| Previous changeset 10:3f31c0eb7539 (2012-01-12) Next changeset 12:d0722148cb59 (2012-03-22) |
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Commit message:
Imports simplified, new tool for inference added |
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modified:
OPPL/README OPPL/oppl.xml |
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added:
OPPL/inference.jar OPPL/inference.xml OPPL/inference_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar OPPL/inference_lib/HermiT.jar OPPL/inference_lib/antlr-runtime-3.2.jar OPPL/inference_lib/aterm-java-1.6.jar OPPL/inference_lib/commons-logging-1.1.1.jar OPPL/inference_lib/jgrapht-jdk1.5.jar OPPL/inference_lib/junit-4.8.2.jar OPPL/inference_lib/junit.jar OPPL/inference_lib/log4j-1.2.15.jar OPPL/inference_lib/oboformat.jar OPPL/inference_lib/org.coode.oppl-API.jar OPPL/inference_lib/owlapi-bin.jar OPPL/inference_lib/owlapi-bin_2.jar OPPL/inference_lib/owllink-bin.jar OPPL/inference_lib/parsers.jar OPPL/inference_lib/pellet-core.jar OPPL/inference_lib/pellet-datatypes.jar OPPL/inference_lib/pellet-el.jar OPPL/inference_lib/pellet-owlapiv3.jar OPPL/inference_lib/pellet-query.jar OPPL/inference_lib/pellet-rules.jar OPPL/oppl_galaxy.jar OPPL/oppl_galaxy_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar OPPL/oppl_galaxy_lib/HermiT.jar OPPL/oppl_galaxy_lib/antlr-runtime-3.2.jar OPPL/oppl_galaxy_lib/aterm-java-1.6.jar OPPL/oppl_galaxy_lib/commons-logging-1.1.1.jar OPPL/oppl_galaxy_lib/jgrapht-jdk1.5.jar OPPL/oppl_galaxy_lib/junit-4.8.2.jar OPPL/oppl_galaxy_lib/junit.jar OPPL/oppl_galaxy_lib/log4j-1.2.15.jar OPPL/oppl_galaxy_lib/oboformat.jar OPPL/oppl_galaxy_lib/org.coode.oppl-API.jar OPPL/oppl_galaxy_lib/owlapi-bin.jar OPPL/oppl_galaxy_lib/owlapi-bin_2.jar OPPL/oppl_galaxy_lib/owllink-bin.jar OPPL/oppl_galaxy_lib/parsers.jar OPPL/oppl_galaxy_lib/pellet-core.jar OPPL/oppl_galaxy_lib/pellet-datatypes.jar OPPL/oppl_galaxy_lib/pellet-el.jar OPPL/oppl_galaxy_lib/pellet-owlapiv3.jar OPPL/oppl_galaxy_lib/pellet-query.jar OPPL/oppl_galaxy_lib/pellet-rules.jar OPPL/src/GalaxyOWLAPI.java OPPL/src/InferenceGalaxy.java OPPL/src/OPPLGalaxy.java OPPL/test-data/ontology/imports/imports_inference_test.owl OPPL/test-data/ontology/imports/imports_test.owl OPPL/test-data/ontology/single/inference_test.owl OPPL/test-data/ontology/single/test.owl OPPL/test-data/oppl_script/test.oppl |
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removed:
OPPL/Disjoint_localisation.oppl OPPL/Tool.java OPPL/cell.owl OPPL/chebi.owl OPPL/gene_ontology_ext.owl OPPL/oppl.sh OPPL/oppl_galaxy_tool.jar OPPL/oppl_galaxy_tool_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar OPPL/oppl_galaxy_tool_lib/HermiT.jar OPPL/oppl_galaxy_tool_lib/antlr-runtime-3.2.jar OPPL/oppl_galaxy_tool_lib/aterm-java-1.6.jar OPPL/oppl_galaxy_tool_lib/commons-logging-1.1.1.jar OPPL/oppl_galaxy_tool_lib/jgrapht-jdk1.5.jar OPPL/oppl_galaxy_tool_lib/junit-4.8.2.jar OPPL/oppl_galaxy_tool_lib/junit.jar OPPL/oppl_galaxy_tool_lib/log4j-1.2.15.jar OPPL/oppl_galaxy_tool_lib/oboformat.jar OPPL/oppl_galaxy_tool_lib/org.coode.oppl-API.jar OPPL/oppl_galaxy_tool_lib/owlapi-bin.jar OPPL/oppl_galaxy_tool_lib/owlapi-bin_2.jar OPPL/oppl_galaxy_tool_lib/owllink-bin.jar OPPL/oppl_galaxy_tool_lib/parsers.jar OPPL/oppl_galaxy_tool_lib/pellet-core.jar OPPL/oppl_galaxy_tool_lib/pellet-datatypes.jar OPPL/oppl_galaxy_tool_lib/pellet-el.jar OPPL/oppl_galaxy_tool_lib/pellet-owlapiv3.jar OPPL/oppl_galaxy_tool_lib/pellet-query.jar OPPL/oppl_galaxy_tool_lib/pellet-rules.jar OPPL/test.oppl OPPL/test.owl OPPL/test_URI_mappings OPPL/test_new.owl |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/Disjoint_localisation.oppl --- a/OPPL/Disjoint_localisation.oppl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -?localisation_sibling:CLASS -SELECT -ASSERTED ?localisation_sibling SubClassOf GO_0008150 -WHERE ?localisation_sibling != GO_0051179 -BEGIN -ADD ?localisation_sibling DisjointWith GO_0051179 -END; |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/README --- a/OPPL/README Thu Jan 12 10:20:00 2012 +0100 +++ b/OPPL/README Fri Mar 09 16:15:27 2012 +0100 |
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| @@ -1,9 +1,3 @@ - - - - =========== - OPPL-GALAXY - =========== @@ -12,60 +6,52 @@ 1.- Stop Galaxy. -2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ -and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/ +2.- Copy the following files and dirs to +/galaxy-dist/tool-data/shared/jars/: + +oppl_galaxy_tool.jar +oppl_galax_lib/ +FaCT++-linux-v1.5.2/ +FaCT++-OSX-v1.5.2/ +inference.jar +inference_lib/ 3.- Create directory /galaxy-dist/tools/OPPL/ -4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/ +4.- Copy oppl.xml and inference.xml to /galaxy-dist/tools/OPPL/ 5.- Add the following lines to /galaxy-dist/tool_conf.xml: <section name="Ontology Pre Processor Language" id="oppl"> <tool file="OPPL/oppl.xml"/> + <tool file="OPPL/inference.xml"/> </section> 6.- Start Galaxy. -USAGE -===== - -An ontology and an OPPL file are needed (test.owl and test.oppl can be -used as samples). Load both: - -Get Data - >> Upload File from your computer - -Then execute the OPPL file against the OWL file: - -Ontology Pre Processor Language - >> Execute an OPPL file against an OWL file - -An ontology produced by another galaxy tool can also be used. - -Test.oppl and test.owl can be used as examples. More OPPL-Galaxy -examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and -general OPPL script that may be useful to use with OPPL-Galaxy can be -obtained at http://oppl2.sourceforge.net/taggedexamples/. - -A public instance of Galaxy with pre-installed OPPL-Galaxy can be used -at http://sele.inf.um.es:8080/. - - - FORESEEN FEATURES ================= -Choose which inferred axioms to add to the output ontology (Right now -only subsumption between named classes is available). +OPPL: + +- Support for processing ontologies that import other ontologies loaded +in galaxy. + +- Rendering definition (URI fragment, label, etc). -Rendering definition (URI fragment, label, etc). +- Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf +cell). + +- OWLLink and Racer support. + -XML catalog support for imported URIs. +Inference: -OWLLink and Racer support. +- DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals, +... + @@ -74,31 +60,14 @@ Currently Galaxy interprets any information thrown to stderr as a tool error, which is bad since OPPL (And many other tools) throw info to -sdterr even if working properly. In OPPL Galaxy, stderr is redirected to -/dev/null to avoid the problem, but that means that OPPL Galaxy does not -fail gracefully (It simply stops). A wrapper will be implemented. +sdterr even if working properly. In OPPL Galaxy, stderr is redirected +to /dev/null to avoid the problem, but that means that OPPL Galaxy does +not fail gracefully (It simply stops). A wrapper will be implemented. http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -TESTS -===== - -To run the functional test, first complete installation and then: - -1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/ - -2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample - - <section name="Ontology Pre Processor Language" id="oppl"> - <tool file="OPPL/oppl.xml"/> - </section> - -3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl - - - CONTACT ======= @@ -118,10 +87,10 @@ Copyright (c) 2011 Mikel Egaña Aranguren. -OPPL-Galaxy is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. +(OPPL|Inference)-Galaxy is free software: you can redistribute it and/or +modify it under the terms of the GNU General Public License as published +by the Free Software Foundation, either version 3 of the License, or (at +your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/Tool.java --- a/OPPL/Tool.java Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,271 +0,0 @@\n-/**\n- * Copyright (C) 2011, Mikel Ega\xc3\xb1a Aranguren\n- *\n- * This program is free software: you can redistribute it and/or modify\n- * it under the terms of the GNU General Public License as published by\n- * the Free Software Foundation, either version 3 of the License, or\n- * (at your option) any later version.\n- *\n- * This program is distributed in the hope that it will be useful,\n- * but WITHOUT ANY WARRANTY; without even the implied warranty of\n- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n- * GNU General Public License for more details.\n- *\n- * You should have received a copy of the GNU General Public License\n- * along with this program. If not, see <http://www.gnu.org/licenses/>.\n- */\n-\n-package es.upm.fi.dia.oeg.oppl.galaxy;\n-\n-import java.io.BufferedWriter;\n-import java.io.File;\n-//import java.io.PrintWriter;\n-//import java.io.FileNotFoundException;\n-import java.io.IOException;\n-import java.io.OutputStreamWriter;\n-import java.net.URISyntaxException;\n-import java.util.ArrayList;\n-import java.util.List;\n-import java.util.Scanner;\n-//import java.util.logging.Level;\n-import java.util.logging.Logger;\n-\n-import org.coode.oppl.ChangeExtractor;\n-import org.coode.oppl.OPPLParser;\n-import org.coode.oppl.OPPLScript;\n-import org.coode.oppl.ParserFactory;\n-import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler;\n-//import org.coode.oppl.log.Logging;\n-import org.coode.owlapi.obo.parser.OBOOntologyFormat;\n-import org.coode.parsers.ErrorListener;\n-import org.coode.parsers.LoggerErrorListener;\n-//import org.obolibrary.obo2owl.Owl2Obo;\n-//import org.obolibrary.oboformat.model.OBODoc;\n-//import org.obolibrary.oboformat.writer.OBOFormatWriter;\n-import org.semanticweb.owlapi.apibinding.OWLManager;\n-import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;\n-import org.semanticweb.owlapi.io.SystemOutDocumentTarget;\n-import org.semanticweb.owlapi.model.AddAxiom;\n-import org.semanticweb.owlapi.model.IRI;\n-import org.semanticweb.owlapi.model.OWLAnnotation;\n-import org.semanticweb.owlapi.model.OWLAnnotationProperty;\n-import org.semanticweb.owlapi.model.OWLAxiom;\n-import org.semanticweb.owlapi.model.OWLAxiomChange;\n-import org.semanticweb.owlapi.model.OWLClass;\n-import org.semanticweb.owlapi.model.OWLDataFactory;\n-import org.semanticweb.owlapi.model.OWLLiteral;\n-//import org.semanticweb.owlapi.model.OWLObjectProperty;\n-import org.semanticweb.owlapi.model.OWLOntology;\n-import org.semanticweb.owlapi.model.OWLOntologyChange;\n-import org.semanticweb.owlapi.model.OWLOntologyCreationException;\n-import org.semanticweb.owlapi.model.OWLOntologyIRIMapper;\n-import org.semanticweb.owlapi.model.OWLOntologyManager;\n-import org.semanticweb.owlapi.model.OWLOntologyStorageException;\n-//import org.semanticweb.owlapi.owllink.OWLlinkHTTPXMLReasonerFactory;\n-import org.semanticweb.owlapi.reasoner.InferenceType;\n-import org.semanticweb.owlapi.reasoner.OWLReasoner;\n-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;\n-import org.semanticweb.owlapi.util.InferredAxiomGenerator;\n-import org.semanticweb.owlapi.util.InferredOntologyGenerator;\n-import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;\n-import org.semanticweb.owlapi.util.OWLEntityRenamer;\n-import org.semanticweb.owlapi.util.OWLOntologyMerger;\n-import org.semanticweb.owlapi.util.SimpleIRIMapper;\n-import org.semanticweb.owlapi.vocab.OWL2Datatype;\n-import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;\n-\n-import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;\n-\n-import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;\n-\n-import org.semanticweb.HermiT.Reasoner;\n-\n-/**\n- * @author Mikel Ega\xc3\xb1a Aranguren\n- */\n-public class Tool {\n-\n-\t/**\n-\t * @throws OWLOntologyCreationException \n-\t * @throws OWLOntologyStorageException \n-\t * @throws IOException \n-\t * @throws URISyntaxException \n-\t */\n-\tpublic static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException, URISyntaxExcepti'..b'recomputeInferences(InferenceType.CLASS_HIERARCHY);\n-\t\t\tList<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();\n-\t\t\tgens.add(new InferredSubClassAxiomGenerator());\n-\t\t\tInferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);\n-\t\t\tiog.fillOntology(manager, OWL_ontology);\t\n-\t\t}\n-\t\t\n-\t\t// Print the ontology to the standard output so other galaxy tools can operate on it\n-\t\t\n-\t\t// Merge ontologies (Only in case there are imports)\n-\t\tif(!merge_URI.equals("NoMerge") && !imports_file_path.equals("NoImports")){\n-\t\t\tOWLOntologyMerger merger = new OWLOntologyMerger(manager);\n-\t\t\tIRI mergedOntologyIRI = IRI.create(merge_URI);\n-\t\t\tOWLOntology merged = merger.createMergedOntology(manager, mergedOntologyIRI);\n-\t\t\tsaveOntology(manager, merged, Output_format);\n-\t\t}\n-\t\t// Do not merge ontologies (Even in the case in which a URI is provided, if there are not imports do not merge)\t\n-\t\telse{\t\n-\t\t\tsaveOntology(manager, OWL_ontology, Output_format);\n-\t\t}\n-\t}\n-\t\n-\tprivate static void saveOntology (OWLOntologyManager manager, OWLOntology ontology, String Format) throws OWLOntologyStorageException, IOException, URISyntaxException {\n-\t\t\n-\t\t// OBO format\n-\t\tif(Format.equals("OBO")){\n-\t\t\t\n-\t\t\t// OWL API generates bad OBO but OBOformat doesn\'t work either so I correct the OWL API problems (More predictable) in a temporary file\n-\t\t\t// Very inefficient but no time for another solution\n-\t\t\t\n-\t\t\tOWLDataFactory factory = manager.getOWLDataFactory();\n-\t\t\t\n-\t\t\tOWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());\n-\t\t\tOWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());\n-\t\t\t\n-\t\t\tfor(OWLClass cls : ontology.getClassesInSignature()){\n-\t\t\t\t// Remove annotations (OWL API generates bad OBO annotations)\n-\t\t\t\t\n-\t\t\t\t// Keep rdfs:label\n-\t\t\t\tString class_name = null;\n-\t\t\t\tfor (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){\n-\t\t\t\t\tif (annotation.getValue() instanceof OWLLiteral) {\n-\t\t\t\t\t\tOWLLiteral val = (OWLLiteral) annotation.getValue();\n-\t\t\t\t\t\tclass_name = val.getLiteral();\n-\t\t\t\t\t}\n-\t\t\t\t}\n-\t\t\t\t\t\t\t\n-//\t\t\t\tI have to remove all the annotations cause I don\'t know which ones are rendered properly\n-\t\t\t\tmanager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));\n-\t\t\t\t\n-\t\t\t\t// Add rdfs:label again\n-\t\t\t\tOWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(\n-\t\t\t\tOWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));\n-\t\t\t\tOWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);\n-\t\t\t\tmanager.applyChange(new AddAxiom(ontology, ax));\n-\t\t\t\t\n-\t\t\t\t// Rename entities\n-\t\t\t\tString cls_IRI = cls.getIRI().toString();\n-\t\t\t\tString cls_proper_IRI = cls_IRI.replace("_", ":");\n-\t\t\t\tList<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));\n-\t\t\t\tmanager.applyChanges(changes);\n-\t\t\t}\n-\t\t\t\n-\t\t\tFile file = new File("tmp.obo");\n-\t\t\tmanager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));\n-\t\t\tBufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));\t\t\n-\t\t\tScanner input = new Scanner(file);\n-\t\t\tString buffer = "";\n-\n-\t\t\twhile(input.hasNext()){\n-\t\t\t\tString nextLine = input.nextLine();\n-\t\t\t\tif(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){\n-\t\t\t\t\tif(buffer.isEmpty()){\n-\t\t\t\t\t\tbw.write(buffer);\n-\t\t\t\t\t\tbw.newLine();\n-\t\t\t\t\t}\n-\t\t\t\t}\n-\t\t\t\tif(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){\n-\t\t\t\t\tif(!nextLine.isEmpty() && !buffer.contains("relationship:")){\n-\t\t\t\t\t\tbw.write(nextLine);\n-\t\t\t\t\t\tbw.newLine();\n-\t\t\t\t\t}\n-\t\t\t\t}\n-\t\t\t\tbuffer = nextLine;\n-\t\t\t}\n-\t\t\tinput.close();\n-\t\t\tbw.close();\n-\t\t\tfile.delete();\n-\t\t}\n-\t\t\n-\t\t//OWL format\n-\t\telse{\n-\t\t\tmanager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());\n-\t\t}\n-\t}\n-}\n' |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/cell.owl --- a/OPPL/cell.owl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,39919 +0,0 @@\n-<?xml version="1.0"?>\n-\n-\n-<!DOCTYPE rdf:RDF [\n- <!ENTITY owl "http://www.w3.org/2002/07/owl#" >\n- <!ENTITY obo "http://purl.obolibrary.org/obo/" >\n- <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >\n- <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >\n- <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >\n-]>\n-\n-\n-<rdf:RDF xmlns="&obo;UBERON_uberon#"\n- xml:base="&obo;UBERON_uberon"\n- xmlns:obo="http://purl.obolibrary.org/obo/"\n- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"\n- xmlns:owl="http://www.w3.org/2002/07/owl#"\n- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n- <owl:Ontology rdf:about="&obo;UBERON_uberon">\n- <obo:remark rdf:datatype="&xsd;string">$Revision: 1.52 $ See PMID:15693950, PMID:12799354, PMID:20123131, Contact Alexander Diehl, addiehl@buffalo.edu, University of Buffalo.</obo:remark>\n- <obo:format-version rdf:datatype="&xsd;string">1.2</obo:format-version>\n- <obo:data-version rdf:datatype="&xsd;string">2011-06-03</obo:data-version>\n- <obo:date rdf:datatype="&xsd;string">24:08:2011 09:07</obo:date>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd;string">AAO part_of NCBITaxon:8292</obo:treat-xrefs-as-genus-differentia>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">ATTRIBUTION_REQUIRED "expert consultation and attribution required"</obo:synonymtypedef>\n- <obo:treat-xrefs-as-equivalent rdf:datatype="&xsd;string">BILA</obo:treat-xrefs-as-equivalent>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">BRAND_NAME "BRAND NAME"</obo:synonymtypedef>\n- <obo:treat-xrefs-as-equivalent rdf:datatype="&xsd;string">BSPO</obo:treat-xrefs-as-equivalent>\n- <obo:treat-xrefs-as-equivalent rdf:datatype="&xsd;string">CARO</obo:treat-xrefs-as-equivalent>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">DUBIOUS "dubious or contested synonym"</obo:synonymtypedef>\n- <obo:treat-xrefs-as-has-subclass rdf:datatype="&xsd;string">EHDAA</obo:treat-xrefs-as-has-subclass>\n- <obo:treat-xrefs-as-has-subclass rdf:datatype="&xsd;string">EHDAA2</obo:treat-xrefs-as-has-subclass>\n- <obo:treat-xrefs-as-has-subclass rdf:datatype="&xsd;string">EMAPA</obo:treat-xrefs-as-has-subclass>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd;string">FBbt part_of NCBITaxon:7227</obo:treat-xrefs-as-genus-differentia>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd;string">FMA part_of NCBITaxon:9606</obo:treat-xrefs-as-genus-differentia>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">FORMULA "FORMULA"</obo:synonymtypedef>\n- <obo:treat-xrefs-as-equivalent rdf:datatype="&xsd;string">GO</obo:treat-xrefs-as-equivalent>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd;string">HAO part_of NCBITaxon:7399</obo:treat-xrefs-as-genus-differentia>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">HOMOLOGY "a synonym made on the basis of a possibly homologous structure in another species"</obo:synonymtypedef>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">INCONSISTENT "indicates that a synonym is used in an inconsistent or confusing way, typically between species"</obo:synonymtypedef>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">INN "INN"</obo:synonymtypedef>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">IUPAC_NAME "IUPAC NAME"</obo:synonymtypedef>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">InChI "InChI"</obo:synonymtypedef>\n- <obo:synonymtypedef rdf:datatype="&xsd;string">InChIKey "InChIKey"</obo:synonymtypedef>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd;string">KUPO part_of NCBITaxon:9606</obo:treat-xrefs-as-genus-differentia>\n- <obo:treat-xrefs-as-genus-differentia rdf:datatype="&xsd'..b'bo;UBERON_located_in">\n- <rdfs:label rdf:datatype="&xsd;string">located_in</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_exists_during">\n- <rdfs:label rdf:datatype="&xsd;string">exists_during</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_not_completed">\n- <rdfs:label rdf:datatype="&xsd;string">has_not_completed</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_parent_hydride">\n- <rdfs:label rdf:datatype="&xsd;string">has parent hydride</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_similar_in_magnitude_relative_to">\n- <rdfs:label rdf:datatype="&xsd;string">similar_in_magnitude_relative_to</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_modification">\n- <rdfs:label rdf:datatype="&xsd;string">has_modification</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_derives_from">\n- <rdfs:label rdf:datatype="&xsd;string">derives_from</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_singly_occurring_form_of">\n- <rdfs:label rdf:datatype="&xsd;string">singly_occurring_form_of</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_existence_starts_with">\n- <rdfs:label rdf:datatype="&xsd;string">existence_starts_with</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_branch_of">\n- <rdfs:label rdf:datatype="&xsd;string">branch_of</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_precedes">\n- <rdfs:label rdf:datatype="&xsd;string">precedes</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_ratio_quality">\n- <rdfs:label rdf:datatype="&xsd;string">has_ratio_quality</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_participates_in">\n- <rdfs:label rdf:datatype="&xsd;string">participates in</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_deep_to">\n- <rdfs:label rdf:datatype="&xsd;string">deep_to</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_inheres_in_progenitor_of">\n- <rdfs:label rdf:datatype="&xsd;string">inheres_in_progenitor_of</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_never_in_taxon">\n- <rdfs:label rdf:datatype="&xsd;string">never_in_taxon</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_output_of">\n- <rdfs:label rdf:datatype="&xsd;string">output_of</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_part">\n- <rdfs:label rdf:datatype="&xsd;string">has part</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_divisor_entity">\n- <rdfs:label rdf:datatype="&xsd;string">has_divisor_entity</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_is_unit_of">\n- <rdfs:label rdf:datatype="&xsd;string">is_unit_of</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_has_function_in">\n- <rdfs:label rdf:datatype="&xsd;string">has_function_in</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_existence_ends_during">\n- <rdfs:label rdf:datatype="&xsd;string">existence_ends_during</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_lacks_part">\n- <rdfs:label rdf:datatype="&xsd;string">lacks_part</rdfs:label>\n- </rdf:Description>\n- <rdf:Description rdf:about="&obo;UBERON_finishes">\n- <rdfs:label rdf:datatype="&xsd;string">finishes</rdfs:label>\n- </rdf:Description>\n-</rdf:RDF>\n-\n-\n-\n-<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net -->\n-\n' |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/chebi.owl --- a/OPPL/chebi.owl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1078327 +0,0 @@\n-<?xml version="1.0"?>\n-\n-\n-<!DOCTYPE rdf:RDF [\n- <!ENTITY owl "http://www.w3.org/2002/07/owl#" >\n- <!ENTITY obo "http://purl.obolibrary.org/obo/" >\n- <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >\n- <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >\n- <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >\n-]>\n-\n-\n-<rdf:RDF xmlns="&obo;CHEBI_ONTOLOGY_chebi_ontology#"\n- xml:base="&obo;CHEBI_ONTOLOGY_chebi_ontology"\n- xmlns:obo="http://purl.obolibrary.org/obo/"\n- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"\n- xmlns:owl="http://www.w3.org/2002/07/owl#"\n- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n- <owl:Ontology rdf:about="&obo;CHEBI_ONTOLOGY_chebi_ontology"/>\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Annotation properties\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- <owl:AnnotationProperty rdf:about="&obo;synonymtype"/>\n- <owl:AnnotationProperty rdf:about="&obo;xref"/>\n- <owl:AnnotationProperty rdf:about="&obo;def"/>\n- <owl:AnnotationProperty rdf:about="&obo;is_obsolete"/>\n- <owl:AnnotationProperty rdf:about="&obo;synonym"/>\n- <owl:AnnotationProperty rdf:about="&obo;is_cyclic"/>\n- <owl:AnnotationProperty rdf:about="&obo;alt_id"/>\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Datatypes\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Object Properties\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_has_functional_parent -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_has_functional_parent">\n- <rdfs:label rdf:datatype="&xsd;string">has functional parent</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_has_parent_hydride -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_has_parent_hydride">\n- <rdfs:label rdf:datatype="&xsd;string">has parent hydride</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_has_part -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_has_part">\n- <rdf:type rdf:resource="&owl;TransitiveProperty"/>\n- <rdfs:label rdf:datatype="&xsd;string">has part</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_has_role -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_has_role">\n- <rdfs:label rdf:datatype="&xsd;string">has role</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_is_conjugate_acid_of -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_is_conjugate_acid_of">\n- <rdfs:label rdf:datatype="&xsd;string">is conjugate acid of</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_is_conjugate_base_of -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_is_conjugate_base_of">\n- <rdfs:label rdf:datatype="&xsd;string">is conjugate base of</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_is_enantiomer_of -->\n-\n- <owl:ObjectProperty rdf:about="&obo;CHEBI_ONTOLOGY_is_enantiomer_of">\n- <rdfs:label rdf:datatype="&xsd;string">is enantiomer of</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_is_subs'..b'd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>Velban (TN)</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9984"/>\n- <obo:xref rdf:resource="&obo;KEGG%20DRUG:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/CHEBI_9985 -->\n-\n- <owl:Class rdf:about="&obo;CHEBI_9985">\n- <rdfs:label rdf:datatype="&xsd;string">vincamine</rdfs:label>\n- <rdfs:subClassOf rdf:resource="&obo;CHEBI_27288"/>\n- <rdfs:subClassOf rdf:resource="&obo;CHEBI_38481"/>\n- <rdfs:subClassOf>\n- <owl:Restriction>\n- <owl:onProperty rdf:resource="&obo;CHEBI_ONTOLOGY_has_role"/>\n- <owl:someValuesFrom rdf:resource="&obo;CHEBI_35620"/>\n- </owl:Restriction>\n- </rdfs:subClassOf>\n- <rdfs:subClassOf>\n- <owl:Restriction>\n- <owl:onProperty rdf:resource="&obo;CHEBI_ONTOLOGY_has_role"/>\n- <owl:someValuesFrom rdf:resource="&obo;CHEBI_35674"/>\n- </owl:Restriction>\n- </rdfs:subClassOf>\n- <rdfs:subClassOf>\n- <owl:Restriction>\n- <owl:onProperty rdf:resource="&obo;CHEBI_ONTOLOGY_has_functional_parent"/>\n- <owl:someValuesFrom rdf:resource="&obo;CHEBI_35644"/>\n- </owl:Restriction>\n- </rdfs:subClassOf>\n- <obo:xref>KEGG COMPOUND:1617-90-9 "CAS Registry Number"</obo:xref>\n- <obo:synonym>(+)-Vincamine</obo:synonym>\n- <obo:xref>Beilstein:52767 "Beilstein Registry Number"</obo:xref>\n- <obo:synonym>Pervincamine</obo:synonym>\n- <obo:synonym>Methyl vincaminate</obo:synonym>\n- <obo:def>"An alkaloid ester that has formula C21H26N2O3." []</obo:def>\n- <obo:synonym>Vincamidol</obo:synonym>\n- <obo:xref>ChemIDplus:1617-90-9 "CAS Registry Number"</obo:xref>\n- <obo:synonym>Vincamine</obo:synonym>\n- <obo:xref>KEGG COMPOUND:C09251 "KEGG COMPOUND"</obo:xref>\n- </owl:Class>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>(+)-Vincamine</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9985"/>\n- <obo:xref rdf:resource="&obo;ChemIDplus:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>Methyl vincaminate</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9985"/>\n- <obo:xref rdf:resource="&obo;ChemIDplus:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>Vincamidol</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9985"/>\n- <obo:xref rdf:resource="&obo;ChemIDplus:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>Pervincamine</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9985"/>\n- <obo:xref rdf:resource="&obo;ChemIDplus:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">EXACT</obo:synonymtype>\n- <owl:annotatedTarget>Vincamine</owl:annotatedTarget>\n- <owl:annotatedSource rdf:resource="&obo;CHEBI_9985"/>\n- <obo:xref rdf:resource="&obo;KEGG%20COMPOUND:"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n-</rdf:RDF>\n-\n-\n-\n-<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net -->\n-\n' |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/gene_ontology_ext.owl --- a/OPPL/gene_ontology_ext.owl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,1139966 +0,0 @@\n-<?xml version="1.0"?>\n-\n-\n-<!DOCTYPE rdf:RDF [\n- <!ENTITY owl "http://www.w3.org/2002/07/owl#" >\n- <!ENTITY obo "http://purl.obolibrary.org/obo/" >\n- <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >\n- <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >\n- <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >\n-]>\n-\n-\n-<rdf:RDF xmlns="&obo;go#"\n- xml:base="&obo;go"\n- xmlns:obo="http://purl.obolibrary.org/obo/"\n- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"\n- xmlns:owl="http://www.w3.org/2002/07/owl#"\n- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">\n- <owl:Ontology rdf:about="&obo;go">\n- <owl:imports rdf:resource="&obo;CHEBI_ONTOLOGY_chebi_ontology"/>\n- <owl:imports rdf:resource="&obo;UBERON_uberon"/>\n- </owl:Ontology>\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Annotation properties\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- <owl:AnnotationProperty rdf:about="&obo;consider"/>\n- <owl:AnnotationProperty rdf:about="&obo;synonymtype"/>\n- <owl:AnnotationProperty rdf:about="&obo;def"/>\n- <owl:AnnotationProperty rdf:about="&obo;subset"/>\n- <owl:AnnotationProperty rdf:about="&obo;comment"/>\n- <owl:AnnotationProperty rdf:about="&obo;alt_id"/>\n- <owl:AnnotationProperty rdf:about="&obo;replaced_by"/>\n- <owl:AnnotationProperty rdf:about="&obo;transitive_over"/>\n- <owl:AnnotationProperty rdf:about="&obo;namespace"/>\n- <owl:AnnotationProperty rdf:about="&obo;xref"/>\n- <owl:AnnotationProperty rdf:about="&obo;is_obsolete"/>\n- <owl:AnnotationProperty rdf:about="&obo;synonym"/>\n- <owl:AnnotationProperty rdf:about="&obo;created_by"/>\n- <owl:AnnotationProperty rdf:about="&obo;creation_date"/>\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Datatypes\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- \n-\n-\n- <!-- \n- ///////////////////////////////////////////////////////////////////////////////////////\n- //\n- // Object Properties\n- //\n- ///////////////////////////////////////////////////////////////////////////////////////\n- -->\n-\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GENE_ONTOLOGY_has_part -->\n-\n- <owl:ObjectProperty rdf:about="&obo;GENE_ONTOLOGY_has_part">\n- <rdf:type rdf:resource="&owl;TransitiveProperty"/>\n- <rdfs:label rdf:datatype="&xsd;string">has_part</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GENE_ONTOLOGY_negatively_regulates -->\n-\n- <owl:ObjectProperty rdf:about="&obo;GENE_ONTOLOGY_negatively_regulates">\n- <rdfs:label rdf:datatype="&xsd;string">negatively_regulates</rdfs:label>\n- <rdfs:subPropertyOf rdf:resource="&obo;GENE_ONTOLOGY_regulates"/>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GENE_ONTOLOGY_occurs_in -->\n-\n- <owl:ObjectProperty rdf:about="&obo;GENE_ONTOLOGY_occurs_in">\n- <rdfs:label rdf:datatype="&xsd;string">occurs in</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GENE_ONTOLOGY_part_of -->\n-\n- <owl:ObjectProperty rdf:about="&obo;GENE_ONTOLOGY_part_of">\n- <rdf:type rdf:resource="&owl;TransitiveProperty"/>\n- <rdfs:label rdf:datatype="&xsd;string">part_of</rdfs:label>\n- </owl:ObjectProperty>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GENE_ONTOLOGY_positively_regulates -->\n-\n- <owl:ObjectProperty rdf:about="&obo;GENE_ONTOLOGY_positively_regulates">\n- <rdfs:label rdf:datatype="&xsd;string">positively_regulates</rdfs:label>\n- <rdfs:subPropertyOf rdf:resource="&obo;GENE_ONTOLOGY_regulates"/>'..b' <obo:creation_date>2011-09-14T12:01:06Z</obo:creation_date>\n- </owl:Class>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>animal starch binding</owl:annotatedTarget>\n- <obo:xref rdf:resource="&obo;GOC_obol"/>\n- <owl:annotatedSource rdf:resource="&obo;GO_2001069"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>liver starch binding</owl:annotatedTarget>\n- <obo:xref rdf:resource="&obo;GOC_obol"/>\n- <owl:annotatedSource rdf:resource="&obo;GO_2001069"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GO_2001070 -->\n-\n- <owl:Class rdf:about="&obo;GO_2001070">\n- <rdfs:label rdf:datatype="&xsd;string">starch binding</rdfs:label>\n- <rdfs:subClassOf rdf:resource="&obo;GO_0030247"/>\n- <obo:synonym>amidon binding</obo:synonym>\n- <obo:created_by>jane</obo:created_by>\n- <obo:namespace>molecular_function</obo:namespace>\n- <obo:def>"Interacting selectively and non-covalently with starch." [GOC:mengo_curators]</obo:def>\n- <obo:creation_date>2011-09-14T12:02:50Z</obo:creation_date>\n- <obo:synonym>amylum binding</obo:synonym>\n- </owl:Class>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>amylum binding</owl:annotatedTarget>\n- <obo:xref rdf:resource="&obo;GOC_obol"/>\n- <owl:annotatedSource rdf:resource="&obo;GO_2001070"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- <owl:Axiom>\n- <obo:synonymtype rdf:datatype="&xsd;string">RELATED</obo:synonymtype>\n- <owl:annotatedTarget>amidon binding</owl:annotatedTarget>\n- <obo:xref rdf:resource="&obo;GOC_obol"/>\n- <owl:annotatedSource rdf:resource="&obo;GO_2001070"/>\n- <owl:annotatedProperty rdf:resource="&obo;synonym"/>\n- </owl:Axiom>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GO_2001071 -->\n-\n- <owl:Class rdf:about="&obo;GO_2001071">\n- <rdfs:label rdf:datatype="&xsd;string">maltoheptaose binding</rdfs:label>\n- <rdfs:subClassOf rdf:resource="&obo;GO_0070492"/>\n- <obo:def>"Interacting selectively and non-covalently with maltoheptaose." [GOC:mengo_curators]</obo:def>\n- <obo:namespace>molecular_function</obo:namespace>\n- <obo:created_by>jane</obo:created_by>\n- <obo:creation_date>2011-09-14T12:04:30Z</obo:creation_date>\n- </owl:Class>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GO_2001072 -->\n-\n- <owl:Class rdf:about="&obo;GO_2001072">\n- <rdfs:label rdf:datatype="&xsd;string">galactomannan binding</rdfs:label>\n- <rdfs:subClassOf rdf:resource="&obo;GO_0010297"/>\n- <obo:namespace>molecular_function</obo:namespace>\n- <obo:creation_date>2011-09-14T12:12:02Z</obo:creation_date>\n- <obo:def>"Interacting selectively and non-covalently with galactomannan." [GOC:mengo_curators]</obo:def>\n- <obo:created_by>jane</obo:created_by>\n- </owl:Class>\n- \n-\n-\n- <!-- http://purl.obolibrary.org/obo/GO_2001073 -->\n-\n- <owl:Class rdf:about="&obo;GO_2001073">\n- <rdfs:label rdf:datatype="&xsd;string">cyclodextrin binding</rdfs:label>\n- <rdfs:subClassOf rdf:resource="&obo;GO_0030247"/>\n- <obo:created_by>jane</obo:created_by>\n- <obo:namespace>molecular_function</obo:namespace>\n- <obo:creation_date>2011-09-14T12:24:30Z</obo:creation_date>\n- <obo:def>"Interacting selectively and non-covalently with cyclodextrin." [GOC:mengo_curators]</obo:def>\n- </owl:Class>\n-</rdf:RDF>\n-\n-\n-\n-<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net -->\n-\n' |
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| @@ -0,0 +1,80 @@ +<tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1"> + <description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description> + + <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + + <command> + java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output + </command> + + <inputs> + <param format="text" name="input" type="data" label="Input ontology file"/> + <param name="reasoner" type="select" label="Choose reasoner"> + <option value="Pellet" selected="true">Pellet</option> + <option value="HermiT">HermiT</option> + <option value="FaCTPlusPlus">FaCT++</option> + </param> + <param name="axioms" type="select" display="checkboxes" multiple="true" label="Select what axioms to add as asserted"> + <option value="CLASS_ASSERTIONS">CLASS_ASSERTIONS</option> + <option value="CLASS_HIERARCHY">CLASS_HIERARCHY</option> + <option value="DATA_PROPERTY_HIERARCHY">DATA_PROPERTY_HIERARCHY</option> + <option value="DISJOINT_CLASSES">DISJOINT_CLASSES</option> + <option value="OBJECT_PROPERTY_HIERARCHY">OBJECT_PROPERTY_HIERARCHY</option> + </param> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="input" value="test.owl"/> + <param name="reasoner" value="Pellet"/> + <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/> + <output name="out_file" file="test_new.owl"/> + </test> + </tests> + <help> + +**About Inference-Galaxy** + + Inference galaxy offers the possibility of performing automated reasoning in an ontology and then injecting the inferred axioms as asserted axioms, generating a new OWL ontology. + +**Formats** + + Inference-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is OWL (RDF/XML). + +**Usage** + + An ontology is needed as input: load it with Get Data >> Upload File from your computer or redirect the output of another galaxy tool. In case the ontology includes imports, they should be resolvable. + + The reasoner can be Pellet, HermiT or FaCT++. + + The inferred axioms to add as asserted axioms can be chosen. + +**More information** + + Galaxy public instances with Inference-Galaxy pre-installed: + + http://sele.inf.um.es:8080/ + + http://linkeddata2.dia.fi.upm.es:8080 + + Links of interest: + + http://owlapi.sourceforge.net/ + + http://www.w3.org/TR/owl2-manchester-syntax/ + + http://clarkparsia.com/pellet + + http://hermit-reasoner.com/ + + http://code.google.com/p/factplusplus/ + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + </help> + +</tool> |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/oppl.sh --- a/OPPL/oppl.sh Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -#!/bin/sh - -java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar oppl_galaxy_tool.jar test.owl test.oppl > test_new.owl - - - |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/oppl.xml --- a/OPPL/oppl.xml Thu Jan 12 10:20:00 2012 +0100 +++ b/OPPL/oppl.xml Fri Mar 09 16:15:27 2012 +0100 |
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| b'@@ -1,92 +1,57 @@\n-\xef\xbb\xbf<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.7">\n+\xef\xbb\xbf<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.8">\n \t<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>\n \n \t<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->\n \t<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->\n+\t<!-- Testing with wrapper.sh but no success so far -->\n \t\n-\n-\t<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that\'s too much for your machine simply delete or modify at will -->\n-\n-\t<!--<command>\n-\t\t#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null\n-\t\t#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null\n-\t\t#end if\n-\t</command>-->\n+\t\n \t\n+\t<!-- DEFAULT SETTINGS -->\n+\t\n+\t<!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that\'s too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory -->\n \n \t<command>\n-\t\t#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null\n-\t\t#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $import_opts.imports $reasoner $import_opts.merge_opts.merged > $output 2>/dev/null\n-\t\t#end if\n+\t\tjava -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null\n \t</command>\n \t\n \t\n-\t<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the one above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->\n+\t\n+\t<!-- FACT++ -->\n+\t\n+\t<!-- If you are planning to use FaCT++ you have to uncomment bellow (And comment the default settings above) and replace the -Djava.library.path with the appropiate JNI library path for your platform:FaCT++-linux-v1.5.2/64bit, FaCT++-linux-v1.5.2/32bit, FaCT++-OSX-v1.5.2/64bit, ...... -->\n \t<!-- Using this setting doesn\'t upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT -->\n \t\n \t<!--<command>\n-\t\t#if $import_opts.imports_select==False #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner NoMerge > $output 2>/dev/null\n-\t\t#else #java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner $merged > $output 2>/dev/null\n-\t\t#end if\n-\t</command>-->\n+\t\tjava -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/de'..b'bel="Type an URI or use the default URI" /> \n-\t\t\t\t </when>\n-\t\t\t\t</conditional> \n- \t\t</when>\n-\t\t</conditional>\n+\t\t<param name="reasoner" type="select" label="Choose reasoner">\n+\t\t\t<option value="Pellet" selected="true">Pellet</option>\n+\t\t\t<option value="HermiT">HermiT</option>\n+\t\t\t<option value="FaCTPlusPlus">FaCT++</option>\n+\t\t</param>\n \t\t<param format="text" name="OPPL" type="data" label="OPPL file"/>\n \t\t<param name="format" type="select" label="Choose ontology output format">\n \t\t\t<option value="OWL" selected="true">OWL</option>\n \t\t\t<option value="OBO">OBO</option>\n \t\t</param>\n-\t\t<param name="inferred" type="boolean" value="False" truevalue="AddInferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>\n-<!-- \t\t<param name="merged" type="text" size="100" value="NoMerge" label="To merge ontologies (If there are imports), type an URI for the new ontology (Leave NoMerge for not merging)" /> -->\n-\t\t<param name="reasoner" type="select" label="Choose reasoner">\n-\t\t\t<option value="Pellet" selected="true">Pellet</option>\n-\t\t\t<option value="HermiT">HermiT</option>\n-\t\t\t<option value="FaCTPlusPlus">FaCT++</option>\n-\t\t</param>\n-\n \t</inputs>\n \t<outputs>\n \t\t<data format="text" name="output" />\n@@ -95,11 +60,8 @@\n \t\t<test>\n \t\t\t<param name="input" value="test.owl"/>\n \t\t\t<param name="OPPL" value="test.oppl"/>\n-\t\t\t<param name="imports" value="NoImports"/>\n \t\t\t<param name="format" value="OWL"/>\n-\t\t\t<param name="inferred" value="False"/>\n \t\t\t<param name="reasoner" value="Pellet"/>\n-\t\t\t<param name="merged" value="no_merge"/>\n \t\t\t<output name="out_file" file="test_new.owl"/>\t\n \t\t</test>\n \t</tests>\n@@ -115,27 +77,33 @@\n \n **Usage**\n \n- An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer. \n+ An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples, both available in the bundle). Load both with Get Data >> Upload File from your computer, or redirect from another Galaxy tool.\n \n Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file. A new output ontology will be generated.\n \n- In case the loaded ontology includes OWL imports, a file that maps the imported ontologies\' URIs to actual physical URIs is needed. The file (See the file test_URI_mappings provided in the bundle) follows the convention URI-tab-physical URI:\n- \n- http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology\t/home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl\n-\n- http://purl.obolibrary.org/obo/UBERON_uberon\t/home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl\n+ In case the loaded ontology includes OWL imports, OPPL-Galaxy will try to resolve them. \n \n The output ontology can be OBO or OWL (RDF/XML).\n- \n- The inferred subsumption axioms can be added to the output ontology as asserted axioms. \n-\n+ \n The reasoner can be Pellet, HermiT FaCT++. Sometimes, if an execution fails it can be fixed by using a different reasoner. \n \n- If OWL imports are used, all the ontologies (Main one and imported ones) can be merged in a single ontology for the output.\n-\n **More information**\n \n+ Galaxy public instances with OPPL-Galaxy pre-installed:\n+ \n+ http://sele.inf.um.es:8080/\n+ \n+ http://linkeddata2.dia.fi.upm.es:8080\n+ \n+ OPPL-Galaxy Examples: \n+ \n http://miuras.inf.um.es/OPPL-Galaxy/\n+ \n+ OPPL examples:\n+ \n+ http://oppl2.sourceforge.net/taggedexamples/\n+ \n+ Links of interest:\n \n http://oppl.sf.net/\n \n@@ -151,7 +119,7 @@\n \n **Citation**\n \n- Mikel Ega\xc3\xb1a Aranguren, Jesualdo Tom\xc3\xa1s Fern\xc3\xa1ndez-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011 (To appear in ACM proceedings).\n+ Mikel Ega\xc3\xb1a Aranguren, Jesualdo Tom\xc3\xa1s Fern\xc3\xa1ndez-Breis and Erick Antezana. OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL. SWAT4LS 2011.\n \n **Contact**\n \n' |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/src/GalaxyOWLAPI.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/src/GalaxyOWLAPI.java Fri Mar 09 16:15:27 2012 +0100 |
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| b'@@ -0,0 +1,265 @@\n+/**\n+ * \n+ */\n+package es.upm.fi.dia.oeg.oppl.galaxy;\n+\n+import java.io.BufferedWriter;\n+import java.io.File;\n+import java.io.IOException;\n+import java.io.OutputStreamWriter;\n+import java.util.ArrayList;\n+import java.util.List;\n+import java.util.Scanner;\n+\n+import org.coode.owlapi.obo.parser.OBOOntologyFormat;\n+import org.semanticweb.HermiT.Reasoner;\n+import org.semanticweb.owlapi.apibinding.OWLManager;\n+import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;\n+import org.semanticweb.owlapi.io.SystemOutDocumentTarget;\n+import org.semanticweb.owlapi.model.AddAxiom;\n+import org.semanticweb.owlapi.model.IRI;\n+import org.semanticweb.owlapi.model.OWLAnnotation;\n+import org.semanticweb.owlapi.model.OWLAnnotationProperty;\n+import org.semanticweb.owlapi.model.OWLAxiom;\n+import org.semanticweb.owlapi.model.OWLClass;\n+import org.semanticweb.owlapi.model.OWLDataFactory;\n+import org.semanticweb.owlapi.model.OWLLiteral;\n+import org.semanticweb.owlapi.model.OWLOntology;\n+import org.semanticweb.owlapi.model.OWLOntologyChange;\n+import org.semanticweb.owlapi.model.OWLOntologyCreationException;\n+import org.semanticweb.owlapi.model.OWLOntologyManager;\n+import org.semanticweb.owlapi.model.OWLOntologyStorageException;\n+import org.semanticweb.owlapi.reasoner.InferenceType;\n+import org.semanticweb.owlapi.reasoner.OWLReasoner;\n+import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;\n+import org.semanticweb.owlapi.util.InferredAxiomGenerator;\n+import org.semanticweb.owlapi.util.InferredClassAssertionAxiomGenerator;\n+import org.semanticweb.owlapi.util.InferredDisjointClassesAxiomGenerator;\n+import org.semanticweb.owlapi.util.InferredOntologyGenerator;\n+import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;\n+import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator;\n+import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator;\n+import org.semanticweb.owlapi.util.OWLEntityRenamer;\n+import org.semanticweb.owlapi.util.OWLOntologyMerger;\n+import org.semanticweb.owlapi.vocab.OWL2Datatype;\n+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;\n+\n+import uk.ac.manchester.cs.factplusplus.owlapiv3.FaCTPlusPlusReasonerFactory;\n+\n+import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;\n+\n+/**\n+ * A wrapper of the OWL API \n+ * \n+ * @author Mikel Ega\xc3\xb1a Aranguren\n+ */\n+public class GalaxyOWLAPI {\n+\tprivate OWLOntologyManager manager;\n+\tprivate OWLOntology ontology;\n+\tprivate OWLReasonerFactory reasonerFactory;\n+\tprivate OWLReasoner reasoner;\n+\t\n+\tpublic GalaxyOWLAPI (){\n+\t\tmanager = OWLManager.createOWLOntologyManager();\n+\t}\n+\tpublic OWLOntologyManager getOWLManager(){\n+\t\treturn manager;\n+\t}\n+\tpublic OWLOntology getMainOntology(){\n+\t\treturn ontology;\n+\t}\n+\tpublic OWLReasoner getReasoner(){\n+\t\treturn reasoner;\n+\t}\n+\t\n+\tpublic void loadMainOntology(String OWLFilePath) throws OWLOntologyCreationException{\n+\t\tFile owl_file = new File(OWLFilePath);\n+\t\tontology = manager.loadOntologyFromOntologyDocument(owl_file);\n+\t}\n+\t\n+//\tpublic void loadImportedOntology(IRI importedOntologyIRI) throws OWLOntologyCreationException{\n+//\t\tmanager.loadOntologyFromOntologyDocument(importedOntologyIRI);\n+//\t}\n+\t\n+\t// OWLLink: The problem is that Racer, for example, listens in 8080, the same port as Galaxy\n+\t// I have to change Racer settings and OWLLink settings\n+//\t\tOWLlinkHTTPXMLReasonerFactory factory = new OWLlinkHTTPXMLReasonerFactory();\n+//\t\treasoner = factory.createReasoner(OWL_ontology);\n+\t\n+\tpublic void setReasonerPellet (){\n+\t\treasonerFactory = new PelletReasonerFactory(); \n+\t\treasoner = reasonerFactory.createReasoner(ontology);\n+\t}\n+\tpublic void setReasonerFaCT (){\n+\t\treasonerFactory = new FaCTPlusPlusReasonerFactory();\n+\t\treasoner = reasonerFactory.createReasoner(ontology);\n+\t}\n+\tpublic void setReasonerHermit (){\n+\t\treasonerFactory = new Reasoner.ReasonerFactory();\n+\t\treasoner = reasonerFactory.createReasoner(ontology);\n+\t}\n+\tpublic void merge () throws OWLOntologyCreationException{\n+\t\tOWLOntologyMerger merger '..b'/\t\tiog.fillOntology(manager, ontology);\n+//\t}\n+\t\n+\t//\tOBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy.\n+\t\n+\tpublic void addOBJECT_PROPERTY_HIERARCHY(){\n+\t\treasoner.precomputeInferences(InferenceType.OBJECT_PROPERTY_HIERARCHY);\n+\t\tList<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();\n+\t\tgens.add(new InferredSubObjectPropertyAxiomGenerator());\n+\t\tInferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);\n+\t\tiog.fillOntology(manager, ontology);\n+\t}\n+\t\n+\t//\tSAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology.\n+\t\n+//\tpublic void addSAME_INDIVIDUAL(){\n+//\t\treasoner.precomputeInferences(InferenceType.SAME_INDIVIDUAL);\n+//\t\tList<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();\n+//\t\tgens.add(new Infer);\n+//\t\tInferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);\n+//\t\tiog.fillOntology(manager, ontology);\n+//\t}\n+\t\n+\tpublic void saveOntology (boolean OWL) throws OWLOntologyStorageException, IOException, OWLOntologyCreationException{\n+\t\t// OWL format\n+\t\tif(OWL){\n+\t\t\tmanager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());\n+\t\t}\n+\t\t// OBO format\n+\t\telse{\n+\t\t\t// OWL API generates bad OBO but OBOformat doesn\'t work either so I correct the OWL API problems (More predictable) in a temporary file\n+\t\t\t// Very inefficient but no time for another solution\n+\t\t\t\t\t\t\n+\t\t\tOWLDataFactory factory = manager.getOWLDataFactory();\n+\t\t\tOWLEntityRenamer renamer = new OWLEntityRenamer (manager, manager.getOntologies());\n+\t\t\tOWLAnnotationProperty label = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());\n+\t\t\tfor(OWLClass cls : ontology.getClassesInSignature()){\n+\t\t\t// Remove annotations (OWL API generates bad OBO annotations)\n+\t\t\t\t\t\t\t\n+\t\t\t// Keep rdfs:label\n+\t\t\tString class_name = null;\n+\t\t\tfor (OWLAnnotation annotation : cls.getAnnotations(ontology, label)){\n+\t\t\t\tif (annotation.getValue() instanceof OWLLiteral) {\n+\t\t\t\t\tOWLLiteral val = (OWLLiteral) annotation.getValue();\n+\t\t\t\t\tclass_name = val.getLiteral();\n+\t\t\t\t}\n+\t\t\t}\n+\t\t\t\t\t\t\t\t\t\t\n+//\t\t\tI have to remove all the annotations cause I don\'t know which ones are rendered properly\n+\t\t\tmanager.removeAxioms(ontology,ontology.getAnnotationAssertionAxioms(cls.getIRI()));\n+\t\t\t\t\t\t\t\n+\t\t\t// Add rdfs:label again\n+\t\t\tOWLAnnotation labelAnno = factory.getOWLAnnotation(factory.getOWLAnnotationProperty(\n+\t\t\tOWLRDFVocabulary.RDFS_LABEL.getIRI()),factory.getOWLLiteral(class_name,OWL2Datatype.XSD_STRING));\n+\t\t\tOWLAxiom ax = factory.getOWLAnnotationAssertionAxiom(cls.getIRI(), labelAnno);\n+\t\t\tmanager.applyChange(new AddAxiom(ontology, ax));\n+\t\t\t\t\t\t\t\n+\t\t\t// Rename entities\n+\t\t\tString cls_IRI = cls.getIRI().toString();\n+\t\t\tString cls_proper_IRI = cls_IRI.replace("_", ":");\n+\t\t\tList<OWLOntologyChange> changes = renamer.changeIRI(cls, IRI.create(cls_proper_IRI));\n+\t\t\tmanager.applyChanges(changes);\n+\t\t\t}\n+\t\t\t\t\t\t\n+\t\t\tFile file = new File("tmp.obo");\n+\t\t\tmanager.saveOntology(ontology, new OBOOntologyFormat(), IRI.create(file.toURI()));\n+\t\t\tBufferedWriter bw = new BufferedWriter(new OutputStreamWriter(System.out));\t\t\n+\t\t\tScanner input = new Scanner(file);\n+\t\t\tString buffer = "";\n+\n+\t\t\twhile(input.hasNext()){\n+\t\t\t\tString nextLine = input.nextLine();\n+\t\t\t\tif(nextLine.contains("[Term]") || nextLine.contains("[Typedef]")){\n+\t\t\t\t\tif(buffer.isEmpty()){\n+\t\t\t\t\t\tbw.write(buffer);\n+\t\t\t\t\t\tbw.newLine();\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t\tif(!nextLine.contains("is_a: Thing") && !nextLine.contains("auto-generated-by:") && !nextLine.contains("id_space:") && !nextLine.contains("! ----")){\n+\t\t\t\t\tif(!nextLine.isEmpty() && !buffer.contains("relationship:")){\n+\t\t\t\t\t\tbw.write(nextLine);\n+\t\t\t\t\t\tbw.newLine();\n+\t\t\t\t\t}\n+\t\t\t\t}\n+\t\t\t\tbuffer = nextLine;\n+\t\t\t}\n+\t\t\tinput.close();\n+\t\t\tbw.close();\n+\t\t\tfile.delete();\n+\t\t}\n+\t}\t\n+}\n' |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/src/InferenceGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/src/InferenceGalaxy.java Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,105 @@ +/** + * + */ +package es.upm.fi.dia.oeg.oppl.galaxy; + + +import java.io.IOException; + +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + + +/** + * @author Mikel Egaña Aranguren + * + */ +public class InferenceGalaxy { + + /** + * @param args + * @throws IOException + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + */ + public static void main(String[] args) throws OWLOntologyStorageException, OWLOntologyCreationException, IOException { + // Get the arguments from command-line + String OWLFilePath = args [0]; + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT + String axioms_to_inject = args [2]; // CLASS_ASSERTIONS,CLASS_HIERARCHY,DATA_PROPERTY_ASSERTIONS + +// CLASS_ASSERTIONS Denotes the computation of the direct types of individuals for each individual in the signature of the imports closure of the root ontology. +// CLASS_HIERARCHY Denotes the computation of the class hierarchy. +// DATA_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals and data property values for each individual in the signature of the imports closure of the root ontology. +// DATA_PROPERTY_HIERARCHY Denotes the computation of the data property hierarchy. +// DIFFERENT_INDIVIDUALS Denotes the computation of sets of individuals that are different from each individual in the signature of the imports closure of the root ontology. +// DISJOINT_CLASSES Denotes the computation of sets of classes that are disjoint for each class in the signature of the imports closure of the root ontology. +// OBJECT_PROPERTY_ASSERTIONS Denotes the computation of relationships between individuals in the signature of the imports closure of the root ontology. +// OBJECT_PROPERTY_HIERARCHY Denotes the computation of the object property hierarchy. +// SAME_INDIVIDUAL Denotes the computation of individuals that are interpreted as the same object for each individual in the imports closure of the root ontology. + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Add the inferred axioms as asserted axioms to the original ontology + + if(axioms_to_inject.contains(",")){ + String[] axioms = axioms_to_inject.split(","); + for(int i =0; i < axioms.length ; i++) + injectAxiom (axioms[i], galaxyowlapi); + } + else{ + injectAxiom (axioms_to_inject, galaxyowlapi); + } + + // Merge imported ontologies if requested +// if(merge.equals("Merge")){ +// galaxyowlapi.merge(); +// } + + // Save the ontology in OWL + galaxyowlapi.saveOntology(true); + + } + + static void injectAxiom (String axiom_to_inject, GalaxyOWLAPI galaxyowlapi){ + if(axiom_to_inject.equals("CLASS_HIERARCHY")){ + galaxyowlapi.addCLASS_HIERARCHY(); +// System.out.println("CLASS_HIERARCHY"); + } + if(axiom_to_inject.equals("CLASS_ASSERTIONS")){ + galaxyowlapi.addCLASS_ASSERTIONS(); +// System.out.println("CLASS_ASSERTIONS"); + } + if(axiom_to_inject.equals("DATA_PROPERTY_HIERARCHY")){ + galaxyowlapi.addDATA_PROPERTY_HIERARCHY(); +// System.out.println("DATA_PROPERTY_HIERARCHY"); + } + if(axiom_to_inject.equals("DISJOINT_CLASSES")){ + galaxyowlapi.addDISJOINT_CLASSES(); +// System.out.println("DISJOINT_CLASSES"); + } + if(axiom_to_inject.equals("OBJECT_PROPERTY_HIERARCHY")){ + galaxyowlapi.addOBJECT_PROPERTY_HIERARCHY(); +// System.out.println("OBJECT_PROPERTY_HIERARCHY"); + } + } +} |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/src/OPPLGalaxy.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/src/OPPLGalaxy.java Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,108 @@ +/** + * + */ +package es.upm.fi.dia.oeg.oppl.galaxy; + +import java.io.File; +import java.io.IOException; +import java.util.List; +import java.util.Scanner; +import java.util.logging.Logger; + +import org.coode.oppl.ChangeExtractor; +import org.coode.oppl.OPPLParser; +import org.coode.oppl.OPPLScript; +import org.coode.oppl.ParserFactory; +import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; +import org.coode.parsers.ErrorListener; +import org.coode.parsers.LoggerErrorListener; +import org.semanticweb.owlapi.model.OWLAxiomChange; +import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.reasoner.OWLReasoner; + + +/** + * @author Mikel Egaña Aranguren + * + */ +public class OPPLGalaxy { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + * @throws IOException + */ + public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + // Get the arguments from command-line + String OWLFilePath = args [0]; + String reasoner_type = args [1]; // Pellet|FaCTPlusPlus|HermiT + + String OPPL_script_file = args [2]; + String OWL = args [3]; // OWL|OBO + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Set the reasoner + + // Pellet + if(reasoner_type.equals("Pellet")){ + galaxyowlapi.setReasonerPellet(); + } + // FaCTPlusPlus + else if (reasoner_type.equals("FaCTPlusPlus")){ + galaxyowlapi.setReasonerFaCT(); + } + // HermiT + else{ + galaxyowlapi.setReasonerHermit(); + } + + // Load the OPPL flat file with script in memory + String OPPL_script_source = ""; + File file = new File(OPPL_script_file); + Scanner input = new Scanner(file); + while(input.hasNext()) { + String nextToken = input.next(); + OPPL_script_source = OPPL_script_source + " " + nextToken; + } + input.close(); + + OWLOntologyManager manager = galaxyowlapi.getOWLManager(); + OWLOntology ontology = galaxyowlapi.getMainOntology(); + OWLReasoner reasoner = galaxyowlapi.getReasoner(); + + // Parse the OPPL script + ParserFactory parserFactory = new ParserFactory(manager, ontology, reasoner); + Logger logger = Logger.getLogger(Tool.class.getName()); +// Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null) + ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); + OPPLParser opplparser = parserFactory.build(errorListener); + OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); + + // Execute the script + ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true); + List<OWLAxiomChange> changes = extractor.visit(OPPLscript); + manager.applyChanges(changes); + + // Merge imported ontologies if requested +// if(merge.equals("Merge")){ +// galaxyowlapi.merge(); +// } + + // Save the ontology + if(OWL.equals("OWL")){ + galaxyowlapi.saveOntology(true); + } + else{ + galaxyowlapi.saveOntology(false); + } + } +} |
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| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test-data/ontology/imports/imports_inference_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/imports/imports_inference_test.owl Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,196 @@ +<?xml version="1.0"?> + + +<!DOCTYPE rdf:RDF [ + <!ENTITY owl "http://www.w3.org/2002/07/owl#" > + <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > + <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > + <!ENTITY inference_test "http://www.oeg-upm.net/inference_test.owl/" > + <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > + <!ENTITY biopax-level3 "http://www.biopax.org/release/biopax-level3.owl#" > +]> + + +<rdf:RDF xmlns="http://www.oeg-upm.net/inference_test.owl#" + xml:base="http://www.oeg-upm.net/inference_test.owl" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:biopax-level3="http://www.biopax.org/release/biopax-level3.owl#" + xmlns:inference_test="http://www.oeg-upm.net/inference_test.owl/"> + <owl:Ontology rdf:about="http://www.oeg-upm.net/inference_test.owl"> + <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/> + </owl:Ontology> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Annotation properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Datatypes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/p --> + + <owl:ObjectProperty rdf:about="&inference_test;p"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/q --> + + <owl:ObjectProperty rdf:about="&inference_test;q"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Classes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/a --> + + <owl:Class rdf:about="&inference_test;a"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </owl:equivalentClass> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/b --> + + <owl:Class rdf:about="&inference_test;b"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/c --> + + <owl:Class rdf:about="&inference_test;c"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/d --> + + <owl:Class rdf:about="&inference_test;d"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&biopax-level3;Entity"/> + </owl:Restriction> + </owl:equivalentClass> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/e --> + + <owl:Class rdf:about="&inference_test;e"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&biopax-level3;Entity"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.w3.org/2002/07/owl#Thing --> + + <rdf:Description rdf:about="&owl;Thing"> + <rdfs:comment>Expected inferences: + +aa memberOf a + +c subClassOf a + +(imports) + +d subClassOf e</rdfs:comment> + </rdf:Description> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Individuals + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/aa --> + + <owl:Thing rdf:about="&inference_test;aa"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + <inference_test:p rdf:resource="&inference_test;bb"/> + </owl:Thing> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/bb --> + + <owl:NamedIndividual rdf:about="&inference_test;bb"> + <rdf:type rdf:resource="&inference_test;b"/> + </owl:NamedIndividual> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/cc --> + + <owl:Thing rdf:about="&inference_test;cc"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + </owl:Thing> +</rdf:RDF> + + + +<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net --> + |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test-data/ontology/imports/imports_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/imports/imports_test.owl Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,208 @@ +<?xml version="1.0"?> + + +<!DOCTYPE rdf:RDF [ + <!ENTITY owl "http://www.w3.org/2002/07/owl#" > + <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > + <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > + <!ENTITY inference_test "http://www.oeg-upm.net/inference_test.owl/" > + <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > + <!ENTITY biopax-level3 "http://www.biopax.org/release/biopax-level3.owl#" > +]> + + +<rdf:RDF xmlns="http://www.oeg-upm.net/inference_test.owl#" + xml:base="http://www.oeg-upm.net/inference_test.owl" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:biopax-level3="http://www.biopax.org/release/biopax-level3.owl#" + xmlns:inference_test="http://www.oeg-upm.net/inference_test.owl/"> + <owl:Ontology rdf:about="http://www.oeg-upm.net/inference_test.owl"> + <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl"/> + </owl:Ontology> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Annotation properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Datatypes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/p --> + + <owl:ObjectProperty rdf:about="&inference_test;p"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/part_of --> + + <owl:ObjectProperty rdf:about="&inference_test;part_of"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/q --> + + <owl:ObjectProperty rdf:about="&inference_test;q"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Classes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/a --> + + <owl:Class rdf:about="&inference_test;a"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </owl:equivalentClass> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/b --> + + <owl:Class rdf:about="&inference_test;b"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/c --> + + <owl:Class rdf:about="&inference_test;c"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/d --> + + <owl:Class rdf:about="&inference_test;d"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&biopax-level3;Entity"/> + </owl:Restriction> + </owl:equivalentClass> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/e --> + + <owl:Class rdf:about="&inference_test;e"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;part_of"/> + <owl:someValuesFrom rdf:resource="&biopax-level3;Entity"/> + </owl:Restriction> + </rdfs:subClassOf> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&biopax-level3;Entity"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.w3.org/2002/07/owl#Thing --> + + <rdf:Description rdf:about="&owl;Thing"> + <rdfs:comment>Expected inferences: + +aa memberOf a + +c subClassOf a + +(imports) + +d subClassOf e</rdfs:comment> + </rdf:Description> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Individuals + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/aa --> + + <owl:Thing rdf:about="&inference_test;aa"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + <inference_test:p rdf:resource="&inference_test;bb"/> + </owl:Thing> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/bb --> + + <owl:NamedIndividual rdf:about="&inference_test;bb"> + <rdf:type rdf:resource="&inference_test;b"/> + </owl:NamedIndividual> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/cc --> + + <owl:Thing rdf:about="&inference_test;cc"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + </owl:Thing> +</rdf:RDF> + + + +<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net --> + |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test-data/ontology/single/inference_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/single/inference_test.owl Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,162 @@ +<?xml version="1.0"?> + + +<!DOCTYPE rdf:RDF [ + <!ENTITY owl "http://www.w3.org/2002/07/owl#" > + <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > + <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > + <!ENTITY inference_test "http://www.oeg-upm.net/inference_test.owl/" > + <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > +]> + + +<rdf:RDF xmlns="http://www.oeg-upm.net/inference_test.owl#" + xml:base="http://www.oeg-upm.net/inference_test.owl" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" + xmlns:inference_test="http://www.oeg-upm.net/inference_test.owl/"> + <owl:Ontology rdf:about="http://www.oeg-upm.net/inference_test.owl"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Annotation properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Datatypes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/p --> + + <owl:ObjectProperty rdf:about="&inference_test;p"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/q --> + + <owl:ObjectProperty rdf:about="&inference_test;q"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Classes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/a --> + + <owl:Class rdf:about="&inference_test;a"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </owl:equivalentClass> + </owl:Class> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/b --> + + <owl:Class rdf:about="&inference_test;b"/> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/c --> + + <owl:Class rdf:about="&inference_test;c"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&inference_test;p"/> + <owl:someValuesFrom rdf:resource="&inference_test;b"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.w3.org/2002/07/owl#Thing --> + + <rdf:Description rdf:about="&owl;Thing"> + <rdfs:comment>Expected inferences: + +aa memberOf a + +c subClassOf a</rdfs:comment> + </rdf:Description> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Individuals + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.oeg-upm.net/inference_test.owl/aa --> + + <owl:Thing rdf:about="&inference_test;aa"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + <inference_test:p rdf:resource="&inference_test;bb"/> + </owl:Thing> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/bb --> + + <owl:NamedIndividual rdf:about="&inference_test;bb"> + <rdf:type rdf:resource="&inference_test;b"/> + </owl:NamedIndividual> + + + + <!-- http://www.oeg-upm.net/inference_test.owl/cc --> + + <owl:Thing rdf:about="&inference_test;cc"> + <rdf:type rdf:resource="&owl;NamedIndividual"/> + </owl:Thing> +</rdf:RDF> + + + +<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net --> + |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test-data/ontology/single/test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/single/test.owl Fri Mar 09 16:15:27 2012 +0100 |
| [ |
| @@ -0,0 +1,130 @@ +<?xml version="1.0"?> + + +<!DOCTYPE rdf:RDF [ + <!ENTITY owl "http://www.w3.org/2002/07/owl#" > + <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > + <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > + <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > + <!ENTITY Ontology1314715036188 "http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" > +]> + + +<rdf:RDF xmlns="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#" + xml:base="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + xmlns:Ontology1314715036188="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" + xmlns:owl="http://www.w3.org/2002/07/owl#" + xmlns:xsd="http://www.w3.org/2001/XMLSchema#" + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> + <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of --> + + <owl:ObjectProperty rdf:about="&Ontology1314715036188;part_of"/> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop --> + + <owl:ObjectProperty rdf:about="&Ontology1314715036188;prop"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Classes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test --> + + <owl:Class rdf:about="&Ontology1314715036188;OPPL_test"/> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test --> + + <owl:Class rdf:about="&Ontology1314715036188;Taxonomy_test"/> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/child_class --> + + <owl:Class rdf:about="&Ontology1314715036188;child_class"> + <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/> + <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler --> + + <owl:Class rdf:about="&Ontology1314715036188;filler"> + <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> + </owl:Class> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/parent_class --> + + <owl:Class rdf:about="&Ontology1314715036188;parent_class"> + <owl:equivalentClass> + <owl:Restriction> + <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/> + <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/> + </owl:Restriction> + </owl:equivalentClass> + <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> + </owl:Class> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part --> + + <owl:Class rdf:about="&Ontology1314715036188;part"> + <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="&Ontology1314715036188;part_of"/> + <owl:someValuesFrom rdf:resource="&Ontology1314715036188;whole"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> + + + + <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole --> + + <owl:Class rdf:about="&Ontology1314715036188;whole"> + <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/> + </owl:Class> +</rdf:RDF> + + + +<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net --> + |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test-data/oppl_script/test.oppl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/oppl_script/test.oppl Fri Mar 09 16:15:27 2012 +0100 |
| b |
| @@ -0,0 +1,8 @@ +?whole:CLASS, +?part:CLASS +SELECT +?part SubClassOf part_of some ?whole WHERE ?part != Nothing +BEGIN +ADD ?part SubClassOf part_of only ?whole +END; + |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test.oppl --- a/OPPL/test.oppl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -?whole:CLASS, -?part:CLASS -SELECT -?part SubClassOf part_of some ?whole WHERE ?part != Nothing -BEGIN -ADD ?part SubClassOf part_of only ?whole -END; - |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test.owl --- a/OPPL/test.owl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,130 +0,0 @@ -<?xml version="1.0"?> - - -<!DOCTYPE rdf:RDF [ - <!ENTITY owl "http://www.w3.org/2002/07/owl#" > - <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" > - <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" > - <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" > - <!ENTITY Ontology1314715036188 "http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" > -]> - - -<rdf:RDF xmlns="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#" - xml:base="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:Ontology1314715036188="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" - xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"/> - - - - <!-- - /////////////////////////////////////////////////////////////////////////////////////// - // - // Object Properties - // - /////////////////////////////////////////////////////////////////////////////////////// - --> - - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of --> - - <owl:ObjectProperty rdf:about="&Ontology1314715036188;part_of"/> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop --> - - <owl:ObjectProperty rdf:about="&Ontology1314715036188;prop"/> - - - - <!-- - /////////////////////////////////////////////////////////////////////////////////////// - // - // Classes - // - /////////////////////////////////////////////////////////////////////////////////////// - --> - - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test --> - - <owl:Class rdf:about="&Ontology1314715036188;OPPL_test"/> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test --> - - <owl:Class rdf:about="&Ontology1314715036188;Taxonomy_test"/> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/child_class --> - - <owl:Class rdf:about="&Ontology1314715036188;child_class"> - <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> - <rdfs:subClassOf> - <owl:Restriction> - <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/> - <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/> - </owl:Restriction> - </rdfs:subClassOf> - </owl:Class> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler --> - - <owl:Class rdf:about="&Ontology1314715036188;filler"> - <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> - </owl:Class> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/parent_class --> - - <owl:Class rdf:about="&Ontology1314715036188;parent_class"> - <owl:equivalentClass> - <owl:Restriction> - <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/> - <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/> - </owl:Restriction> - </owl:equivalentClass> - <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/> - </owl:Class> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part --> - - <owl:Class rdf:about="&Ontology1314715036188;part"> - <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/> - <rdfs:subClassOf> - <owl:Restriction> - <owl:onProperty rdf:resource="&Ontology1314715036188;part_of"/> - <owl:someValuesFrom rdf:resource="&Ontology1314715036188;whole"/> - </owl:Restriction> - </rdfs:subClassOf> - </owl:Class> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole --> - - <owl:Class rdf:about="&Ontology1314715036188;whole"> - <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/> - </owl:Class> -</rdf:RDF> - - - -<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net --> - |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test_URI_mappings --- a/OPPL/test_URI_mappings Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology /home/pik/UPM/OPPL_galaxy/oppl/OPPL/chebi.owl -http://purl.obolibrary.org/obo/UBERON_uberon /home/pik/UPM/OPPL_galaxy/oppl/OPPL/cell.owl -# Comments can be added with # - |
| b |
| diff -r 3f31c0eb7539 -r 6ca67b155e32 OPPL/test_new.owl --- a/OPPL/test_new.owl Thu Jan 12 10:20:00 2012 +0100 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,68 +0,0 @@ -<?xml version="1.0"?> -<rdf:RDF xmlns="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#" - xml:base="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl" - xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:Ontology1314715036188="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" - xmlns:owl="http://www.w3.org/2002/07/owl#" - xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"> - <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"/> - - - - <!-- - /////////////////////////////////////////////////////////////////////////////////////// - // - // Object Properties - // - /////////////////////////////////////////////////////////////////////////////////////// - --> - - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of --> - - <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/> - - - - <!-- - /////////////////////////////////////////////////////////////////////////////////////// - // - // Classes - // - /////////////////////////////////////////////////////////////////////////////////////// - --> - - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part --> - - <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part"> - <rdfs:subClassOf> - <owl:Restriction> - <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/> - <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/> - </owl:Restriction> - </rdfs:subClassOf> - <rdfs:subClassOf> - <owl:Restriction> - <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/> - <owl:allValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/> - </owl:Restriction> - </rdfs:subClassOf> - </owl:Class> - - - - <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole --> - - <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/> -</rdf:RDF> - - - -<!-- Generated by the OWL API (version 3.2.4.1806) http://owlapi.sourceforge.net --> - |