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

To: "[ontolog-forum]" <ontolog-forum@xxxxxxxxxxxxxxxx>
From: Patrick Cassidy <pcassidy@xxxxxxxxxxxxxxxx>
Date: Sun, 21 Nov 2004 15:42:46 -0500
Message-id: <41A0FDC6.7050400@xxxxxxxxxxxxxxxx>
The latest version of the combined SUMO+Mid-Level+Quality of Service 
together with the Core components representations that Adam Pease has provided, 
is now available at:
    ftp://micra.com/ontolog/CContology/    (01)

   The Protege files containing the combined concepts of those
ontologies are:
     SMQCC.pont    (02)

    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 
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).    (03)

    The contents of other files in that directory are described below, and in 
the readme.txt file in that directory.    (04)

   The Core-Components-specific concepts in the SKIF format are in the file:
        CCTrep2.txt    (05)

    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.    (06)

    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    (07)

    In the import process for each of these files, there were some format 
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 anyone
notices any errors or omissions in the import, I would much appreciate a note so
I can correct the problem.    (08)

    As usual, I will be happy to answer any questions about the import process 
the results.    (09)

     Pat    (010)

My daytime phone now is (703)883-8976 (McLean, Virginia) or
(732)578-6340 (Eatontown, NJ).  E-mail there is pcassidy (at) mitre.org.    (011)

Patrick Cassidy    (012)

MICRA, Inc.                      || (908) 561-3416
735 Belvidere Ave.               || (908) 668-5252 (if no answer above)
Plainfield, NJ 07062-2054    (013)

internet:   cassidy@xxxxxxxxx
=============================================    (014)

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.    (015)

The Protege ontology containing the SUMO and  Mid-Level combined ontologies 
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.pont    (016)

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 
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.pont    (017)

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.pont    (018)

    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 problems.    (019)

============================================    (020)

   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 
  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 
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 
collected in a single block of sequential lines, and separated from other 
by one or more blank lines.
   (2) class definition blocks will have a subclass proposition as the first 
   (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 
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 
line    (021)

   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.    (022)

   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.    (023)

   At present the program cannot correctly export all information from a 
file to a SKIF-format file, and this program is therefore usable at present 
as a visualizing tool, not for development or editing.    (024)

    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 
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 
of Protege will manage to avoid the conditions that cause this bug to surface.    (025)

    Pat Cassidy
   cassidy@xxxxxxxxx    (026)

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