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Re: [ontolog-forum] CCTONT work progress: Protege version

To: cassidy@xxxxxxxxx, "[ontolog-forum] " <ontolog-forum@xxxxxxxxxxxxxxxx>, "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Adam Pease <adampease@xxxxxxxxxxxxx>
Date: Sun, 21 Nov 2004 12:49:11 -0800
Message-id: <>
   If you could let me know of any typos you found, that would be of great 
help.  I can then fix and redistribute.    (01)

Adam    (02)

At 12:42 PM 11/21/2004, Patrick Cassidy wrote:
>The latest version of the combined SUMO+Mid-Level+Quality of Service 
>ontologies, together with the Core components representations that Adam 
>Pease has provided, is now available at:
>    ftp://micra.com/ontolog/CContology/
>   The Protege files containing the combined concepts of those
>ontologies are:
>     SMQCC.pprj
>     SMQCC.pins
>     SMQCC.pont
>    These have loaded properly in Protege version 2.1.2 (the latest full 
> release) on three computers, but have not been tested in other releases 
> of Protege.
>The problem of mangling the axiom text has been resolved, and
>the axioms should be viewable as instances of the class :SKIF-AXIOM.
>They also appear in the windows for classes and relations to which they
>are most relevant (but not, as in some viewers, in the windows for
>every concept mentioned in the axioms).
>    The contents of other files in that directory are described below, and 
> in the readme.txt file in that directory.
>   The Core-Components-specific concepts in the SKIF format are in the file:
>        CCTrep2.txt
>    Note that this file contains, in addition to the latest concepts 
> provided by
>Adam Pease (in CCTrep.kif), some additional concepts provided earlier
>by Adam for the CCT work.  Some of these have been reformatted to import
>properly using the SkifTab.
>    The latest set of concepts in the format provided by Adam are, as he
>has mentioned, in the file:
>       http://ontolog.cim3.net/file/work/ontology/UBLONT/CCTrep.kif
>    In the import process for each of these files, there were some format 
> changes
>made, mostly a reorganization of propositions by clustering the propositions
>according to the first argument.  Some standardized documentation was provided
>for some concepts without documentation.  A few apparent typographical errors
>were also corrected, and in a few cases this required some interpretation of
>the intent of the data, but in each case the intention seemed clear.  If 
>notices any errors or omissions in the import, I would much appreciate a 
>note so
>I can correct the problem.
>    As usual, I will be happy to answer any questions about the import 
> process or
>the results.
>     Pat
>My daytime phone now is (703)883-8976 (McLean, Virginia) or
>(732)578-6340 (Eatontown, NJ).  E-mail there is pcassidy (at) mitre.org.
>Patrick Cassidy
>MICRA, Inc.                      || (908) 561-3416
>735 Belvidere Ave.               || (908) 668-5252 (if no answer above)
>Plainfield, NJ 07062-2054
>internet:   cassidy@xxxxxxxxx
>Readme file to accompany the Protege import versions of the SUMO ontology, 
>plus the SUMO supplemented with the Quality of Service ontology (from Adam 
>Pease and Teknowledge) and the Core Components mappings created by Adam 
>Pease Nov. 2004.
>     This information is current as of November 21, 2004.
>The Protege ontology containing the SUMO and  Mid-Level combined 
>ontologies (KIF format is file SAM156b.txt), plus the Quality of Service 
>ontology (KIF file QOSONT.KIF), plus the Core Components classes suggested 
>by Adam Pease, (collected in the KIF file CCTrep2.txt) is contained in the 
>three Protege files:
>     SMQCC.pprj
>     SMQCC.pins
>     SMQCC.pont
>This ontology was constructed by adding the concepts in the Core 
>Components mappings provided by Adam Pease (in KIF file CCTrep2.txt) to 
>the SMQ ontology.  The SMQ ontology contains the SUMO and  Mid-Level 
>combined ontologies (KIF format is file SAM156b.txt), plus the Quality of 
>Service ontology (KIF file QOSONT.KIF).  The KIF-format classes in file 
>CCTrep2.txt correspond logically to the KIF-format classes provided by 
>Adam Pease, but in some cases  the format of the classes and relations 
>provided by Adam Pease was reorganized to conform to the format expected 
>by the SkifTab import program, mostly by adding a standard documentation 
>proposition to each subclass declaration..  The , or by changing some 
>apparent typographical errors.  The base Protege ontology containing the 
>SUMO and  Mid-Level combined ontologies (KIF format is file SAM156b.txt), 
>which was used to import these concepts is called SMQ and is contained in 
>the three Protege files :
>     SMQ.pprj
>     SMQ.pins
>     SMQ.pont
>The SMQ ontology was constructed by adding the concepts in the Quality of 
>Service ontology provided by Adam Pease (KIF file QOSONT.KIF) to 
>the  SAM156bX3 ontology, which contains the concepts in the combined SUMO 
>and Mid-Level ontologies.  The Protege ontology containing the SUMO 
>and  Mid-Level combined ontologies (KIF format is file SAM156b.txt),  is 
>contained in the three Protege files :
>     SAM156bX3.pprj
>     SAM156bX3.pins
>     SAM156bX3.pont
>    If any errors or omissions are present in any of these files -- KIF 
> format or Protege format -- please let me know and I will correct the 
>   NOTE about the import program:  The importation of KIF files into 
> Protege is performed by use of a Protege plug-in called SkifTab.  The 
> present version of this program has been tested only within Protege 
> version 2.1.2, using the Java run-time environment provided with the 
> Protege download.  The java files SkifTab.java and Predicates.java 
> contain the source code for the import program.  This program is still 
> crude, but appears at present to convert all of the logical information 
> in the original SKIF-format file into some Protege representation.  The 
> axioms are saved only as strings, and higher-arity relations are 
> represented as slots with additional facets -- but instances of 
> higher-arity relations need to be reified as instances of special classes.
>     The import program makes some assumptions about the format of the 
> SKIF file, with the result that a logically correct SKIF file in which 
> the propositions are not in a particular order will give errors during 
> the importing process.  Thus reorganization of a SKIF file may be 
> required to get the importation to proceed correctly.  The most important 
> format assumptions are:
>   (1) all propositions with a specific constant  in argument 1 position 
> must be collected in a single block of sequential lines, and separated 
> from other blocks by one or more blank lines.
>   (2) class definition blocks will have a subclass proposition as the 
> first proposition
>   (3) relation definition blocks will have either an instance proposition 
> or a subrelation proposition as the first proposition of the block
>   (4) instance definition blocks will have an instance proposition as the 
> first proposition of the block
>   (5) all blocks must have a documentation proposition as the final 
> proposition, unless they are bounded by special tags
>   (6) every proposition other than a documentation proposition must be a 
> single line
>   This was the format followed by the original SUMO SKIF file, but it is 
> not followed in all subsequent ontologies provided by Teknowledge.  Some 
> reorganization of those SKIF files is thus usually necessary for the 
> import process.
>   The import program can be made more flexible, but it was decided that 
> requiring a specific format is better, because certain types of errors in 
> the import files are easier to detect when they are organized in this manner.
>   At present the program cannot correctly export all information from a 
> Protege file to a SKIF-format file, and this program is therefore usable 
> at present only as a visualizing tool, not for development or editing.
>    Recently an additional problem has arisen.  Under certain 
> circumstances (frequently, recently), an internal Java interpreter error 
> occurs, in which the program exits without any useful error 
> information.  This is apparently a bug in the optimization routine of the 
> Java run-time program, and can be avoided by running the program in 
> interpret-only (no optimization) mode, at the cost of a substantially 
> slower execution.  I do not know at present whether later versions of 
> Protege will manage to avoid the conditions that cause this bug to surface.
>    Pat Cassidy
>   cassidy@xxxxxxxxx
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