[DL-Learner SVN] SF.net SVN: dl-learner:[1596] trunk

[<jen...@us...>]

Revision: 1596
          http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1596&view=rev
Author:   jenslehmann
Date:     2009-02-12 16:17:41 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
manual continued

Modified Paths:
--------------
    trunk/doc/configOptions.txt
    trunk/doc/manual/bibliography.bib
    trunk/doc/manual/manual.tex
    trunk/src/dl-learner/org/dllearner/cli/Start.java

Modified: trunk/doc/configOptions.txt
===================================================================
--- trunk/doc/configOptions.txt	2009-02-12 13:04:36 UTC (rev 1595)
+++ trunk/doc/configOptions.txt	2009-02-12 16:17:41 UTC (rev 1596)
@@ -11,7 +11,7 @@
 
 option name: url
 description: URL pointer to the KB file
-values: class org.dllearner.core.config.URLConfigOption
+values: class org.dllearner.core.options.URLConfigOption
 default value: null
 CLI usage: null.url = null;
 
@@ -29,7 +29,7 @@
 
 option name: url
 description: URL pointing to the OWL file
-values: class org.dllearner.core.config.URLConfigOption
+values: class org.dllearner.core.options.URLConfigOption
 default value: null
 CLI usage: owlfile.url = null;
 
@@ -41,139 +41,139 @@
 
 option name: url
 description: URL of SPARQL Endpoint
-values: class org.dllearner.core.config.URLConfigOption
+values: class org.dllearner.core.options.URLConfigOption
 default value: null
 CLI usage: sparql.url = null;
 
 option name: cacheDir
 description: dir of cache
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: sparql.instances = null;
 
 option name: recursionDepth
 description: recursion depth of KB fragment selection
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 1
 CLI usage: sparql.recursionDepth = 1;
 
 option name: predefinedFilter
 description: the mode of the SPARQL Filter, use one of YAGO,SKOS,YAGOSKOS , YAGOSPECIALHIERARCHY, TEST
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: null
 CLI usage: sparql.predefinedFilter = null;
 
 option name: predefinedEndpoint
 description: the mode of the SPARQL Filter, use one of DBPEDIA, LOCAL, GOVTRACK, REVYU, MYOPENLINK, FACTBOOK
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: []
 CLI usage: sparql.predList = [];
 
 option name: objList
 description: list of all ignored objects
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: []
 CLI usage: sparql.objList = [];
 
 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.saveExtractedFragment = true;
+values: class org.dllearner.core.options.BooleanConfigOption
+default value: false
+CLI usage: sparql.saveExtractedFragment = false;
 
 option name: replacePredicate
 description: rule for replacing predicates
-values: class org.dllearner.core.config.StringTupleListConfigOption
+values: class org.dllearner.core.options.StringTupleListConfigOption
 default value: []
 CLI usage: sparql.replacePredicate = [];
 
 option name: replaceObject
 description: rule for replacing predicates
-values: class org.dllearner.core.config.StringTupleListConfigOption
+values: class org.dllearner.core.options.StringTupleListConfigOption
 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
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 1000
 CLI usage: sparql.breakSuperClassRetrievalAfter = 1000;
 
 option name: useLits
 description: use Literals in SPARQL query
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.BooleanConfigOption
 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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.StringConfigOption
 default value: warning
 CLI usage: sparql.verbosity = warning;
 
 option name: defaultGraphURIs
 description: a list of all default Graph URIs
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: []
 CLI usage: sparql.defaultGraphURIs = [];
 
 option name: namedGraphURIs
 description: a list of all named Graph URIs
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: []
 CLI usage: sparql.namedGraphURIs = [];
 
@@ -189,19 +189,19 @@
 
 option name: reasonerUrl
 description: URL of the DIG reasoner
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: null
 CLI usage: digReasoner.reasonerUrl = null;
 
 option name: writeDIGProtocol
 description: specifies whether or not to write a protocoll of send and received DIG requests
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: digReasoner.writeDIGProtocol = false;
 
 option name: digProtocolFile
 description: the file to store the DIG protocol
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: log/digProtocol.txt
 CLI usage: digReasoner.digProtocolFile = log/digProtocol.txt;
 
@@ -213,13 +213,13 @@
 
 option name: reasonerType
 description: FaCT++ or Pellet to dematerialize
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: fastInstanceChecker.defaultNegation = true;
 
@@ -237,7 +237,7 @@
 
 option name: reasonerType
 description: FaCT++ or Pellet, which means "pellet" or "fact"
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: pellet
 CLI usage: owlAPIReasoner.reasonerType = pellet;
 
@@ -246,6 +246,24 @@
 * Learning Problems *
 *********************
 
+component: unnamed component (org.dllearner.learningproblems.ClassLearningProblem)
+==================================================================================
+
+CLI usage: null = null;
+
+option name: classToDescribe
+description: class of which a description should be learned
+values: class org.dllearner.core.options.StringConfigOption
+default value: null
+CLI usage: null.classToDescribe = null;
+
+option name: type
+description: Whether to learn an equivalence class or super class axiom.
+values: class org.dllearner.core.options.StringConfigOption
+default value: equivalence
+CLI usage: null.type = equivalence;
+
+
 component: two valued definition learning problem (org.dllearner.learningproblems.PosNegDefinitionLP)
 =====================================================================================================
 
@@ -253,31 +271,31 @@
 
 option name: positiveExamples
 description: positive examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: posNegDefinitionLP.positiveExamples = null;
 
 option name: negativeExamples
 description: negative examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: posNegDefinitionLP.negativeExamples = null;
 
 option name: useRetrievalForClassficiation
 description: Specifies whether to use retrieval or instance checks for testing a concept.
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 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
-values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.05
 CLI usage: posNegDefinitionLP.percentPerLenghtUnit = 0.05;
 
 option name: useMultiInstanceChecks
 description: See UseMultiInstanceChecks enum.
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: twoChecks
 CLI usage: posNegDefinitionLP.useMultiInstanceChecks = twoChecks;
 
@@ -289,49 +307,49 @@
 
 option name: positiveExamples
 description: positive examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: null.positiveExamples = null;
 
 option name: negativeExamples
 description: negative examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: null.negativeExamples = null;
 
 option name: useRetrievalForClassficiation
 description: Specifies whether to use retrieval or instance checks for testing a concept.
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: null.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
-values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.DoubleConfigOption
 default value: 3.0
 CLI usage: null.errorPenalty = 3.0;
 
@@ -343,31 +361,31 @@
 
 option name: positiveExamples
 description: positive examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: posNegInclusionLP.positiveExamples = null;
 
 option name: negativeExamples
 description: negative examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: posNegInclusionLP.negativeExamples = null;
 
 option name: useRetrievalForClassficiation
 description: Specifies whether to use retrieval or instance checks for testing a concept.
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 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
-values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.05
 CLI usage: posNegInclusionLP.percentPerLenghtUnit = 0.05;
 
 option name: useMultiInstanceChecks
 description: See UseMultiInstanceChecks enum.
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: twoChecks
 CLI usage: posNegInclusionLP.useMultiInstanceChecks = twoChecks;
 
@@ -379,7 +397,7 @@
 
 option name: positiveExamples
 description: positive examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: posOnlyDefinitionLP.positiveExamples = null;
 
@@ -391,7 +409,7 @@
 
 option name: positiveExamples
 description: positive examples
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: null.positiveExamples = null;
 
@@ -407,13 +425,13 @@
 
 option name: maxLength
 description: maximum length of generated concepts
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 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.
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: null
 CLI usage: bruteForce.returnType = null;
 
@@ -425,175 +443,175 @@
 
 option name: writeSearchTree
 description: specifies whether to write a search tree
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: null
 CLI usage: dbpediaNavigationSuggestor.forceRefinementLengthIncrease = null;
 
@@ -605,13 +623,13 @@
 
 option name: numberOfTrees
 description: number of randomly generated concepts/trees
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 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
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 5
 CLI usage: random.maxDepth = 5;
 
@@ -622,6 +640,18 @@
 CLI usage: null = null;
 
 
+component: unnamed component (org.dllearner.algorithms.celoe.CELOE)
+===================================================================
+
+CLI usage: null = null;
+
+
+component: standard EL learning algorithm (org.dllearner.algorithms.el.ELLearningAlgorithm)
+===========================================================================================
+
+CLI usage: null = el;
+
+
 component: genetic programming learning algorithm (org.dllearner.algorithms.gp.GP)
 ==================================================================================
 
@@ -629,311 +659,347 @@
 
 option name: selectionType
 description: selection type
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: rankSelection
 CLI usage: gp.selectionType = rankSelection;
 
 option name: tournamentSize
 description: tournament size (applies only to tournament selection)
-values: class org.dllearner.core.config.IntegerConfigOption min 2 max 20
+values: class org.dllearner.core.options.IntegerConfigOption min 2 max 20
 default value: 3
 CLI usage: gp.tournamentSize = 3;
 
 option name: elitism
 description: specifies whether to use elitism in selection
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: gp.elitism = true;
 
 option name: algorithmType
 description: algorithm type
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.03
 CLI usage: gp.mutationProbability = 0.03;
 
 option name: crossoverProbability
 description: crossover probability
-values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.95
 CLI usage: gp.crossoverProbability = 0.95;
 
 option name: hillClimbingProbability
 description: hill climbing probability
-values: class org.dllearner.core.config.DoubleConfigOption min 0.0 max 1.0
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.0
 CLI usage: gp.hillClimbingProbability = 0.0;
 
 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
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.0
 CLI usage: gp.refinementProbability = 0.0;
 
 option name: numberOfIndividuals
 description: number of individuals
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 100
 CLI usage: gp.numberOfIndividuals = 100;
 
 option name: numberOfSelectedIndividuals
 description: number of selected individuals
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 92
 CLI usage: gp.numberOfSelectedIndividuals = 92;
 
 option name: useFixedNumberOfGenerations
 description: specifies whether to use a fixed number of generations
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: gp.useFixedNumberOfGenerations = false;
 
 option name: generations
 description: number of generations (only valid if a fixed number of generations is used)
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 20
 CLI usage: gp.generations = 20;
 
 option name: postConvergenceGenerations
 description: number of generations after which to stop if no improvement wrt. the best solution has been achieved
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 50
 CLI usage: gp.postConvergenceGenerations = 50;
 
 option name: adc
 description: whether to use automatically defined concept (this invents new helper concepts, but enlarges the search space
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: gp.adc = false;
 
 option name: initMinDepth
 description: minimum depth to use when creating the initial population
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 4
 CLI usage: gp.initMinDepth = 4;
 
 option name: initMaxDepth
 description: maximum depth to use when creating the initial population
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 6
 CLI usage: gp.initMaxDepth = 6;
 
 option name: maxConceptLength
 description: maximum concept length (higher length means lowest possible fitness)
-values: class org.dllearner.core.config.IntegerConfigOption min 1
+values: class org.dllearner.core.options.IntegerConfigOption min 1
 default value: 75
 CLI usage: gp.maxConceptLength = 75;
 
 
-component: example driven refinement operator based learning algorithm (org.dllearner.algorithms.refexamples.ExampleBasedROLComponent)
-======================================================================================================================================
+component: refinement operator based learning algorithm II (org.dllearner.algorithms.refexamples.ExampleBasedROLComponent)
+==========================================================================================================================
 
 CLI usage: null = refexamples;
 
 option name: writeSearchTree
 description: specifies whether to write a search tree
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: refexamples.writeSearchTree = false;
 
 option name: searchTreeFile
 description: file to use for the search tree
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: log/searchTree.txt
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: refexamples.replaceSearchTree = false;
 
 option name: heuristic
 description: specifiy the heuristic to use
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: lexicographic
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.useOverlyGeneralList = true;
 
 option name: useShortConceptConstruction
 description: shorten concept to see whether they already exist
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.6
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.improveSubsumptionHierarchy = true;
 
 option name: allowedConcepts
 description: concepts the algorithm is allowed to use
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refexamples.allowedConcepts = null;
 
 option name: ignoredConcepts
 description: concepts the algorithm must ignore
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refexamples.ignoredConcepts = null;
 
 option name: allowedRoles
 description: roles the algorithm is allowed to use
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refexamples.allowedRoles = null;
 
 option name: ignoredRoles
 description: roles the algorithm must ignore
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.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
+values: class org.dllearner.core.options.BooleanConfigOption
 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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.useCardinalityRestrictions = true;
 
+option name: cardinalityLimit
+description: Gives the maximum number used in cardinality restrictions.
+values: class org.dllearner.core.options.IntegerConfigOption
+default value: 5
+CLI usage: refexamples.cardinalityLimit = 5;
+
 option name: useNegation
 description: specifies whether negation is used in the learning algorothm
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refexamples.useNegation = true;
 
 option name: useBooleanDatatypes
 description: specifies whether boolean datatypes are used in the learning algorothm
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 0
 CLI usage: refexamples.maxExecutionTimeInSeconds = 0;
 
 option name: minExecutionTimeInSeconds
 description: algorithm will run at least specified seconds
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 0
 CLI usage: refexamples.minExecutionTimeInSeconds = 0;
 
 option name: guaranteeXgoodDescriptions
 description: algorithm will run until X good (100%) concept descritpions are found
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 100.0
 default value: 0.0
 CLI usage: refexamples.noisePercentage = 0.0;
 
+option name: terminateOnNoiseReached
+description: specifies whether to terminate when noise criterion is met
+values: class org.dllearner.core.options.BooleanConfigOption
+default value: true
+CLI usage: refexamples.terminateOnNoiseReached = true;
+
 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
+values: class org.dllearner.core.options.StringConfigOption
 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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: null
 CLI usage: refexamples.forceRefinementLengthIncrease = null;
 
+option name: negativeWeight
+description: Used to penalise errors on negative examples different from those of positive examples (lower = less importance for negatives).
+values: class org.dllearner.core.options.DoubleConfigOption
+default value: 1.0
+CLI usage: refexamples.negativeWeight = 1.0;
 
+option name: startNodeBonus
+description: You can use this to give a heuristic bonus on the start node (= initially broader exploration of search space).
+values: class org.dllearner.core.options.DoubleConfigOption
+default value: 0.0
+CLI usage: refexamples.startNodeBonus = 0.0;
+
+option name: negationPenalty
+description: Penalty on negations (TODO: better explanation).
+values: class org.dllearner.core.options.IntegerConfigOption
+default value: 0
+CLI usage: refexamples.negationPenalty = 0;
+
+option name: expansionPenaltyFactor
+description: describes the reduction in heuristic score one is willing to accept for reducing the length of the concept by one
+values: class org.dllearner.core.options.DoubleConfigOption
+default value: 0.02
+CLI usage: refexamples.expansionPenaltyFactor = 0.02;
+
+
 component: refinement operator based learning algorithm (org.dllearner.algorithms.refinement.ROLearner)
 =======================================================================================================
 
@@ -941,151 +1007,151 @@
 
 option name: writeSearchTree
 description: specifies whether to write a search tree
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: refinement.writeSearchTree = false;
 
 option name: searchTreeFile
 description: file to use for the search tree
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: log/searchTree.txt
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: refinement.replaceSearchTree = false;
 
 option name: heuristic
 description: specifiy the heuristic to use
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: lexicographic
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.useOverlyGeneralList = true;
 
 option name: useShortConceptConstruction
 description: shorten concept to see whether they already exist
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.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
+values: class org.dllearner.core.options.DoubleConfigOption min 0.0 max 1.0
 default value: 0.6
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.improveSubsumptionHierarchy = true;
 
 option name: quiet
 description: may be deprecated soon
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: false
 CLI usage: refinement.quiet = false;
 
 option name: allowedConcepts
 description: concepts the algorithm is allowed to use
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refinement.allowedConcepts = null;
 
 option name: ignoredConcepts
 description: concepts the algorithm must ignore
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refinement.ignoredConcepts = null;
 
 option name: allowedRoles
 description: roles the algorithm is allowed to use
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refinement.allowedRoles = null;
 
 option name: ignoredRoles
 description: roles the algorithm must ignore
-values: class org.dllearner.core.config.StringSetConfigOption
+values: class org.dllearner.core.options.StringSetConfigOption
 default value: null
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.useExistsConstructor = true;
 
 option name: useNegation
 description: specifies whether negation is used in the learning algorothm
-values: class org.dllearner.core.config.BooleanConfigOption
+values: class org.dllearner.core.options.BooleanConfigOption
 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
+values: class org.dllearner.core.options.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
+values: class org.dllearner.core.options.BooleanConfigOption
 default value: true
 CLI usage: refinement.useBooleanDatatypes = true;
 
 option name: maxExecutionTimeInSeconds
 description: algorithm will stop after specified seconds
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 0
 CLI usage: refinement.maxExecutionTimeInSeconds = 0;
 
 option name: minExecutionTimeInSeconds
 description: algorithm will run at least specified seconds
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 0
 CLI usage: refinement.minExecutionTimeInSeconds = 0;
 
 option name: guaranteeXgoodDescriptions
 description: algorithm will run until X good (100%) concept descritpions are found
-values: class org.dllearner.core.config.IntegerConfigOption
+values: class org.dllearner.core.options.IntegerConfigOption
 default value: 1
 CLI usage: refinement.guaranteeXgoodDescriptions = 1;
 
 option name: logLevel
 description: determines the logLevel for this component, can be {TRACE, DEBUG, INFO}
-values: class org.dllearner.core.config.StringConfigOption
+values: class org.dllearner.core.options.StringConfigOption
 default value: DEBUG
 CLI usage: refinement.logLevel = DEBUG;
 

Modified: trunk/doc/manual/bibliography.bib
===================================================================
--- trunk/doc/manual/bibliography.bib	2009-02-12 13:04:36 UTC (rev 1595)
+++ trunk/doc/manual/bibliography.bib	2009-02-12 16:17:41 UTC (rev 1596)
@@ -5,3 +5,35 @@
 	publisher = {Cambridge University Press},
 	isbn = {0-521-78176-0},
 } 
+
+@article{2009_ijswis,
+	title = "Learning of {OWL} Class Descriptions on Very Large Knowledge Bases",
+	author = "Sebastian Hellmann and Jens Lehmann and Sören Auer",
+	journal = "International Journal On Semantic Web and Information Systems",
+	year = "2009",
+}
+
+@inproceedings{2008_dbpedia,
+	title = "{DB}pedia: A Nucleus for a Web of Open Data",
+	author = "Sören Auer and Chris Bizer and Georgi Kobilarov and Jens Lehmann and Richard Cyganiak and Zachary Ives",
+	publisher = "Springer",
+	booktitle = "Proceedings of the 6th International Semantic Web Conference (ISWC)",
+	series = "Lecture Notes in Computer Science",
+	volume = "4825",
+	pages = "722-735",
+	year = "2008",
+}
+
+@InProceedings{cheng00,
+  author =  "Liviu Badea and Shan-Hwei Nienhuys-Cheng",
+  title =   "A Refinement Operator for Description Logics",
+  booktitle =   "Proceedings of the 10th International Conference on
+         Inductive Logic Programming",
+  series =  "Lecture Notes in Artificial Intelligence",
+  volume =  "1866",
+  editor =  "J. Cussens and A. Frisch",
+  publisher =   "Springer-Verlag",
+  year =    "2000",
+  ISBN =    "3-540-67795-X",
+  pages =   "40--59",
+}
\ No newline at end of file

Modified: trunk/doc/manual/manual.tex
===================================================================
--- trunk/doc/manual/manual.tex	2009-02-12 13:04:36 UTC (rev 1595)
+++ trunk/doc/manual/manual.tex	2009-02-12 16:17:41 UTC (rev 1596)
@@ -20,6 +20,8 @@
 \urldef{\wsjavadoc}{\url}{http://dl-learner.org/javadoc/org/dllearner/server/DLLearnerWS.html}
 \urldef{\wsphpexamples}{\url}{http://dl-learner.svn.sourceforge.net/viewvc/dl-learner/trunk/src/php-examples/}
 \urldef{\wikiprotplugin}{\url}{http://dl-learner.org/wiki/ProtegePlugin}
+\urldef{\owlapi}{\url}{http://owlapi.sourceforge.net}
+\urldef{\dig}{\url}{http://dl.kr.org/dig/}
 
 \title{DL-Learner Manual [Draft]}
 \author{Jens Lehmann}
@@ -124,16 +126,49 @@
 \section{DL-Learner Components}
 \label{sec:components}
 
+In this part, we describe concrete components currently implemented in DL-Learner. Each of the subsections contains a list of components of type specified in the subsection heading. Note that this constitute a full description, i.e.~we omit some components and many configuration options. The purpose of the manual is to obtain a general understanding of the implemented components. A full list of components, which is generated automatically from the source code, can be found in \verb|doc/configOptions.txt| including the default values for all options and their usage in conf files. \todo{ConfigDocumentationGenerator seems partially broken, because it prints things like CLI usage: null = owlAPIReasoner;}
 
-
 \subsection{Knowledge Sources}
 
+Knowledge sources have a URI and can be included in conf files using \verb|import("$url");|, e.g.~\verb|import("ontology.owl")|. Depending on the file ending, DL-Learner will guess the correct type of knowledge source. If you want to overwrite this, you can use a second parameter with value \verb|OWL|, \verb|KB|, or \verb|SPARQL|, e.g.~\verb|import("ontology.owl","OWL")|.
+
+\begin{description}
+ \item[OWL File] DL-Learner supports OWL files in different formats, e.g. RDF/XML or N-Triples. If there is a standard OWL format, you want to use, but is not supported by DL-Learner please let us know.
+ \item[KB File] KB files are an internal non-standardised knowledge representation format, which corresponds to description logic syntax except that the special symbols have been replaced by ASCII strings, e.g.~\verb|AND| instead of $\sqcap$. You can find several KB files in the examples folder.
+ \item[SPARQL Endpoint] DL-Learner allows to use SPARQL endpoints as background knowledge source, which enables the incorporation of very large knowledge bases, e.g. DBpedia\cite{2008_dbpedia}, in DL-Learner. This works by using a set of start instances, which usually correspond to the examples in a learning problem, and then retrieving knowledge about these instances via SPARQL queries. The obtained knowledge base fragment can be converted to OWL and consumed by a reasoner later since it is now sufficiently to be processed in reasonable time. Please see \cite{2009_ijswis} for details. Some options of the SPARQL component are:
+\begin{itemize}
+ \item instances: Set of individuals to use for starting the knowledge fragment extraction. Example use in conf file: \begin{verbatim}sparql.instances = {"http://dbpedia.org/resource/Matt_Stone",
+ "http://dbpedia.org/resource/Sarah_Silverman"};\end{verbatim}
+ \item recursionDepth: Maximum distance of an extracted individual from a start individual. This influences the size of the extracted fragment and depends on the maximum property depth you want the learned class expression to have. Example use in conf file: \verb|sparql.recursionDepth = 3;|.
+\end{itemize}
+ Many further options allow to modify the extracted fragment on the fly or fine-tune the extraction process.
+\end{description}
+
 \subsection{Reasoner Components}
 
+Several reasoner components are implemented, which can be interfaces to concrete reasoner implementations. To select a component in a conf file, use \verb|reasoner=$value;|, where  \verb|$value| is one of \verb|digReasoner|, \verb|fastInstanceChecker|, or \verb|owlAPIReasoner|, which are explained below.
+
+\begin{description}
+ \item[OWL API] The OWL API\footnote{\owlapi} reasoner interface can be used in conjunction with the Pellet and FaCT++ reasoners. The only option allows to switch between both:
+ \begin{itemize}
+  \item reasonerType: Selects the desired reasoner. By default, Pellet is used. Usage: \verb|owlAPIReasoner.reasonerType = fact;|. Note that FaCT++ is written in C++ and we currently ship the 32 bit version of the JNI layer. This may change to 64 bit in the future.
+ \end{itemize}
+ \item[DIG] DIG 1.1\footnote{\dig} is an interface to description logic reasoners and supported by a large variety of reasoners including Pellet, FaCT++, KAON2, and Racer Pro. The major drawback is that the current version DIG 1.1 is not aligned with the OWL specification and therefore lacks several features, which are crucial to the more recent learning algorithms in DL-Learner. If you still want to use the DIG interface, you have to download a DIG capable reasoner and start the DIG server there. DL-Learner communicates with the reasoner using the XML based protocol over HTTP.
+ \item[Fast Instance Checker] Instance checks, i.e.~testing whether an individual is inst...
 
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