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[DL-Learner SVN] SF.net SVN: dl-learner:[1828] trunk
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From: <lor...@us...> - 2009-08-18 15:32:44
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Revision: 1828
http://dl-learner.svn.sourceforge.net/dl-learner/?rev=1828&view=rev
Author: lorenz_b
Date: 2009-08-18 15:32:20 +0000 (Tue, 18 Aug 2009)
Log Message:
-----------
added closed world assumption option to PelletReasoner as it is used in FastInstanceChecker
integrated modularity approach to compute explanations in a smaller set of logical axioms
provided recentmanager for former used knowledgebases
renamed main application class to OREApplication
cleaned up ORE-helper class and renamed it to OREManager
Modified Paths:
--------------
trunk/doc/configOptions.txt
trunk/src/dl-learner/org/dllearner/core/configurators/PelletReasonerConfigurator.java
trunk/src/dl-learner/org/dllearner/reasoning/OWLAPIReasoner.java
trunk/src/dl-learner/org/dllearner/reasoning/PelletReasoner.java
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ORE.java
trunk/src/dl-learner/org/dllearner/tools/ore/SPARQLTest.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/laconic/LaconicExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/relevance/SyntacticRelevanceBasedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/DescriptionLabel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ExplanationTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ImpactTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/OWLSyntaxTableCellRenderer.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairDialog.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RepairTable.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatusBar.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/StatusBarSimulator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardController.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/WizardModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/ClassPanelOWLDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/InconsistencyExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/KnowledgeSourcePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/LearningPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/RepairPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/SavePanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/descriptors/UnsatisfiableExplanationPanelDescriptor.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/DescriptionPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/KnowledgeSourcePanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/wizard/panels/UnsatisfiableExplanationPanel.java
Added Paths:
-----------
trunk/endpoints.txt
trunk/examples/ore/tambis.owl
trunk/src/dl-learner/org/dllearner/tools/ore/ExplanationManagerListener.java
trunk/src/dl-learner/org/dllearner/tools/ore/OREApplication.java
trunk/src/dl-learner/org/dllearner/tools/ore/OREManager.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/CachedExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/explanation/ExplanationGenerator.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/LinkLabel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MetricsPanel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/MetricsTableModel.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/ReasonerProgressUI.java
trunk/src/dl-learner/org/dllearner/tools/ore/ui/RecentManager.java
Removed Paths:
-------------
trunk/src/dl-learner/org/dllearner/tools/ore/Main.java
Modified: trunk/doc/configOptions.txt
===================================================================
--- trunk/doc/configOptions.txt 2009-08-17 17:45:45 UTC (rev 1827)
+++ trunk/doc/configOptions.txt 2009-08-18 15:32:20 UTC (rev 1828)
@@ -215,6 +215,18 @@
conf file usage: owlAPIReasoner.reasonerType = pellet;
+component: unnamed component (org.dllearner.reasoning.PelletReasoner)
+=====================================================================
+
+conf file usage: reasoner = null;
+
+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.
+allowed values: boolean
+default value: true
+conf file usage: null.defaultNegation = true;
+
+
*********************
* Learning Problems *
*********************
@@ -236,7 +248,13 @@
default value: equivalence
conf file usage: classLearning.type = equivalence;
+option name: useApproximations
+description: whether to use stochastic approximations for computing accuracy
+allowed values: boolean
+default value: true
+conf file usage: classLearning.useApproximations = true;
+
component: pos neg learning problem (org.dllearner.learningproblems.PosNegLPStandard)
=====================================================================================
@@ -469,6 +487,24 @@
conf file usage: algorithm = el;
+component: disjunctive EL learning algorithm (org.dllearner.algorithms.el.ELLearningAlgorithmDisjunctive)
+=========================================================================================================
+
+conf file usage: algorithm = disjunctiveEL;
+
+option name: noisePercentage
+description: the (approximated) percentage of noise within the examples
+allowed values: double min 0.0 max 100.0
+default value: 0.0
+conf file usage: disjunctiveEL.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)
+allowed values: String []
+default value: not set
+conf file usage: disjunctiveEL.startClass = ;
+
+
component: genetic programming learning algorithm (org.dllearner.algorithms.gp.GP)
==================================================================================
@@ -882,6 +918,12 @@
default value: true
conf file usage: refexamples.useDoubleDatatypes = true;
+option name: useStringDatatypes
+description: specifies whether string datatypes are used in the learning algorothm
+allowed values: boolean
+default value: false
+conf file usage: refexamples.useStringDatatypes = false;
+
option name: maxExecutionTimeInSeconds
description: algorithm will stop after specified seconds
allowed values: int
Added: trunk/endpoints.txt
===================================================================
--- trunk/endpoints.txt (rev 0)
+++ trunk/endpoints.txt 2009-08-18 15:32:20 UTC (rev 1828)
@@ -0,0 +1,12 @@
+DEBUG - sending query: length: 44 | ENDPOINT: http://www4.wiwiss.fu-berlin.de/dblp/sparql
+INFO - finished 1 of 19
+DEBUG - sending query: length: 44 | ENDPOINT: http://dbpedia.org/sparql
+INFO - finished 2 of 19
+DEBUG - sending query: length: 44 | ENDPOINT: http://doapspace.org/sparql
+DEBUG - RuntimeException in SparqlQuery (see /log/sparql.txt): HttpException: HttpException: 404 Not Found: rethrew: HttpException: 404 Not Found
+DEBUG - query was (max. 300 chars displayed) SELECT DISTINCT ?c WHERE {[] a ?c }LIMIT 10
+WARN - rethrew: HttpException: 404 Not Found
+INFO - **************
+INFO - endpoint working: http://dbpedia.org/sparql (more than 100 concepts ) needed 20405 ms
+INFO - endpoint working: http://www4.wiwiss.fu-berlin.de/dblp/sparql (about 4 concepts ) needed 1756 ms
+INFO - endpoint NOT working: http://doapspace.org/sparql needed 583 ms
Added: trunk/examples/ore/tambis.owl
===================================================================
--- trunk/examples/ore/tambis.owl (rev 0)
+++ trunk/examples/ore/tambis.owl 2009-08-18 15:32:20 UTC (rev 1828)
@@ -0,0 +1,6051 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<rdf:RDF
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns="http://krono.act.uji.es/Links/ontologies/tambis.owl#"
+ xml:base="http://krono.act.uji.es/Links/ontologies/tambis.owl">
+ <owl:Ontology rdf:about=""/>
+ <owl:Class rdf:about="#physical-substance">
+ <rdfs:subClassOf>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#physical"/>
+ <owl:Class rdf:about="#substance"/>
+ </owl:intersectionOf>
+ </owl:Class>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#enzyme-inhibitor">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#regulation"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#sodium">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#biological-compartment">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#biological-space"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#vanadium">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#amino-transfer">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#inter-molecule-transfer"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#physicochemical-selector">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#selector"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#nucleus">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#biological-structure"/>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#cell"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#cell"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-classification"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#eukaryote"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-classification"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#eukaryote"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#species">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#organism-classification"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#hydrophilic">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#hydrophobicity-property"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#hydrophobic">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#hydrophobicity-property"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#time-unit">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#unit"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#biological-classification">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#mental-organisation"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#complement-dna">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#macromolecular-compound"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#polymer-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#deoxy-nucleotide"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#polymer-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#deoxy-nucleotide"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#strandedness"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#single-stranded"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#reverse-transcribed-from"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#reverse-transcribed-from"/>
+ <owl:allValuesFrom>
+ <owl:Class>
+ <owl:unionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#messenger-rna"/>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#messenger-rna"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:unionOf>
+ </owl:Class>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#small-organic-molecular-compound">
+ <rdfs:subClassOf>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#organic-molecular-compound"/>
+ <owl:Class rdf:about="#small-molecular-compound"/>
+ </owl:intersectionOf>
+ </owl:Class>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#sulphur">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#journal-name">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#name"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#name-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#journal"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#name-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#journal"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#structure">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://www.w3.org/2002/07/owl#Thing"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#trivalent-cation">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-charge"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">3</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-charge"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#positive-charge"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#hydrophobicity-property">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#physicochemical-property"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#nucleotide">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#small-organic-molecular-compound"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#storage-protein">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#biological-function"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#gene-name">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#name"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#name-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#gene"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#name-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#gene"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#gene-part">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#dna-part"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#gene"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#gene"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#property">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#modifier"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#physical">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://www.w3.org/2002/07/owl#Thing"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#restriction-endonuclease-site">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#dna-site"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#alkali-metal">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#ether-bond-hydrolysis">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#reaction"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#hydrolysis-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#ether-bond"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#small-nuclear-rna-function">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#biological-function"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#prosthetic-group">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#cofactor"/>
+ <owl:Class>
+ <owl:complementOf>
+ <owl:Class rdf:about="#metal-ion"/>
+ </owl:complementOf>
+ </owl:Class>
+ </owl:intersectionOf>
+ </owl:Class>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#binds-strongly"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#protein"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#binds-strongly"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#protein"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#macromolecular-compound">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#molecule"/>
+ <owl:Class rdf:about="#compound"/>
+ </owl:intersectionOf>
+ </owl:Class>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-molecular-weight"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-molecular-weight"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#polymer-of"/>
+ <owl:someValuesFrom>
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+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#sulphation-site">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#modification-site"/>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#target-for"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#inter-molecule-transfer"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#target-for"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#inter-molecule-transfer"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#endoplasmic-reticulum">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#organelle"/>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#cytosol"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#covalent-bond">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#chemical-bond"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#electrical-charge">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#physicochemical-property"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#zinc-divalent-cation">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <owl:Class rdf:about="#chemical"/>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#atomic-number"/>
+ <owl:someValuesFrom rdf:resource="http://www.w3.org/2001/XMLSchema#integer"/>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-metal-class"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#metal"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-charge"/>
+ <owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">2</owl:cardinality>
+ </owl:Restriction>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#has-charge"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#positive-charge"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="#spliceosome">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#biological-structure"/>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:someValuesFrom>
+ <owl:Class rdf:about="#nucleus"/>
+ </owl:someValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty rdf:resource="#part-of"/>
+ <owl:allValuesFrom>
+ <owl:Class rdf:about="#nucleus"/>
+ </owl:allValuesFrom>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="#carbon-nitrogen-bond">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="#covalent-bond"/>
+ ...
[truncated message content] |
