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commit 93e5be892786aba0e1dfb1efdd1121da6762ff20 1 parent 5af44f8
@gofranshukair gofranshukair authored
Showing with 14 additions and 1,974 deletions.
  1. +14 −0 .classpath
  2. +0 −5 module/MOD-INF/classes/com/.svn/all-wcprops
  3. +0 −31 module/MOD-INF/classes/com/.svn/entries
  4. +0 −5 module/MOD-INF/classes/com/google/.svn/all-wcprops
  5. +0 −31 module/MOD-INF/classes/com/google/.svn/entries
  6. +0 −5 module/MOD-INF/classes/com/google/refine/.svn/all-wcprops
  7. +0 −31 module/MOD-INF/classes/com/google/refine/.svn/entries
  8. +0 −11 module/MOD-INF/classes/com/google/refine/granatumExtension/.svn/all-wcprops
  9. +0 −62 module/MOD-INF/classes/com/google/refine/granatumExtension/.svn/entries
  10. +0 −8 module/MOD-INF/classes/com/google/refine/granatumExtension/.svn/text-base/SampleUtil.java.svn-base
  11. BIN  module/MOD-INF/classes/com/google/refine/granatumExtension/commands/ApplyGranatumRDFOperationsCommand.class
  12. BIN  module/MOD-INF/classes/com/google/refine/granatumExtension/util/GranatumOntology.class
  13. BIN  module/MOD-INF/classes/com/google/refine/granatumExtension/util/StudyAttribute.class
  14. +0 −694 module/MOD-INF/classes/ontologies/1.owl
  15. +0 −111 module/scripts/index/granatum-data-insertion.js
  16. +0 −694 resources/ontologies/1.owl
  17. +0 −119 src/com/google/refine/granatumExtension/commands/ApplyGranatumRDFOperationsCommand.java
  18. +0 −129 src/com/google/refine/granatumExtension/util/GranatumOntology.java
  19. +0 −38 src/com/google/refine/granatumExtension/util/StudyAttribute.java
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14 .classpath
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<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" path="src"/>
+ <classpathentry kind="src" path="resources"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"/>
<classpathentry kind="src" path="/grefine"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/xercesImpl-2.7.1.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/wstx-asl-3.2.9.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/stax-api-1.0.1.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/slf4j-log4j12-1.5.8.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/slf4j-api-1.5.8.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/lucene-core-2.3.1.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/log4j-1.2.13.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/junit-4.5.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/jena-2.6.4-tests.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/jena-2.6.4.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/iri-0.8.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/icu4j-3.4.4.jar"/>
+ <classpathentry kind="lib" path="/home/gofran/Downloads/jars/Jena-2.6.4/lib/arq-2.8.7.jar"/>
<classpathentry kind="output" path="module/MOD-INF/classes"/>
</classpath>
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5 module/MOD-INF/classes/com/.svn/all-wcprops
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-K 25
-svn:wc:ra_dav:version-url
-V 50
-/svn/!svn/ver/1542/trunk/extensions/sample/src/com
-END
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31 module/MOD-INF/classes/com/.svn/entries
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-https://google-refine.googlecode.com/svn/trunk/extensions/sample/src/com
-https://google-refine.googlecode.com/svn
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5 module/MOD-INF/classes/com/google/.svn/all-wcprops
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-K 25
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-V 57
-/svn/!svn/ver/1542/trunk/extensions/sample/src/com/google
-END
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31 module/MOD-INF/classes/com/google/.svn/entries
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5 module/MOD-INF/classes/com/google/refine/.svn/all-wcprops
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-K 25
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-V 64
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11 module/MOD-INF/classes/com/google/refine/granatumExtension/.svn/all-wcprops
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-K 25
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-V 80
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-K 25
-svn:wc:ra_dav:version-url
-V 96
-/svn/!svn/ver/1542/trunk/extensions/sample/src/com/google/refine/sampleExtension/SampleUtil.java
-END
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62 module/MOD-INF/classes/com/google/refine/granatumExtension/.svn/entries
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8 ...D-INF/classes/com/google/refine/granatumExtension/.svn/text-base/SampleUtil.java.svn-base
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-package com.google.refine.sampleExtension;
-
-
-public class SampleUtil {
- static public int stringArrayLength(String[] a) {
- return a.length;
- }
-}
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BIN  ...sses/com/google/refine/granatumExtension/commands/ApplyGranatumRDFOperationsCommand.class
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BIN  module/MOD-INF/classes/com/google/refine/granatumExtension/util/GranatumOntology.class
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694 module/MOD-INF/classes/ontologies/1.owl
@@ -1,694 +0,0 @@
-<?xml version="1.0"?>
-<rdf:RDF
- xmlns:UO="http://purl.org/obo/owl/UO#"
- xmlns:obo="http://purl.obolibrary.org/obo/"
- xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
- xmlns:p1="http://granatum.org/ns/"
- xmlns:kegg="http://kegg.bio2rdf.org/"
- xmlns:ncithesaurus="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
- xmlns:dbpedia="http://dbpedia.org/"
- xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:pubchem2="http://bio2rdf.org/ns/ns/ns/pubchem#"
- xmlns:s3db="http://s3db.org/core#"
- xmlns:void="http://granatum.org/schema/http://rdfs.org/ns/void#"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
- xmlns:drugbank="http://www4.wiwiss.fu-berlin.de/drugbank/"
- xmlns:bio2rdf="http://bio2rdf.org/ns/bio2rdf#"
- xmlns="http://granatum.org/schema/"
- xmlns:skos="http://www.w3.org/2004/02/skos/core#"
- xmlns:pubchem="http://granatum.org/schema/http://pubchem.bio2rdf.org/"
- xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
- xmlns:void2="http://rdfs.org/ns/void#"
- xmlns:chebi="http://chebi.bio2rdf.org/"
- xmlns:linkedlifedata="http://linkedlifedata.com/"
- xmlns:EFO_0000311="http://www.ebi.ac.uk/efo/EFO_0000311#"
- xmlns:go="http://go.bio2rdf.org/"
- xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
- xmlns:efo="http://www.ebi.ac.uk/efo/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:swrl="http://www.w3.org/2003/11/swrl#"
- xmlns:acgt="http://www.ifomis.org/acgt/1.0#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xml:base="http://granatum.org/schema/">
- <owl:Ontology rdf:about="">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Created by Helena F. Deus</rdfs:comment>
- <owl:imports rdf:resource="http://www.ifomis.org/acgt/1.0"/>
- <owl:imports rdf:resource="http://www.ebi.ac.uk/efo/"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Granaum Biomedical Semantic Data Model</rdfs:label>
- </owl:Ontology>
- <rdfs:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Tumor">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer"/>
- </rdfs:subClassOf>
- </rdfs:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Source"/>
- <owl:Class rdf:about="http://granatum.org/schema/dbpediaURI">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Resources"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_silico_assay">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Bioassay"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/COX1IC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Cox-1 inhibition IC50 [µM]</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/IC50"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubmedURL">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/epigeneticsStudy">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Study"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ORAC">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Measurement of oxygen radical absorbance capacity</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >one ORAC unit equals the net protection of -PE produced by 1 µM Trolox.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/IC50">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration"/>
- </rdfs:subClassOf>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >half-maximal inhibitory concentration</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ChemopreventiveAgent">
- <owl:equivalentClass>
- <owl:Class rdf:about="http://granatum.org/schema/cma"/>
- </owl:equivalentClass>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://s3db.org/core#Collection"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/XXOSC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >xanthine oxidase SC50</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/SC50"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/IC">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Maximum Inhibitory concentration</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/CancerType">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/max_percent_inhibition">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition"/>
- </rdfs:subClassOf>
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubmedURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/cell_activity">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Organism"/>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://purl.org/obo/owl/UO#UO_0000064">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >micromolar</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Cyp1AIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >IC50 of Cyp1A</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/CD">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >concentration required to double the specific activity of quinone reductase</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Bioassay">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Assay"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/QRIC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >IC50 of Quinone Reductase</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >measurementUnit</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/inhibitory_concentration">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Natural">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Source"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Databases">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/iNOSIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of iNOS induction A-IC50</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/goURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Author">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >author of a publication</rdfs:comment>
- <rdfs:subClassOf>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ProfessionalRole">
- <rdfs:subClassOf rdf:resource="http://www.ifomis.org/acgt/1.0#HumanBeing"/>
- </rdf:Description>
- </rdfs:subClassOf>
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- <owl:disjointWith>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </owl:disjointWith>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Protocol">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/carcinogenActivating">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/chemopreventionStudy"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >e.g. Inhibition of cytochrome P450 (Cyp) 1A activity </rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Synthetic">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Source"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/biologicalMechanism"/>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chebiURI">
- <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >http://chebi.bio2rdf.org/sparql</rdfs:seeAlso>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chemSpiderURL">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_vivo_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/drugbankURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/max_inhibitory_concentration">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/inhibitory_concentration"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/mechanism_based">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/user_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/iNOSTIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of iNOS induction A-IC50 [µM]a T-IC50 [µM]b</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Study">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >A study is a collection of bioassays sharing a protocol</rdfs:comment>
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/toxicityStudy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/HL60IC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced superoxide anion radical generation in differentiated HL-60 cells (HL-60 assay)</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubchemURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/fractionation_guided">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://purl.org/obo/owl/UO#UO_0000062">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >molar</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ORACOH">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ORAC"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chemopreventionStudy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/enzymeInduction">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/chemopreventionStudy"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >e.g. NAD(P)H:quinone reductase (quinone reductase, QR) activity</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://rdfs.org/ns/void#Dataset">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Dataset</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/BioMaterial">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_vitro_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/keggURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/OCDIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of ODC induction IC50 [µM]</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Pathway">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Instances can come from any of the pathway databases. Instances should be indexed with those URI. </rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Publication">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/cma">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/DPPHSC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >1,1-diphenyl-2 picrylhydrazyl SC50</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/SC50"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/SC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >half-maximal scavenging concentration</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Assay">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Organ"/>
- <owl:Class rdf:about="http://granatum.org/schema/ORACROO">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ORAC"/>
- </owl:Class>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/similar_to"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/http://rdfs.org/ns/void#uriLookupEndpoint">
- <rdfs:domain rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/part_of">
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/part_of"/>
- </owl:Restriction>
- </rdfs:domain>
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/part_of"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Restriction>
- </rdfs:range>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_cma">
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_cma"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </owl:Restriction>
- </rdfs:range>
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_cma"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/topic"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/max_inhibitory_conc">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >concentration values in Molar</rdfs:comment>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/measures">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >what is being measured in a certain study. E.g. quinone reductase activity. Values are GO terms</rdfs:label>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#isPublishedBy"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/target_mechanism">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/topic"/>
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Study"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/target_mechanism"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#hasStatus">
- <rdfs:range>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001742">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </rdf:Description>
- </rdfs:range>
- <rdfs:domain rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_organism">
- <rdfs:domain>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_organism"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/user_assay"/>
- </owl:Restriction>
- </rdfs:domain>
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_organism"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Organism"/>
- </owl:Restriction>
- </rdfs:range>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_protocol">
- <rdfs:range>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Protocol"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_protocol"/>
- </owl:Restriction>
- </rdfs:range>
- <rdfs:domain>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_protocol"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/naturalVsSynthetic"/>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#hasPublication">
- <rdfs:range rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- <owl:inverseOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#isPublishedBy"/>
- <rdfs:domain rdf:resource="http://granatum.org/schema/Author"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/study_part"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/activity"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/publicationNumber">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >How many times has this compound been cited in the literature?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/antiOxidantActivity">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Does this compound have antioxidative properties?</rdfs:comment>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/actionMechanism">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >What is the action mechanism of the component?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/publication"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/source">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If this compound is normally found in a natural substatnce, indicate which in the domain</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/PDB_id">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you know the PDB Id of this component, insert it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/toxicity">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
- >false</rdfs:comment>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/hashedFingerprint"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/toxicConcentration">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If toxic, at which concentration has it been deemed toxic? </rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/chemopreventionMechanism">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/actionMechanism"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/SMILESnotation">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have the SMILES notation for this agent, insert it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/study_reference">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Paper describing a study</rdfs:label>
- <rdfs:subPropertyOf>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/references"/>
- </rdfs:subPropertyOf>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/go:0003960">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >NAD(P)H:quinone reductase (quinone reductase, QR) activity </rdfs:label>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/MDLmolfile">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have an MDL Molfile for this component, insert it here</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/references">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Introduce here the reference to the publications where this component has been cited</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/efficacyInVivo">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >In this chemopreventative agent has been tested in vivo, what was the measured efficacy?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/pathwayAction">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Which metabolic pathways is this agent know to affect?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/targetOrgan">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Indicate whether there is a known target orgain for this chemopreventative agent</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/output"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/structuralKey"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/cma_reference">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Paper where cma is references</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/references"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/connectionTable">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have a connection table for this chemical component, indicate it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/input"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/diagram2D">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have a link to an image with the 2D representation of this molecular, indicate its URL here</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/published">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Has this been component been published before? Answer yes or no.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/used_cellLine">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/go:0015034">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >cytochrome P450 (Cyp) 1A activity </rdfs:label>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/ns/ns/ns/pubchem#InChI"/>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/ns/bio2rdf#inchi">
- <owl:equivalentProperty rdf:resource="http://bio2rdf.org/ns/ns/ns/pubchem#InChI"/>
- </owl:DatatypeProperty>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/pubmed">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://www4.wiwiss.fu-berlin.de/drugbank/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >drugbank sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
- <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/natural">
- <rdf:type rdf:resource="http://granatum.org/schema/Source"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003863">
- <rdfs:subClassOf>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- </rdfs:subClassOf>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/enzymeModulation"/>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Assay"/>
- </rdf:Description>
- <owl:AllDisjointClasses/>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003826">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/chebi">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://purl.org/obo/owl/UO#UO:0000000">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#hasProtocol">
- <rdfs:domain rdf:resource="http://granatum.org/schema/Study"/>
- <rdfs:range rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001639">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000272">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
- <rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://dbpedia.org/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >dbpedia sparql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#CancerTreatment">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#MeasurementUnit">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/synthetic">
- <rdf:type rdf:resource="http://granatum.org/schema/Source"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Disease">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000808">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organ"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Publication">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000408">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Protocol">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Organism">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#describes">
- <rdfs:range rdf:resource="http://granatum.org/schema/Study"/>
- <rdfs:domain>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001426">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </rdf:Description>
- </rdfs:domain>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ChemotherapyDrug">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000635">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003860">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://kegg.bio2rdf.org/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >kegg spaql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Chemotherapy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://linkedlifedata.com/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >linked life data sparql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001444">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003869">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://chebi.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >chebi sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/pubchem">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/drugbank">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >drugbank</rdfs:label>
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/bioassay1">
- <used_organism>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/Mouse">
- <rdf:type rdf:resource="http://granatum.org/schema/Organism"/>
- </owl:NamedIndividual>
- </used_organism>
- <rdf:type rdf:resource="http://granatum.org/schema/user_assay"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of carcinogen-induced development of precancerous lesions in the mouse mammary grand organ culture model (MMOC)</rdfs:comment>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/kegg">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/http://pubchem.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://granatum.org/schema/pubchemURI"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003897">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ChemotherapyRegime">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://go.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >go sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
-</rdf:RDF>
-
-<!-- Created with Protege (with OWL Plugin 3.4.7, Build 620) http://protege.stanford.edu -->
View
111 module/scripts/index/granatum-data-insertion.js
@@ -1,111 +0,0 @@
-/*
-
-Copyright 2010, Google Inc.
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
- * Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above
-copyright notice, this list of conditions and the following disclaimer
-in the documentation and/or other materials provided with the
-distribution.
- * Neither the name of Google Inc. nor the names of its
-contributors may be used to endorse or promote products derived from
-this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
-SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
-LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
-DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
-THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
-(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-*/
-
-// This file is added to the /project page
-
-var granatumExtension = {};
-
-
-
-function GranatumImportingSourceUI(controller) {
- this._controller = controller;
- this._controller._format = "text/line-based/*sv";
- }
- Refine.DefaultImportingController.sources.push({
- "label": "Granatum",
- "id": "granatum",
- "uiClass": GranatumImportingSourceUI
- });
-
- GranatumImportingSourceUI.prototype.attachUI = function(bodyDiv) {
- var self = this;
-
- bodyDiv.html(DOM.loadHTML("granatum", "scripts/index/granatum-insertion-form.html"));
-
- this._elmts = DOM.bind(bodyDiv);
- this._elmts.nextButton.click(function(evt) {
- self._guidGenerator();
-
- // collect the data from the inputs and format them in CSV format .
- //headers
- var datastr="Compound;uuid";//NAD(P)H:quinone reductase (QR) induction CD [µM]a;NAD(P)H:quinone reductase (QR) induction IC50 [µM];Cyp1A inhibition IC50 [µM]";
- var num = $('.clonedRecord').length;
- //combine records is one string
- for (var i=0;i<num;i++){
- var compound_name =$('input[name="compound_name"]')[i].value;
- var compound_uuid =$('input[name="compound_uuid"]')[i].value;
- // var nadcd =$('input[name="nadcd"]')[i].value;
- // var nadic =$('input[name="nadic"]')[i].value;
- // var cyp1aic =$('input[name="cyp1aic"]')[i].value;
- datastr+="\n"+compound_name+";"+compound_uuid;//nadcd+";"+nadic+";"+cyp1aic;
- }
-
- self._elmts.textInput[0].value= datastr;
- self._controller.startImportJob(self._elmts.form, "Uploading pasted data ...");
-
- });
- this._elmts.btnAdd.click(function(evt) {
-
-
- var num = $('.clonedRecord').length; // how many "duplicatable" input fields we currently have
- var newNum = new Number(num + 1); // the numeric ID of the new input field being added
-
- var recordsDiv=$('#recordsDiv');
- self._guidGenerator();
- // create the new element via clone(), and manipulate it's ID using newNum value
- var newClonedRecord = $('#clonedRecord'+num).clone().attr("id","clonedRecord"+newNum).addClass("clonedRecord");
- // manipulate the name/id values of the input inside the new element
- newClonedRecord.children().each(function(){
- var kid = $(this);
- kid.attr('id', kid.attr('id').replace(/\d+/g, '') + newNum);
- kid.val('');
- });
- newClonedRecord.appendTo(recordsDiv);
-
- });
- };
-
- GranatumImportingSourceUI.prototype.focus = function() {
- this._elmts.textInput.focus();
- };
-
- GranatumImportingSourceUI.prototype._guidGenerator= function () {
-
- var S4 = function() {
- return (((1+Math.random())*0x10000)|0).toString(16).substring(1);
- };
- var uuid= (S4()+S4()+"-"+S4()+"-"+S4()+"-"+S4()+"-"+S4()+S4()+S4());
-
- var num = $('.clonedRecord').length; // how many "duplicatable" input fields we currently have
- $('input[name="compound_uuid"]')[num-1].value=uuid;
- };
View
694 resources/ontologies/1.owl
@@ -1,694 +0,0 @@
-<?xml version="1.0"?>
-<rdf:RDF
- xmlns:UO="http://purl.org/obo/owl/UO#"
- xmlns:obo="http://purl.obolibrary.org/obo/"
- xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
- xmlns:p1="http://granatum.org/ns/"
- xmlns:kegg="http://kegg.bio2rdf.org/"
- xmlns:ncithesaurus="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
- xmlns:dbpedia="http://dbpedia.org/"
- xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:pubchem2="http://bio2rdf.org/ns/ns/ns/pubchem#"
- xmlns:s3db="http://s3db.org/core#"
- xmlns:void="http://granatum.org/schema/http://rdfs.org/ns/void#"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
- xmlns:drugbank="http://www4.wiwiss.fu-berlin.de/drugbank/"
- xmlns:bio2rdf="http://bio2rdf.org/ns/bio2rdf#"
- xmlns="http://granatum.org/schema/"
- xmlns:skos="http://www.w3.org/2004/02/skos/core#"
- xmlns:pubchem="http://granatum.org/schema/http://pubchem.bio2rdf.org/"
- xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
- xmlns:void2="http://rdfs.org/ns/void#"
- xmlns:chebi="http://chebi.bio2rdf.org/"
- xmlns:linkedlifedata="http://linkedlifedata.com/"
- xmlns:EFO_0000311="http://www.ebi.ac.uk/efo/EFO_0000311#"
- xmlns:go="http://go.bio2rdf.org/"
- xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
- xmlns:efo="http://www.ebi.ac.uk/efo/"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:swrl="http://www.w3.org/2003/11/swrl#"
- xmlns:acgt="http://www.ifomis.org/acgt/1.0#"
- xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
- xml:base="http://granatum.org/schema/">
- <owl:Ontology rdf:about="">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Created by Helena F. Deus</rdfs:comment>
- <owl:imports rdf:resource="http://www.ifomis.org/acgt/1.0"/>
- <owl:imports rdf:resource="http://www.ebi.ac.uk/efo/"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Granaum Biomedical Semantic Data Model</rdfs:label>
- </owl:Ontology>
- <rdfs:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Tumor">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer"/>
- </rdfs:subClassOf>
- </rdfs:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Source"/>
- <owl:Class rdf:about="http://granatum.org/schema/dbpediaURI">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Resources"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_silico_assay">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Bioassay"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/COX1IC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Cox-1 inhibition IC50 [µM]</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/IC50"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubmedURL">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/epigeneticsStudy">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Study"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ORAC">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Measurement of oxygen radical absorbance capacity</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >one ORAC unit equals the net protection of -PE produced by 1 µM Trolox.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/IC50">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration"/>
- </rdfs:subClassOf>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >half-maximal inhibitory concentration</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ChemopreventiveAgent">
- <owl:equivalentClass>
- <owl:Class rdf:about="http://granatum.org/schema/cma"/>
- </owl:equivalentClass>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://s3db.org/core#Collection"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/XXOSC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >xanthine oxidase SC50</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/SC50"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/IC">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Maximum Inhibitory concentration</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/CancerType">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/max_percent_inhibition">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition"/>
- </rdfs:subClassOf>
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubmedURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/cell_activity">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Organism"/>
- <owl:Class rdf:about="http://granatum.org/schema/Concentration">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://purl.org/obo/owl/UO#UO_0000064">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >micromolar</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Cyp1AIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >IC50 of Cyp1A</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/CD">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >concentration required to double the specific activity of quinone reductase</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Bioassay">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Assay"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/QRIC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >IC50 of Quinone Reductase</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Measurement">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >measurementUnit</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/inhibitory_concentration">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Natural">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Source"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Databases">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/iNOSIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of iNOS induction A-IC50</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/goURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Author">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >author of a publication</rdfs:comment>
- <rdfs:subClassOf>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ProfessionalRole">
- <rdfs:subClassOf rdf:resource="http://www.ifomis.org/acgt/1.0#HumanBeing"/>
- </rdf:Description>
- </rdfs:subClassOf>
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- <owl:disjointWith>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </owl:disjointWith>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Protocol">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/carcinogenActivating">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/chemopreventionStudy"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >e.g. Inhibition of cytochrome P450 (Cyp) 1A activity </rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Synthetic">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Source"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/biologicalMechanism"/>
- <owl:Class rdf:about="http://granatum.org/schema/Cancer">
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdfs:subClassOf>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chebiURI">
- <rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >http://chebi.bio2rdf.org/sparql</rdfs:seeAlso>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chemSpiderURL">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_vivo_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/drugbankURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/max_inhibitory_concentration">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/inhibitory_concentration"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/percent_inhibition">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/mechanism_based">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/user_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/iNOSTIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of iNOS induction A-IC50 [µM]a T-IC50 [µM]b</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Study">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >A study is a collection of bioassays sharing a protocol</rdfs:comment>
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/toxicityStudy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/HL60IC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced superoxide anion radical generation in differentiated HL-60 cells (HL-60 assay)</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/pubchemURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/fractionation_guided">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://purl.org/obo/owl/UO#UO_0000062">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >molar</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/ORACOH">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ORAC"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/chemopreventionStudy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/enzymeInduction">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/chemopreventionStudy"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >e.g. NAD(P)H:quinone reductase (quinone reductase, QR) activity</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://rdfs.org/ns/void#Dataset">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Dataset</rdfs:label>
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/BioMaterial">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/in_vitro_assay">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/keggURI">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/OCDIC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/IC50"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of ODC induction IC50 [µM]</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Pathway">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Instances can come from any of the pathway databases. Instances should be indexed with those URI. </rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Publication">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/cma">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/DPPHSC50">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >1,1-diphenyl-2 picrylhydrazyl SC50</rdfs:label>
- <rdfs:subClassOf>
- <owl:Class rdf:about="http://granatum.org/schema/SC50"/>
- </rdfs:subClassOf>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Numbers in parentheses indicate the percentage of scavenging or inhibition at the indicated concentrations.</rdfs:comment>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/SC50">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Concentration"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >half-maximal scavenging concentration</rdfs:label>
- </owl:Class>
- <owl:Class rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#Assay">
- <rdfs:subClassOf rdf:resource="http://s3db.org/core#Collection"/>
- </owl:Class>
- <owl:Class rdf:about="http://granatum.org/schema/Organ"/>
- <owl:Class rdf:about="http://granatum.org/schema/ORACROO">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ORAC"/>
- </owl:Class>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/similar_to"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/http://rdfs.org/ns/void#uriLookupEndpoint">
- <rdfs:domain rdf:resource="http://granatum.org/schema/Resources"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/part_of">
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/part_of"/>
- </owl:Restriction>
- </rdfs:domain>
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/part_of"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Study"/>
- </owl:Restriction>
- </rdfs:range>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_cma">
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_cma"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </owl:Restriction>
- </rdfs:range>
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_cma"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/topic"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/max_inhibitory_conc">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >concentration values in Molar</rdfs:comment>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/measures">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >what is being measured in a certain study. E.g. quinone reductase activity. Values are GO terms</rdfs:label>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#isPublishedBy"/>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/target_mechanism">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/topic"/>
- <rdfs:domain>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Study"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/target_mechanism"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#hasStatus">
- <rdfs:range>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001742">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </rdf:Description>
- </rdfs:range>
- <rdfs:domain rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_organism">
- <rdfs:domain>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_organism"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/user_assay"/>
- </owl:Restriction>
- </rdfs:domain>
- <rdfs:range>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_organism"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Organism"/>
- </owl:Restriction>
- </rdfs:range>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/used_protocol">
- <rdfs:range>
- <owl:Restriction>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Protocol"/>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_protocol"/>
- </owl:Restriction>
- </rdfs:range>
- <rdfs:domain>
- <owl:Restriction>
- <owl:onProperty rdf:resource="http://granatum.org/schema/used_protocol"/>
- <owl:someValuesFrom rdf:resource="http://granatum.org/schema/Bioassay"/>
- </owl:Restriction>
- </rdfs:domain>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/naturalVsSynthetic"/>
- <owl:ObjectProperty rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311#hasPublication">
- <rdfs:range rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- <owl:inverseOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#isPublishedBy"/>
- <rdfs:domain rdf:resource="http://granatum.org/schema/Author"/>
- </owl:ObjectProperty>
- <owl:ObjectProperty rdf:about="http://granatum.org/schema/study_part"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/activity"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/publicationNumber">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >How many times has this compound been cited in the literature?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/antiOxidantActivity">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Does this compound have antioxidative properties?</rdfs:comment>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/actionMechanism">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >What is the action mechanism of the component?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/publication"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/source">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If this compound is normally found in a natural substatnce, indicate which in the domain</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/PDB_id">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you know the PDB Id of this component, insert it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/toxicity">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean"
- >false</rdfs:comment>
- <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#boolean"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/hashedFingerprint"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/toxicConcentration">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If toxic, at which concentration has it been deemed toxic? </rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/chemopreventionMechanism">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/actionMechanism"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/SMILESnotation">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have the SMILES notation for this agent, insert it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/study_reference">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Paper describing a study</rdfs:label>
- <rdfs:subPropertyOf>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/references"/>
- </rdfs:subPropertyOf>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/go:0003960">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >NAD(P)H:quinone reductase (quinone reductase, QR) activity </rdfs:label>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/MDLmolfile">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have an MDL Molfile for this component, insert it here</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/references">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Introduce here the reference to the publications where this component has been cited</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/efficacyInVivo">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >In this chemopreventative agent has been tested in vivo, what was the measured efficacy?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/pathwayAction">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Which metabolic pathways is this agent know to affect?</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/targetOrgan">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Indicate whether there is a known target orgain for this chemopreventative agent</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/output"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/structuralKey"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/cma_reference">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Paper where cma is references</rdfs:label>
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/references"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/connectionTable">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have a connection table for this chemical component, indicate it here.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/input"/>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/diagram2D">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >If you have a link to an image with the 2D representation of this molecular, indicate its URL here</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/published">
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Has this been component been published before? Answer yes or no.</rdfs:comment>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://granatum.org/schema/used_cellLine">
- <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/go:0015034">
- <rdfs:subPropertyOf rdf:resource="http://granatum.org/schema/activity"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >cytochrome P450 (Cyp) 1A activity </rdfs:label>
- </owl:DatatypeProperty>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/ns/ns/ns/pubchem#InChI"/>
- <owl:DatatypeProperty rdf:about="http://bio2rdf.org/ns/bio2rdf#inchi">
- <owl:equivalentProperty rdf:resource="http://bio2rdf.org/ns/ns/ns/pubchem#InChI"/>
- </owl:DatatypeProperty>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/pubmed">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://www4.wiwiss.fu-berlin.de/drugbank/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >drugbank sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
- <owl:AnnotationProperty rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/natural">
- <rdf:type rdf:resource="http://granatum.org/schema/Source"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003863">
- <rdfs:subClassOf>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000311">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- </rdfs:subClassOf>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/enzymeModulation"/>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000070">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Assay"/>
- </rdf:Description>
- <owl:AllDisjointClasses/>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003826">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/chebi">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://purl.org/obo/owl/UO#UO:0000000">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#hasProtocol">
- <rdfs:domain rdf:resource="http://granatum.org/schema/Study"/>
- <rdfs:range rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001639">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0000272">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
- <rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://dbpedia.org/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >dbpedia sparql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#CancerTreatment">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Cancer"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#MeasurementUnit">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/synthetic">
- <rdf:type rdf:resource="http://granatum.org/schema/Source"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Disease">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000808">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organ"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Publication">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Publication"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000408">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311#Disease"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Protocol">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Protocol"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Organism">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#describes">
- <rdfs:range rdf:resource="http://granatum.org/schema/Study"/>
- <rdfs:domain>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001426">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Study"/>
- </rdf:Description>
- </rdfs:domain>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ChemotherapyDrug">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0000635">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003860">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://kegg.bio2rdf.org/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >kegg spaql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#Chemotherapy">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://linkedlifedata.com/sparql">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >linked life data sparql endpoint</rdfs:label>
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0001444">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Measurement"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003869">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://chebi.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >chebi sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/pubchem">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://purl.obolibrary.org/obo/OBI_0100026">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/Organism"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/drugbank">
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >drugbank</rdfs:label>
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/bioassay1">
- <used_organism>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/Mouse">
- <rdf:type rdf:resource="http://granatum.org/schema/Organism"/>
- </owl:NamedIndividual>
- </used_organism>
- <rdf:type rdf:resource="http://granatum.org/schema/user_assay"/>
- <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >Inhibition of carcinogen-induced development of precancerous lesions in the mouse mammary grand organ culture model (MMOC)</rdfs:comment>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/kegg">
- <rdf:type rdf:resource="http://granatum.org/schema/Databases"/>
- </owl:NamedIndividual>
- <owl:NamedIndividual rdf:about="http://granatum.org/schema/http://pubchem.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://granatum.org/schema/pubchemURI"/>
- </owl:NamedIndividual>
- <rdf:Description rdf:about="http://www.ebi.ac.uk/efo/EFO_0003897">
- <rdfs:subClassOf rdf:resource="http://www.ebi.ac.uk/efo/EFO_0000311"/>
- </rdf:Description>
- <rdf:Description rdf:about="http://www.ifomis.org/acgt/1.0#ChemotherapyRegime">
- <rdfs:subClassOf rdf:resource="http://granatum.org/schema/ChemopreventiveAgent"/>
- </rdf:Description>
- <owl:NamedIndividual rdf:about="http://go.bio2rdf.org/sparql">
- <rdf:type rdf:resource="http://rdfs.org/ns/void#Dataset"/>
- <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
- >go sparql endpoint</rdfs:label>
- </owl:NamedIndividual>
-</rdf:RDF>
-
-<!-- Created with Protege (with OWL Plugin 3.4.7, Build 620) http://protege.stanford.edu -->
View
119 src/com/google/refine/granatumExtension/commands/ApplyGranatumRDFOperationsCommand.java
@@ -1,119 +0,0 @@
-package com.google.refine.granatumExtension.commands;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringReader;
-import java.nio.Buffer;
-import java.util.Properties;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
-import org.json.JSONArray;
-import org.json.JSONException;
-import org.json.JSONObject;
-
-import com.google.refine.commands.Command;
-import com.google.refine.commands.history.ApplyOperationsCommand;
-import com.google.refine.model.AbstractOperation;
-import com.google.refine.model.Project;
-import com.google.refine.operations.OperationRegistry;
-import com.google.refine.process.Process;
-import com.google.refine.util.ParsingUtilities;
-
-public class ApplyGranatumRDFOperationsCommand extends ApplyOperationsCommand {
-
- @Override
- public void doPost(HttpServletRequest request, HttpServletResponse response)
- throws ServletException, IOException {
- Project project = getProject(request);
- String jsonString = getGranatumOperationFile();
-
- try {
- JSONArray a = ParsingUtilities
- .evaluateJsonStringToArray(jsonString);
- int count = a.length();
- for (int i = 0; i < count; i++) {
- JSONObject obj = a.getJSONObject(i);
- System.out.println(obj.toString());
- reconstructOperation(project, obj);
- }
-
- if (project.processManager.hasPending()) {
- respond(response, "{ \"code\" : \"pending\" }");
- } else {
- respond(response, "{ \"code\" : \"ok\" }");
- }
- } catch (JSONException e) {
- respondException(response, e);
- }
- }
-
- protected String getGranatumOperationFile() {
-
- // create file object
- BufferedInputStream bin = null;
- StringBuffer buffer=new StringBuffer();
- try {
- // create FileInputStream object
- InputStream fin = this.getClass().getResourceAsStream("/files/jsonop2");
-
- // create object of BufferedInputStream
- bin = new BufferedInputStream(fin);
-
- // create a byte array
- byte[] contents = new byte[1024];
-
- int bytesRead = 0;
- String strFileContents;
-
-
- while ((bytesRead = bin.read(contents)) != -1) {
-
- strFileContents = new String(contents, 0, bytesRead);
- //System.out.print(strFileContents);
- buffer.append(strFileContents);
-
- }
-
- } catch (FileNotFoundException e) {
- System.out.println("File not found" + e);
- } catch (IOException ioe) {
- System.out.println("Exception while reading the file " + ioe);
- } finally {
- // close the BufferedInputStream using close method
- try {
- if (bin != null)
- bin.close();
- } catch (IOException ioe) {
- System.out.println("Error while closing the stream :" + ioe);
- }
-
- }
-
-
- return buffer.toString();
- }
-
- protected void reconstructOperation(Project project, JSONObject obj) {
- AbstractOperation operation = OperationRegistry.reconstruct(project,
- obj);
- if (operation != null) {
- try {
- Process process = operation.createProcess(project,
- new Properties());
-
- project.processManager.queueProcess(process);
- } catch (Exception e) {
- e.printStackTrace();
- }
- }
- }
-
-
-}
View
129 src/com/google/refine/granatumExtension/util/GranatumOntology.java
@@ -1,129 +0,0 @@
-package com.google.refine.granatumExtension.util;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.StringBufferInputStream;
-import java.util.ArrayList;
-
-import org.json.JSONObject;
-import org.json.JSONWriter;
-import org.openjena.atlas.json.JsonString;
-
-
-import com.hp.hpl.jena.query.Query;
-import com.hp.hpl.jena.query.QueryExecution;
-import com.hp.hpl.jena.query.QueryExecutionFactory;
-import com.hp.hpl.jena.query.QueryFactory;
-import com.hp.hpl.jena.query.QuerySolution;
-import com.hp.hpl.jena.query.ResultSet;
-import com.hp.hpl.jena.query.ResultSetFormatter;
-import com.hp.hpl.jena.rdf.model.Model;
-import com.hp.hpl.jena.rdf.model.ModelFactory;
-import com.hp.hpl.jena.sparql.resultset.JSONInput.JSONResultSet;
-import com.hp.hpl.jena.util.FileManager;
-
-
-
-public class GranatumOntology {
-
- static Model model;
-
- public GranatumOntology(){
- this.model=this.readModel();
- }
-
- public Model readModel(){
- // create an empty model
- Model model = ModelFactory.createDefaultModel();
- String inputFileName="/home/gofran/Downloads/tools/2.5-rc1/extensions/granatum/resources/ontologies/1.owl";
- // use the FileManager to find the input file
- InputStream in = FileManager.get().open( inputFileName );
- if (in == null) {
- throw new IllegalArgumentException(
-