[DL-Learner SVN] SF.net SVN: dl-learner:[1368] trunk

[<ku...@us...>]

Revision: 1368
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1368&view=rev
Author:   kurzum
Date:     2008-10-11 13:35:40 +0000 (Sat, 11 Oct 2008)

Log Message:
-----------


Modified Paths:
--------------
    trunk/doc/configOptions.txt
    trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf
    trunk/examples/sparql/scrobble.conf
    trunk/examples/sparql/scrobble.kb
    trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
    trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java
    trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java

Modified: trunk/doc/configOptions.txt
===================================================================
--- trunk/doc/configOptions.txt	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/doc/configOptions.txt	2008-10-11 13:35:40 UTC (rev 1368)
@@ -7,44 +7,56 @@
 component: KB file (org.dllearner.kb.KBFile)
 ============================================
 
-CLI usage: import = ;
+CLI usage: null = null;
 
-option name: filename
-description: pointer to the KB file on local file system
-values: class org.dllearner.core.config.StringConfigOption
-default value: null
-CLI usage: .filename = null;
-
 option name: url
 description: URL pointer to the KB file
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.config.URLConfigOption
 default value: null
-CLI usage: .url = null;
+CLI usage: null.url = null;
 
 
+component: OWL API Ontology (org.dllearner.kb.OWLAPIOntology)
+=============================================================
+
+CLI usage: null = null;
+
+
 component: OWL file (org.dllearner.kb.OWLFile)
 ==============================================
 
-CLI usage: import = ;
+CLI usage: null = owlfile;
 
 option name: url
 description: URL pointing to the OWL file
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.config.URLConfigOption
 default value: null
-CLI usage: .url = null;
+CLI usage: owlfile.url = null;
 
 
 component: SPARQL Endpoint (org.dllearner.kb.sparql.SparqlKnowledgeSource)
 ==========================================================================
 
-CLI usage: import = sparql;
+CLI usage: null = sparql;
 
 option name: url
 description: URL of SPARQL Endpoint
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.config.URLConfigOption
 default value: null
 CLI usage: sparql.url = null;
 
+option name: cacheDir
+description: dir of cache
+values: class org.dllearner.core.config.StringConfigOption
+default value: cache
+CLI usage: sparql.cacheDir = cache;
+
+option name: useCache
+description: If true a Cache is used
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: sparql.useCache = true;
+
 option name: instances
 description: relevant instances e.g. positive and negative examples in a learning problem
 values: class org.dllearner.core.config.StringSetConfigOption
@@ -54,123 +66,99 @@
 option name: recursionDepth
 description: recursion depth of KB fragment selection
 values: class org.dllearner.core.config.IntegerConfigOption
-default value: 2
-CLI usage: sparql.recursionDepth = 2;
+default value: 1
+CLI usage: sparql.recursionDepth = 1;
 
 option name: predefinedFilter
-description: the mode of the SPARQL Filter
-values: class org.dllearner.core.config.IntegerConfigOption
+description: the mode of the SPARQL Filter, use one of YAGO,SKOS,YAGOSKOS , YAGOSPECIALHIERARCHY, TEST
+values: class org.dllearner.core.config.StringConfigOption
 default value: null
 CLI usage: sparql.predefinedFilter = null;
 
 option name: predefinedEndpoint
-description: the mode of the SPARQL Filter
-values: class org.dllearner.core.config.IntegerConfigOption
+description: the mode of the SPARQL Filter, use one of DBPEDIA, LOCAL, GOVTRACK, REVYU, MYOPENLINK, FACTBOOK
+values: class org.dllearner.core.config.StringConfigOption
 default value: null
 CLI usage: sparql.predefinedEndpoint = null;
 
+option name: predefinedManipulator
+description: the mode of the Manipulator, use one of STANDARD, DBPEDIA-NAVIGATOR
+values: class org.dllearner.core.config.StringConfigOption
+default value: null
+CLI usage: sparql.predefinedManipulator = null;
+
 option name: predList
 description: list of all ignored roles
 values: class org.dllearner.core.config.StringSetConfigOption
-default value: null
-CLI usage: sparql.predList = null;
+default value: []
+CLI usage: sparql.predList = [];
 
 option name: objList
 description: list of all ignored objects
 values: class org.dllearner.core.config.StringSetConfigOption
-default value: null
-CLI usage: sparql.objList = null;
+default value: []
+CLI usage: sparql.objList = [];
 
-option name: classList
-description: list of all ignored classes
-values: class org.dllearner.core.config.StringSetConfigOption
-default value: null
-CLI usage: sparql.classList = null;
-
-option name: format
-description: N-TRIPLES or KB format
-values: class org.dllearner.core.config.StringConfigOption
-default value: N-TRIPLES
-CLI usage: sparql.format = N-TRIPLES;
-
-option name: dumpToFile
-description: Specifies whether the extracted ontology is written to a file or not.
+option name: saveExtractedFragment
+description: Specifies whether the extracted ontology is written to a file or not. The OWL file is written to the cache dir.Some DBpedia URI will make the XML invalid
 values: class org.dllearner.core.config.BooleanConfigOption
 default value: true
-CLI usage: sparql.dumpToFile = true;
+CLI usage: sparql.saveExtractedFragment = true;
 
-option name: useLits
-description: use Literals in SPARQL query
-values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: sparql.useLits = null;
-
-option name: getAllSuperClasses
-description: If true then all superclasses are retrieved until the most general class (owl:Thing) is reached.
-values: class org.dllearner.core.config.BooleanConfigOption
-default value: true
-CLI usage: sparql.getAllSuperClasses = true;
-
-option name: learnDomain
-description: learns the Domain for a Role
-values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: sparql.learnDomain = null;
-
-option name: learnRange
-description: learns the Range for a Role
-values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: sparql.learnRange = null;
-
-option name: role
-description: role to learn Domain/Range from
-values: class org.dllearner.core.config.StringConfigOption
-default value: null
-CLI usage: sparql.role = null;
-
-option name: blankNodeIdentifier
-description: used to identify blanknodes in Tripels
-values: class org.dllearner.core.config.StringConfigOption
-default value: null
-CLI usage: sparql.blankNodeIdentifier = null;
-
-option name: example
-description: example
-values: class org.dllearner.core.config.StringTupleListConfigOption
-default value: null
-CLI usage: sparql.example = null;
-
 option name: replacePredicate
 description: rule for replacing predicates
 values: class org.dllearner.core.config.StringTupleListConfigOption
-default value: null
-CLI usage: sparql.replacePredicate = null;
+default value: []
+CLI usage: sparql.replacePredicate = [];
 
 option name: replaceObject
 description: rule for replacing predicates
 values: class org.dllearner.core.config.StringTupleListConfigOption
-default value: null
-CLI usage: sparql.replaceObject = null;
+default value: []
+CLI usage: sparql.replaceObject = [];
 
 option name: breakSuperClassRetrievalAfter
 description: stops a cyclic hierarchy after specified number of classes
 values: class org.dllearner.core.config.IntegerConfigOption
-default value: null
-CLI usage: sparql.breakSuperClassRetrievalAfter = null;
+default value: 1000
+CLI usage: sparql.breakSuperClassRetrievalAfter = 1000;
 
-option name: numberOfInstancesUsedForRoleLearning
-description: 
-values: class org.dllearner.core.config.IntegerConfigOption
-default value: null
-CLI usage: sparql.numberOfInstancesUsedForRoleLearning = null;
+option name: useLits
+description: use Literals in SPARQL query
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: sparql.useLits = true;
 
+option name: getAllSuperClasses
+description: If true then all superclasses are retrieved until the most general class (owl:Thing) is reached.
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: sparql.getAllSuperClasses = true;
+
 option name: closeAfterRecursion
 description: gets all classes for all instances
 values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: sparql.closeAfterRecursion = null;
+default value: true
+CLI usage: sparql.closeAfterRecursion = true;
 
+option name: getPropertyInformation
+description: gets all types for extracted ObjectProperties
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: sparql.getPropertyInformation = false;
+
+option name: dissolveBlankNodes
+description: determines whether Blanknodes are dissolved. This is a costly function.
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: sparql.dissolveBlankNodes = true;
+
+option name: useImprovedSparqlTupelAquisitor
+description: uses deeply nested SparqlQueries, according to recursion depth, still EXPERIMENTAL
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: sparql.useImprovedSparqlTupelAquisitor = false;
+
 option name: verbosity
 description: control verbosity of output for this component
 values: class org.dllearner.core.config.StringConfigOption
@@ -180,14 +168,14 @@
 option name: defaultGraphURIs
 description: a list of all default Graph URIs
 values: class org.dllearner.core.config.StringSetConfigOption
-default value: null
-CLI usage: sparql.defaultGraphURIs = null;
+default value: []
+CLI usage: sparql.defaultGraphURIs = [];
 
 option name: namedGraphURIs
 description: a list of all named Graph URIs
 values: class org.dllearner.core.config.StringSetConfigOption
-default value: null
-CLI usage: sparql.namedGraphURIs = null;
+default value: []
+CLI usage: sparql.namedGraphURIs = [];
 
 
 *************
@@ -197,7 +185,7 @@
 component: DIG reasoner (org.dllearner.reasoning.DIGReasoner)
 =============================================================
 
-CLI usage: reasoner = digReasoner;
+CLI usage: null = digReasoner;
 
 option name: reasonerUrl
 description: URL of the DIG reasoner
@@ -221,7 +209,7 @@
 component: fast instance checker (org.dllearner.reasoning.FastInstanceChecker)
 ==============================================================================
 
-CLI usage: reasoner = fastInstanceChecker;
+CLI usage: null = fastInstanceChecker;
 
 option name: reasonerType
 description: FaCT++ or Pellet to dematerialize
@@ -229,20 +217,26 @@
 default value: pellet
 CLI usage: fastInstanceChecker.reasonerType = pellet;
 
+option name: defaultNegation
+description: Whether to use default negation, i.e. an instance not being in a class means that it is in the negation of the class.
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: fastInstanceChecker.defaultNegation = true;
 
+
 component: fast retrieval reasoner (org.dllearner.reasoning.FastRetrievalReasoner)
 ==================================================================================
 
-CLI usage: reasoner = fastRetrieval;
+CLI usage: null = fastRetrievalReasoner;
 
 
 component: OWL API reasoner (org.dllearner.reasoning.OWLAPIReasoner)
 ====================================================================
 
-CLI usage: reasoner = owlAPIReasoner;
+CLI usage: null = owlAPIReasoner;
 
 option name: reasonerType
-description: FaCT++ or Pellet
+description: FaCT++ or Pellet, which means "pellet" or "fact"
 values: class org.dllearner.core.config.StringConfigOption
 default value: pellet
 CLI usage: owlAPIReasoner.reasonerType = pellet;
@@ -255,7 +249,7 @@
 component: two valued definition learning problem (org.dllearner.learningproblems.PosNegDefinitionLP)
 =====================================================================================================
 
-CLI usage: problem = posNegDefinitionLP;
+CLI usage: null = posNegDefinitionLP;
 
 option name: positiveExamples
 description: positive examples
@@ -272,8 +266,8 @@
 option name: useRetrievalForClassficiation
 description: Specifies whether to use retrieval or instance checks for testing a concept.
 values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: posNegDefinitionLP.useRetrievalForClassficiation = null;
+default value: false
+CLI usage: posNegDefinitionLP.useRetrievalForClassficiation = false;
 
 option name: percentPerLenghtUnit
 description: describes the reduction in classification accuracy in percent one is willing to accept for reducing the length of the concept by one
@@ -284,15 +278,69 @@
 option name: useMultiInstanceChecks
 description: See UseMultiInstanceChecks enum.
 values: class org.dllearner.core.config.StringConfigOption
+default value: twoChecks
+CLI usage: posNegDefinitionLP.useMultiInstanceChecks = twoChecks;
+
+
+component: three valued definition learning problem (org.dllearner.learningproblems.PosNegDefinitionLPStrict)
+=============================================================================================================
+
+CLI usage: null = null;
+
+option name: positiveExamples
+description: positive examples
+values: class org.dllearner.core.config.StringSetConfigOption
 default value: null
-CLI usage: posNegDefinitionLP.useMultiInstanceChecks = null;
+CLI usage: null.positiveExamples = null;
 
+option name: negativeExamples
+description: negative examples
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: null.negativeExamples = null;
 
-component: inclusion learning problem (org.dllearner.learningproblems.PosNegInclusionLP)
-========================================================================================
+option name: useRetrievalForClassficiation
+description: Specifies whether to use retrieval or instance checks for testing a concept.
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: null.useRetrievalForClassficiation = false;
 
-CLI usage: problem = posNegInclusionLP;
+option name: percentPerLenghtUnit
+description: describes the reduction in classification accuracy in percent one is willing to accept for reducing the length of the concept by one
+values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+default value: 0.05
+CLI usage: null.percentPerLenghtUnit = 0.05;
 
+option name: useMultiInstanceChecks
+description: See UseMultiInstanceChecks enum.
+values: class org.dllearner.core.config.StringConfigOption
+default value: twoChecks
+CLI usage: null.useMultiInstanceChecks = twoChecks;
+
+option name: penaliseNeutralExamples
+description: if set to true neutral examples are penalised
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: null
+CLI usage: null.penaliseNeutralExamples = null;
+
+option name: accuracyPenalty
+description: penalty for pos/neg examples which are classified as neutral
+values: class org.dllearner.core.config.DoubleConfigOption
+default value: 1.0
+CLI usage: null.accuracyPenalty = 1.0;
+
+option name: errorPenalty
+description: penalty for pos. examples classified as negative or vice versa
+values: class org.dllearner.core.config.DoubleConfigOption
+default value: 3.0
+CLI usage: null.errorPenalty = 3.0;
+
+
+component: two valued inclusion learning problem (org.dllearner.learningproblems.PosNegInclusionLP)
+===================================================================================================
+
+CLI usage: null = posNegInclusionLP;
+
 option name: positiveExamples
 description: positive examples
 values: class org.dllearner.core.config.StringSetConfigOption
@@ -308,8 +356,8 @@
 option name: useRetrievalForClassficiation
 description: Specifies whether to use retrieval or instance checks for testing a concept.
 values: class org.dllearner.core.config.BooleanConfigOption
-default value: null
-CLI usage: posNegInclusionLP.useRetrievalForClassficiation = null;
+default value: false
+CLI usage: posNegInclusionLP.useRetrievalForClassficiation = false;
 
 option name: percentPerLenghtUnit
 description: describes the reduction in classification accuracy in percent one is willing to accept for reducing the length of the concept by one
@@ -320,14 +368,14 @@
 option name: useMultiInstanceChecks
 description: See UseMultiInstanceChecks enum.
 values: class org.dllearner.core.config.StringConfigOption
-default value: null
-CLI usage: posNegInclusionLP.useMultiInstanceChecks = null;
+default value: twoChecks
+CLI usage: posNegInclusionLP.useMultiInstanceChecks = twoChecks;
 
 
 component: positive only definition learning problem (org.dllearner.learningproblems.PosOnlyDefinitionLP)
 =========================================================================================================
 
-CLI usage: problem = posOnlyDefinitionLP;
+CLI usage: null = posOnlyDefinitionLP;
 
 option name: positiveExamples
 description: positive examples
@@ -336,6 +384,18 @@
 CLI usage: posOnlyDefinitionLP.positiveExamples = null;
 
 
+component: pos only inclusion learning problem (org.dllearner.learningproblems.PosOnlyInclusionLP)
+==================================================================================================
+
+CLI usage: null = null;
+
+option name: positiveExamples
+description: positive examples
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: null.positiveExamples = null;
+
+
 ***********************
 * Learning Algorithms *
 ***********************
@@ -343,13 +403,13 @@
 component: brute force learning algorithm (org.dllearner.algorithms.BruteForceLearner)
 ======================================================================================
 
-CLI usage: algorithm = bruteForce;
+CLI usage: null = bruteForce;
 
 option name: maxLength
 description: maximum length of generated concepts
 values: class org.dllearner.core.config.IntegerConfigOption
-default value: null
-CLI usage: bruteForce.maxLength = null;
+default value: 7
+CLI usage: bruteForce.maxLength = 7;
 
 option name: returnType
 description: Specifies the type which the solution has to belong to (if already) known. This means we inform the learning algorithm that the solution is a subclass of this type.
@@ -358,28 +418,214 @@
 CLI usage: bruteForce.returnType = null;
 
 
+component: DBpedia Navigation Suggestor (org.dllearner.algorithms.DBpediaNavigationSuggestor)
+=============================================================================================
+
+CLI usage: null = dbpediaNavigationSuggestor;
+
+option name: writeSearchTree
+description: specifies whether to write a search tree
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: dbpediaNavigationSuggestor.writeSearchTree = false;
+
+option name: searchTreeFile
+description: file to use for the search tree
+values: class org.dllearner.core.config.StringConfigOption
+default value: log/searchTree.txt
+CLI usage: dbpediaNavigationSuggestor.searchTreeFile = log/searchTree.txt;
+
+option name: replaceSearchTree
+description: specifies whether to replace the search tree in the log file after each run or append the new search tree
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: dbpediaNavigationSuggestor.replaceSearchTree = false;
+
+option name: heuristic
+description: specifiy the heuristic to use
+values: class org.dllearner.core.config.StringConfigOption
+default value: lexicographic
+CLI usage: dbpediaNavigationSuggestor.heuristic = lexicographic;
+
+option name: applyAllFilter
+description: usage of equivalence ALL R.C AND ALL R.D = ALL R.(C AND D)
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.applyAllFilter = true;
+
+option name: applyExistsFilter
+description: usage of equivalence EXISTS R.C OR EXISTS R.D = EXISTS R.(C OR D)
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.applyExistsFilter = true;
+
+option name: useTooWeakList
+description: try to filter out too weak concepts without sending them to the reasoner
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useTooWeakList = true;
+
+option name: useOverlyGeneralList
+description: try to find overly general concept without sending them to the reasoner
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useOverlyGeneralList = true;
+
+option name: useShortConceptConstruction
+description: shorten concept to see whether they already exist
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useShortConceptConstruction = true;
+
+option name: horizontalExpansionFactor
+description: horizontal expansion factor (see publication for description)
+values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+default value: 0.6
+CLI usage: dbpediaNavigationSuggestor.horizontalExpansionFactor = 0.6;
+
+option name: improveSubsumptionHierarchy
+description: simplify subsumption hierarchy to reduce search space (see publication for description)
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.improveSubsumptionHierarchy = true;
+
+option name: allowedConcepts
+description: concepts the algorithm is allowed to use
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.allowedConcepts = null;
+
+option name: ignoredConcepts
+description: concepts the algorithm must ignore
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.ignoredConcepts = null;
+
+option name: allowedRoles
+description: roles the algorithm is allowed to use
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.allowedRoles = null;
+
+option name: ignoredRoles
+description: roles the algorithm must ignore
+values: class org.dllearner.core.config.StringSetConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.ignoredRoles = null;
+
+option name: useAllConstructor
+description: specifies whether the universal concept constructor is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useAllConstructor = true;
+
+option name: useExistsConstructor
+description: specifies whether the existential concept constructor is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useExistsConstructor = true;
+
+option name: useCardinalityRestrictions
+description: specifies whether CardinalityRestrictions is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useCardinalityRestrictions = true;
+
+option name: useHasValueConstructor
+description: specifies whether the hasValue constructor is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: dbpediaNavigationSuggestor.useHasValueConstructor = false;
+
+option name: valueFrequencyThreshold
+description: specifies how often an object must occur as value in order to be considered for hasValue restrictions
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 3
+CLI usage: dbpediaNavigationSuggestor.valueFrequencyThreshold = 3;
+
+option name: useNegation
+description: specifies whether negation is used in the learning algorothm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useNegation = true;
+
+option name: useBooleanDatatypes
+description: specifies whether boolean datatypes are used in the learning algorothm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: dbpediaNavigationSuggestor.useBooleanDatatypes = true;
+
+option name: maxExecutionTimeInSeconds
+description: algorithm will stop after specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: dbpediaNavigationSuggestor.maxExecutionTimeInSeconds = 0;
+
+option name: minExecutionTimeInSeconds
+description: algorithm will run at least specified seconds
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: dbpediaNavigationSuggestor.minExecutionTimeInSeconds = 0;
+
+option name: guaranteeXgoodDescriptions
+description: algorithm will run until X good (100%) concept descritpions are found
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 1
+CLI usage: dbpediaNavigationSuggestor.guaranteeXgoodDescriptions = 1;
+
+option name: logLevel
+description: determines the logLevel for this component, can be {TRACE, DEBUG, INFO}
+values: class org.dllearner.core.config.StringConfigOption
+default value: DEBUG
+CLI usage: dbpediaNavigationSuggestor.logLevel = DEBUG;
+
+option name: noisePercentage
+description: the (approximated) percentage of noise within the examples
+values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 100.0
+default value: 0.0
+CLI usage: dbpediaNavigationSuggestor.noisePercentage = 0.0;
+
+option name: startClass
+description: the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)
+values: class org.dllearner.core.config.StringConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.startClass = null;
+
+option name: forceRefinementLengthIncrease
+description: specifies whether nodes should be expanded until only longer refinements are reached
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: null
+CLI usage: dbpediaNavigationSuggestor.forceRefinementLengthIncrease = null;
+
+
 component: random guesser learning algorithm (org.dllearner.algorithms.RandomGuesser)
 =====================================================================================
 
-CLI usage: algorithm = random;
+CLI usage: null = random;
 
 option name: numberOfTrees
 description: number of randomly generated concepts/trees
 values: class org.dllearner.core.config.IntegerConfigOption
-default value: null
-CLI usage: random.numberOfTrees = null;
+default value: 5
+CLI usage: random.numberOfTrees = 5;
 
 option name: maxDepth
 description: maximum depth of generated concepts/trees
 values: class org.dllearner.core.config.IntegerConfigOption
-default value: null
-CLI usage: random.maxDepth = null;
+default value: 5
+CLI usage: random.maxDepth = 5;
 
 
+component: simple suggestion algorithm (org.dllearner.algorithms.SimpleSuggestionLearningAlgorithm)
+===================================================================================================
+
+CLI usage: null = null;
+
+
 component: genetic programming learning algorithm (org.dllearner.algorithms.gp.GP)
 ==================================================================================
 
-CLI usage: algorithm = gp;
+CLI usage: null = gp;
 
 option name: selectionType
 description: selection type
@@ -399,29 +645,35 @@
 default value: true
 CLI usage: gp.elitism = true;
 
-option name: mutationProbablitiy
+option name: algorithmType
+description: algorithm type
+values: class org.dllearner.core.config.StringConfigOption
+default value: steadyState
+CLI usage: gp.algorithmType = steadyState;
+
+option name: mutationProbability
 description: mutation probability
 values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
 default value: 0.03
-CLI usage: gp.mutationProbablitiy = 0.03;
+CLI usage: gp.mutationProbability = 0.03;
 
-option name: crossoverProbablitiy
+option name: crossoverProbability
 description: crossover probability
 values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
 default value: 0.95
-CLI usage: gp.crossoverProbablitiy = 0.95;
+CLI usage: gp.crossoverProbability = 0.95;
 
-option name: hillClimbingProbablitiy
+option name: hillClimbingProbability
 description: hill climbing probability
 values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
 default value: 0.0
-CLI usage: gp.hillClimbingProbablitiy = 0.0;
+CLI usage: gp.hillClimbingProbability = 0.0;
 
-option name: refinementProbablitiy
+option name: refinementProbability
 description: refinement operator probability (values higher than 0 turn this into a hybrid GP algorithm - see publication)
 values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
 default value: 0.0
-CLI usage: gp.refinementProbablitiy = 0.0;
+CLI usage: gp.refinementProbability = 0.0;
 
 option name: numberOfIndividuals
 description: number of individuals
@@ -481,7 +733,7 @@
 component: example driven refinement operator based learning algorithm (org.dllearner.algorithms.refexamples.ExampleBasedROLComponent)
 ======================================================================================================================================
 
-CLI usage: algorithm = refexamples;
+CLI usage: null = refexamples;
 
 option name: writeSearchTree
 description: specifies whether to write a search tree
@@ -585,6 +837,18 @@
 default value: true
 CLI usage: refexamples.useExistsConstructor = true;
 
+option name: useHasValueConstructor
+description: specifies whether the hasValue constructor is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: refexamples.useHasValueConstructor = false;
+
+option name: valueFrequencyThreshold
+description: specifies how often an object must occur as value in order to be considered for hasValue restrictions
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 3
+CLI usage: refexamples.valueFrequencyThreshold = 3;
+
 option name: useCardinalityRestrictions
 description: specifies whether CardinalityRestrictions is used in the learning algorithm
 values: class org.dllearner.core.config.BooleanConfigOption
@@ -603,6 +867,12 @@
 default value: true
 CLI usage: refexamples.useBooleanDatatypes = true;
 
+option name: useDoubleDatatypes
+description: specifies whether boolean datatypes are used in the learning algorothm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: refexamples.useDoubleDatatypes = true;
+
 option name: maxExecutionTimeInSeconds
 description: algorithm will stop after specified seconds
 values: class org.dllearner.core.config.IntegerConfigOption
@@ -621,17 +891,35 @@
 default value: 1
 CLI usage: refexamples.guaranteeXgoodDescriptions = 1;
 
+option name: maxClassDescriptionTests
+description: The maximum number of candidate hypothesis the algorithm is allowed to test (0 = no limit). The algorithm will stop afterwards. (The real number of tests can be slightly higher, because this criterion usually won't be checked after each single test.)
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 0
+CLI usage: refexamples.maxClassDescriptionTests = 0;
+
 option name: logLevel
 description: determines the logLevel for this component, can be {TRACE, DEBUG, INFO}
 values: class org.dllearner.core.config.StringConfigOption
 default value: DEBUG
 CLI usage: refexamples.logLevel = DEBUG;
 
+option name: usePropernessChecks
+description: specifies whether to check for equivalence (i.e. discard equivalent refinements)
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: false
+CLI usage: refexamples.usePropernessChecks = false;
+
+option name: maxPosOnlyExpansion
+description: specifies how often a node in the search tree of a posonly learning problem needs to be expanded before it is considered as solution candidate
+values: class org.dllearner.core.config.IntegerConfigOption
+default value: 4
+CLI usage: refexamples.maxPosOnlyExpansion = 4;
+
 option name: noisePercentage
 description: the (approximated) percentage of noise within the examples
 values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 100.0
-default value: null
-CLI usage: refexamples.noisePercentage = null;
+default value: 0.0
+CLI usage: refexamples.noisePercentage = 0.0;
 
 option name: startClass
 description: the named class which should be used to start the algorithm (GUI: needs a widget for selecting a class)
@@ -639,11 +927,17 @@
 default value: null
 CLI usage: refexamples.startClass = null;
 
+option name: forceRefinementLengthIncrease
+description: specifies whether nodes should be expanded until only longer refinements are reached
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: null
+CLI usage: refexamples.forceRefinementLengthIncrease = null;
 
+
 component: refinement operator based learning algorithm (org.dllearner.algorithms.refinement.ROLearner)
 =======================================================================================================
 
-CLI usage: algorithm = refinement;
+CLI usage: null = refinement;
 
 option name: writeSearchTree
 description: specifies whether to write a search tree
@@ -759,6 +1053,12 @@
 default value: true
 CLI usage: refinement.useNegation = true;
 
+option name: useCardinalityRestrictions
+description: specifies whether CardinalityRestrictions is used in the learning algorithm
+values: class org.dllearner.core.config.BooleanConfigOption
+default value: true
+CLI usage: refinement.useCardinalityRestrictions = true;
+
 option name: useBooleanDatatypes
 description: specifies whether boolean datatypes are used in the learning algorothm
 values: class org.dllearner.core.config.BooleanConfigOption

Modified: trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf
===================================================================
--- trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/examples/sparql/difference/DBPediaSKOS_kohl_vs_angela.conf	2008-10-11 13:35:40 UTC (rev 1368)
@@ -87,6 +87,6 @@
 
 
 /** examples **/
-+"http://dbpedia.org/resource/Helmut_Kohl"
--"http://dbpedia.org/resource/Angela_Merkel"
+-"http://dbpedia.org/resource/Helmut_Kohl"
++"http://dbpedia.org/resource/Angela_Merkel"
 

Modified: trunk/examples/sparql/scrobble.conf
===================================================================
--- trunk/examples/sparql/scrobble.conf	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/examples/sparql/scrobble.conf	2008-10-11 13:35:40 UTC (rev 1368)
@@ -23,15 +23,28 @@
 refexamples.useNegation = false;
 refexamples.useAllConstructor = false;
 refexamples.useCardinalityRestrictions = false;
+
+refexamples.writeSearchTree = true;
+refexamples.searchTreeFile = "log/searchtree.txt";
+refexamples.replaceSearchTree = true;
+
 reasoner = fastInstanceChecker;
 
 import("http://dbtune.org/musicbrainz/sparql","SPARQL");
 
+
 // we transform tags to classes
 sparql.replacePredicate=[(
 "http://www.holygoat.co.uk/owl/redwood/0.1/tags/taggedWithTag",
 "http://www.w3.org/1999/02/22-rdf-syntax-ns#type")];
 
+/*
+// some consistency transformation
+sparql.replaceObject=[(
+"http://dbtune.org/musicbrainz/resource/tag/",
+"http://dbtune.org/musicbrainz/resource/tag/tag")];
+*/
+
 // some background knowledge about the tags ("semantically enriched tag cloud")
 import("scrobble.kb");
 

Modified: trunk/examples/sparql/scrobble.kb
===================================================================
--- trunk/examples/sparql/scrobble.kb	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/examples/sparql/scrobble.kb	2008-10-11 13:35:40 UTC (rev 1368)
@@ -4,3 +4,12 @@
 "http://dbtune.org/musicbrainz/resource/tag/171" = "http://dbtune.org/musicbrainz/resource/tag/237".
 // progressive rock is rock
 "http://dbtune.org/musicbrainz/resource/tag/29" SUBCLASSOF "http://dbtune.org/musicbrainz/resource/tag/7".
+
+//repetition for valid xml by OWL API
+
+// english implies british
+"http://dbtune.org/musicbrainz/resource/tag/tag1391" SUBCLASSOF  "http://dbtune.org/musicbrainz/resource/tag/tag171".
+// Britain = UK
+"http://dbtune.org/musicbrainz/resource/tag/tag171" = "http://dbtune.org/musicbrainz/resource/tag/tag237".
+// progressive rock is rock
+"http://dbtune.org/musicbrainz/resource/tag/tag29" SUBCLASSOF "http://dbtune.org/musicbrainz/resource/tag/tag7".

Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/ClassNode.java	2008-10-11 13:35:40 UTC (rev 1368)
@@ -178,7 +178,7 @@
 				OWLLabelAnnotation label = factory.getOWLLabelAnnotation(one.getBPart().getLiteral().getString());
 				owlAPIOntologyCollector.addAxiom(factory.getOWLEntityAnnotationAxiom(me, label));
 			}else {
-				tail(true, "in ontology conversion, no other datatypes, but annotation allowed for class"+" data property is: "+one.getURIString()+" connected with: "+one.getBPart().getNTripleForm());
+				tail(true, "in ontology conversion: no other datatypes, but annotation is allowed for classes."+" data property is: "+one.getURIString()+" connected with: "+one.getBPart().getNTripleForm());
 				
 			}
 		

Modified: trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/src/dl-learner/org/dllearner/kb/extraction/Node.java	2008-10-11 13:35:40 UTC (rev 1368)
@@ -40,7 +40,7 @@
 	.getLogger(Node.class);
 	
 	// make sure no information is missed during the transition to OWLAPI
-	public static final boolean DEBUGTAIL = true;
+	public static final boolean DEBUGTAIL = false;
 
 	protected String uri;
 	// protected String type;
@@ -114,7 +114,7 @@
 	
 	public void tail(boolean ignore, String tailmessage){
 		
-		String message = "difficult tuple. Subject is: "+ this.getURIString()+" of class"+this.getClass().getSimpleName()+" " +
+		String message = "difficult tuple. Subject is: "+ this.getURIString()+" of type: "+this.getClass().getSimpleName()+" " +
 				"info: "+tailmessage;
 		if(ignore){
 			if(DEBUGTAIL){

Modified: trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java
===================================================================
--- trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java	2008-10-11 10:25:09 UTC (rev 1367)
+++ trunk/src/dl-learner/org/dllearner/kb/sparql/SparqlKnowledgeSource.java	2008-10-11 13:35:40 UTC (rev 1368)
@@ -59,7 +59,6 @@
 import org.dllearner.utilities.JamonMonitorLogger;
 import org.dllearner.utilities.datastructures.StringTuple;
 import org.dllearner.utilities.statistics.SimpleClock;
-import org.semanticweb.owl.model.OWLAxiom;
 import org.semanticweb.owl.model.OWLOntology;
 
 import com.jamonapi.Monitor;
@@ -178,7 +177,7 @@
 						"Specifies whether the extracted ontology is written to a file or not. " +
 						"The OWL file is written to the cache dir." +
 						"Some DBpedia URI will make the XML invalid",
-						true, false, true));
+						false, false, true));
 		options.add(new StringTupleListConfigOption("replacePredicate",
 				"rule for replacing predicates", new ArrayList<StringTuple>(), false, true));
 		options.add(new StringTupleListConfigOption("replaceObject",


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