store/ ontological and assertional
>> data together
>> in the same RDF graph. I think, in most cases it will be a
>> better strategy
>> to have them separately stored. Then, you can easily reuse the
>> ontology for
>> different knowledge bases, and combine them /on the fly/,
>> whenever you want
>> to work with them.
>> Cheers,
>> Michael
>> [1] http://jena.sourceforge.net/ (JENA project page)
>> --
>> Dipl.-Inform. Michael Schneider
>> FZI Forschungszentrum Informatik Karlsruhe
>> Abtl. Information Process Engineering (IPE)
>> Tel  : +49-721-9654-726
>> Fax  : +49-721-9654-727
>> Email: Michael.Schneider@fzi.de
>> Web  : http://www.fzi.de/ipe/eng/mitarbeiter.php?id=555
>> FZI Forschungszentrum Informatik an der Universität Karlsruhe
>> Haid-und-Neu-Str. 10-14, D-76131 Karlsruhe
>> Tel.: +49-721-9654-0, Fax: +49-721-9654-959
>> Stiftung des bürgerlichen Rechts
>> Az: 14-0563.1 Regierungspräsidium Karlsruhe
>> Vorstand: Rüdiger Dillmann, Michael Flor, Jivka Ovtcharova, Rudi
> Studer
>> Vorsitzender des Kuratoriums: Ministerialdirigent Günther Leßnerkraus
Received on Monday, 1 October 2007 17:55:44 UTC

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