├── .gitignore ├── README.md ├── nb-configuration.xml ├── pom.xml ├── slib-dist ├── pom.xml └── src │ └── main │ └── assembly │ └── all-jar.xml ├── slib-dsm ├── doc │ └── readme.txt ├── pom.xml └── src │ └── main │ └── java │ └── com │ └── github │ └── sharispe │ └── slib │ └── dsm │ ├── core │ ├── README.md │ ├── Tf_Idf.java │ ├── corpus │ │ ├── Corpus.java │ │ ├── CorpusFromFile.java │ │ ├── CorpusFromFileDir.java │ │ ├── Doc.java │ │ └── Document.java │ ├── engine │ │ ├── CoOccurrenceEngineTheads.java │ │ ├── CoOcurrenceEngine.java │ │ ├── CooccEngineResult.java │ │ ├── CoocurenceComputer.java │ │ ├── DMEngine.java │ │ ├── MapIndexer.java │ │ ├── NgramInfo.java │ │ ├── Voc.java │ │ ├── VocStatComputer.java │ │ ├── VocStatComputerThreads.java │ │ ├── VocStatConf.java │ │ ├── VocStatInfo.java │ │ ├── VocStatResult.java │ │ ├── Vocabulary.java │ │ ├── VocabularyIndex.java │ │ ├── Word.java │ │ ├── WordInfo.java │ │ └── wordIterator │ │ │ ├── WordIterator.java │ │ │ ├── WordIteratorAbstract.java │ │ │ ├── WordIteratorAbstractFromFile.java │ │ │ ├── WordIteratorAccessor.java │ │ │ ├── WordIteratorAccessorFromFile.java │ │ │ ├── WordIteratorConstraint.java │ │ │ ├── WordIterator_Allow_Shorter.java │ │ │ ├── WordIterator_Allow_ShorterFromFile.java │ │ │ ├── WordIterator_Dictionary.java │ │ │ ├── WordIterator_DictionaryFromFile.java │ │ │ ├── WordIterator_FixedSize.java │ │ │ └── WordIterator_FixedSizeFromFile.java │ └── model │ │ ├── access │ │ ├── ModelAccessor.java │ │ ├── ModelAccessorUtils.java │ │ └── twodmodels │ │ │ ├── IndexedVectorInfoIterator.java │ │ │ ├── ModelAccessorFullMemory_2D.java │ │ │ ├── ModelAccessorMemory_2D.java │ │ │ ├── ModelAccessorPersistance_2D.java │ │ │ └── ModelAccessor_2D.java │ │ └── utils │ │ ├── ConcurrentHashMapGenerator.java │ │ ├── HashMapGenerator.java │ │ ├── IndexedVector.java │ │ ├── IndexedVectorInfo.java │ │ ├── MapGenerator.java │ │ ├── MatrixUtils.java │ │ ├── ModelUtil.java │ │ ├── SparseMatrix.java │ │ ├── SparseMatrixGenerator.java │ │ ├── compression │ │ └── CompressionUtils.java │ │ └── modelconf │ │ ├── GConstants.java │ │ ├── ModelConf.java │ │ ├── ModelConfUtils.java │ │ └── ModelType.java │ ├── deprecated │ └── kb │ │ └── EntityVectorRepresentationComputer.java │ ├── main │ ├── ActionConf_ReduceTerm2Term.java │ ├── MainCLI.java │ ├── SlibDist_Wrapper.java │ ├── SlidingWindowTest.java │ └── Test.java │ └── utils │ ├── BinarytUtils.java │ ├── FileUtility.java │ ├── MapUtils.java │ ├── RQueue.java │ ├── StanfordLemmatizer.java │ ├── Utils.java │ └── XPUtils.java ├── slib-examples ├── nb-configuration.xml ├── nbactions-GO_groupwise.xml ├── nbactions-PA.xml ├── nbactions-SnomedCT_ex.xml ├── pom.xml └── src │ └── main │ ├── java │ └── slib │ │ └── examples │ │ ├── graph │ │ ├── general │ │ │ ├── BuildGraph.java │ │ │ └── GraphExample.java │ │ └── traversal │ │ │ └── GO_BFS.java │ │ └── sml │ │ ├── README.md │ │ ├── general │ │ ├── GraphExample.java │ │ └── SMComputation.java │ │ ├── go │ │ ├── GO_computation_full_aspects.java │ │ ├── GO_extractions.java │ │ ├── SMComputationGO_extrinsic_IC.java │ │ ├── SMComputationGO_groupwise.java │ │ ├── SMComputationGO_groupwise_BP_restriction.java │ │ ├── SMComputationGO_groupwise_million.java │ │ ├── SMComputationGO_pairwise.java │ │ └── SMComputationGO_pairwise_edge_based.java │ │ ├── mesh │ │ ├── MeSHExample_XML.java │ │ └── MeSHExample_XML_2013.java │ │ ├── obo │ │ └── ComputationIC_OBO.java │ │ ├── owl │ │ └── SMComputationOWL.java │ │ ├── skos │ │ └── SKOSexample.java │ │ ├── snomedct │ │ └── SMComputationSnomedCT.java │ │ ├── wordnet │ │ ├── WordNetExample_FullLoader.java │ │ ├── WordnetExample.java │ │ └── WordnetExample_ExtractionAnimal.java │ │ └── yago │ │ └── SMComputationYago.java │ └── resources │ ├── graph_test.dot │ ├── graph_test.nt │ ├── graph_test.pdf │ └── log4j.xml ├── slib-graph ├── README.md ├── pom.xml ├── slib-graph-algo │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── slib │ │ └── graph │ │ └── algo │ │ ├── accessor │ │ ├── GraphAccessor.java │ │ ├── InstanceAccessor.java │ │ ├── InstanceAccessorGen.java │ │ └── InstanceAccessorTax.java │ │ ├── extraction │ │ ├── metric │ │ │ └── DepthAnalyserAG.java │ │ ├── package-info.java │ │ ├── reduction │ │ │ └── dag │ │ │ │ ├── GraphReduction_DAG_Ranwez_2011.java │ │ │ │ └── GraphReduction_Transitive.java │ │ ├── rvf │ │ │ ├── AncestorEngine.java │ │ │ ├── DescendantEngine.java │ │ │ ├── RVF.java │ │ │ ├── RVF_DAG.java │ │ │ ├── RVF_TAX.java │ │ │ └── instances │ │ │ │ ├── InstancesAccessor.java │ │ │ │ └── impl │ │ │ │ └── InstanceAccessor_RDF_TYPE.java │ │ ├── shortest_path │ │ │ └── Dijkstra.java │ │ ├── traversal │ │ │ ├── GraphTraversal.java │ │ │ └── classical │ │ │ │ ├── BFS.java │ │ │ │ └── DFS.java │ │ ├── utils │ │ │ ├── Color.java │ │ │ ├── GAction.java │ │ │ ├── GActionType.java │ │ │ ├── GActionValidator.java │ │ │ ├── GraphActionExecutor.java │ │ │ └── RooterDAG.java │ │ └── validator │ │ │ └── dag │ │ │ ├── Path.java │ │ │ └── ValidatorDAG.java │ │ ├── metric │ │ └── DepthAnalyserAG.java │ │ ├── package-info.java │ │ ├── reduction │ │ └── dag │ │ │ ├── GraphReduction_DAG_Ranwez_2011.java │ │ │ └── GraphReduction_Transitive.java │ │ ├── shortest_path │ │ └── Dijkstra.java │ │ ├── traversal │ │ ├── GraphTraversal.java │ │ └── classical │ │ │ ├── BFS.java │ │ │ └── DFS.java │ │ ├── utils │ │ ├── Color.java │ │ ├── GAction.java │ │ ├── GActionType.java │ │ ├── GActionValidator.java │ │ ├── GraphActionExecutor.java │ │ └── RooterDAG.java │ │ └── validator │ │ └── dag │ │ ├── Path.java │ │ └── ValidatorDAG.java ├── slib-graph-io │ ├── CheckableValidity.java │ ├── Parametrable.java │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── slib │ │ └── graph │ │ └── io │ │ ├── conf │ │ ├── GDataConf.java │ │ └── GraphConf.java │ │ ├── loader │ │ ├── GraphLoader.java │ │ ├── GraphLoaderGeneric.java │ │ ├── annot │ │ │ └── GraphLoader_TSVannot.java │ │ ├── bio │ │ │ ├── gaf2 │ │ │ │ ├── EvidenceCodeRules.java │ │ │ │ └── GraphLoader_GAF_2.java │ │ │ ├── mesh │ │ │ │ ├── GraphLoader_MESH_XML.java │ │ │ │ ├── MeshConcept.java │ │ │ │ └── MeshXMLHandler.java │ │ │ ├── obo │ │ │ │ ├── GraphLoader_OBO_1_2.java │ │ │ │ └── utils │ │ │ │ │ ├── OboRelationship.java │ │ │ │ │ ├── OboTerm.java │ │ │ │ │ └── OboType.java │ │ │ └── snomedct │ │ │ │ └── GraphLoaderSnomedCT_RF2.java │ │ ├── csv │ │ │ ├── CSV_Mapping.java │ │ │ ├── CSV_StatementTemplate.java │ │ │ ├── CSV_StatementTemplate_Constraint.java │ │ │ ├── GraphLoader_CSV.java │ │ │ ├── StatementTemplateElement.java │ │ │ └── StatementTemplate_Constraint_Type.java │ │ ├── rdf │ │ │ ├── RDFLoader.java │ │ │ └── SlibRdfHandler.java │ │ ├── slibformat │ │ │ └── GraphLoader_SLIB.java │ │ ├── utils │ │ │ └── filter │ │ │ │ └── graph │ │ │ │ ├── Filter.java │ │ │ │ ├── FilterCst.java │ │ │ │ ├── FilterGraph.java │ │ │ │ ├── gaf2 │ │ │ │ ├── FilterGraph_GAF2.java │ │ │ │ └── FilterGraph_GAF2_cst.java │ │ │ │ ├── metrics │ │ │ │ ├── FilterGraph_Metrics.java │ │ │ │ └── FilterGraph_Metrics_cst.java │ │ │ │ └── repo │ │ │ │ └── FilterRepository.java │ │ └── wordnet │ │ │ ├── GraphLoader_Wordnet.java │ │ │ └── GraphLoader_Wordnet_Full.java │ │ ├── plotter │ │ └── GraphPlotter_Graphviz.java │ │ └── util │ │ ├── GActionValidator.java │ │ ├── GDataValidator.java │ │ └── GFormat.java ├── slib-graph-model-impl │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── slib │ │ └── graph │ │ └── model │ │ └── impl │ │ ├── graph │ │ ├── elements │ │ │ └── Edge.java │ │ ├── memory │ │ │ └── GraphMemory.java │ │ └── weight │ │ │ └── GWS_impl.java │ │ ├── repo │ │ ├── GraphRepositoryMemory.java │ │ └── URIFactoryMemory.java │ │ └── utils │ │ └── GraphUtils.java ├── slib-graph-model │ ├── pom.xml │ └── src │ │ └── main │ │ ├── java │ │ └── slib │ │ │ └── graph │ │ │ └── model │ │ │ ├── graph │ │ │ ├── G.java │ │ │ ├── elements │ │ │ │ └── E.java │ │ │ ├── utils │ │ │ │ ├── Direction.java │ │ │ │ └── WalkConstraint.java │ │ │ └── weight │ │ │ │ └── GWS.java │ │ │ └── repo │ │ │ ├── GraphRepository.java │ │ │ └── URIFactory.java │ │ └── resources │ │ └── log4j.xml ├── slib-graph-test │ ├── pom.xml │ └── src │ │ ├── main │ │ └── resources │ │ │ └── log4j.xml │ │ └── test │ │ ├── java │ │ └── slib │ │ │ └── graph │ │ │ └── test │ │ │ └── algo │ │ │ └── graph │ │ │ ├── SLIB_UnitTestValues.java │ │ │ ├── TestSetUtils.java │ │ │ ├── TestUtils.java │ │ │ ├── extraction │ │ │ └── TestReachableVerticesFinder.java │ │ │ ├── metric │ │ │ └── TestDepthAnalyser.java │ │ │ ├── reduction │ │ │ └── dag │ │ │ │ └── Test_GraphReduction_Transitive.java │ │ │ ├── shortest_path │ │ │ └── Test_Shortest_path.java │ │ │ └── validator │ │ │ └── dag │ │ │ └── TestValidatorDAG.java │ │ └── resources │ │ ├── BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt │ │ ├── graph │ │ ├── obo │ │ │ └── gene_ontology_ext.obo │ │ ├── others │ │ │ ├── go │ │ │ ├── gtest │ │ │ ├── gtest.gv │ │ │ └── gtest.pdf │ │ └── sgl │ │ │ ├── g.dot │ │ │ ├── g.pdf │ │ │ └── g.rdf │ │ ├── log4j.xml │ │ └── modules │ │ └── ontoFocus │ │ ├── exemple.csv │ │ ├── orthomamGO.csv │ │ ├── qGO_obo.txt │ │ ├── qGO_owl.txt │ │ ├── qGO_tiny.txt │ │ └── qHPO_obo.txt └── slib-graph-utils │ ├── pom.xml │ └── src │ └── main │ ├── java │ └── slib │ │ └── graph │ │ └── utils │ │ ├── WalkConstraintGeneric.java │ │ └── WalkConstraintUtils.java │ └── resources │ └── log4j.xml ├── slib-indexer ├── pom.xml └── src │ └── main │ └── java │ └── slib │ └── indexer │ ├── IndexHash.java │ ├── URIDescription.java │ ├── URIDescriptionBasic.java │ ├── mesh │ ├── Indexer_MESH_XML.java │ ├── MeshDescriptor.java │ └── MeshXMLHandler.java │ ├── obo │ └── IndexerOBO.java │ ├── snomed_ct │ └── IndexerSNOMEDCT_RF2.java │ └── wordnet │ └── IndexerWordNetBasic.java ├── slib-sml ├── README.md ├── pom.xml └── src │ ├── main │ ├── java │ │ └── slib │ │ │ └── sml │ │ │ ├── package-info.java │ │ │ ├── sm │ │ │ ├── core │ │ │ │ ├── engine │ │ │ │ │ ├── SMProxResultStorage.java │ │ │ │ │ └── SM_Engine.java │ │ │ │ ├── measures │ │ │ │ │ ├── Dist_Pairwise.java │ │ │ │ │ ├── IDist_Pairwise.java │ │ │ │ │ ├── ISim_Pairwise.java │ │ │ │ │ ├── MConstant.java │ │ │ │ │ ├── MType.java │ │ │ │ │ ├── Measure.java │ │ │ │ │ ├── Measure_Groupwise.java │ │ │ │ │ ├── Measure_Pairwise.java │ │ │ │ │ ├── Sim_Groupwise.java │ │ │ │ │ ├── Sim_Groupwise_Direct.java │ │ │ │ │ ├── Sim_Groupwise_Indirect.java │ │ │ │ │ ├── Sim_Pairwise.java │ │ │ │ │ ├── corpus │ │ │ │ │ │ ├── Matrix.java │ │ │ │ │ │ ├── MatrixType.java │ │ │ │ │ │ └── VocContextMatrixBuilder.java │ │ │ │ │ ├── graph │ │ │ │ │ │ ├── framework │ │ │ │ │ │ │ └── dag │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Bader_2003.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Batet_2010.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Braun_Blanquet_1932.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Dice_1945.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Jaccard_1901.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Knappe_2004.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Korbel_2002.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Maryland_Bridge_2003.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Ochiai_1957.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Simpson_1960.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Sokal_Sneath_1963.java │ │ │ │ │ │ │ │ ├── Sim_Framework_DAG_Set_Tversky_1977.java │ │ │ │ │ │ │ │ └── Sim_Framework_DAG_Set_abstract.java │ │ │ │ │ │ ├── groupwise │ │ │ │ │ │ │ └── dag │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_Ali_Deane.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_GIC.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_LP.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_Lee_2004.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_NTO.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_NTO_MAX.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_TO.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_DAG_UI.java │ │ │ │ │ │ │ │ └── Sim_groupwise_DAG_abstract.java │ │ │ │ │ │ └── pairwise │ │ │ │ │ │ │ └── dag │ │ │ │ │ │ │ ├── Dist_Pairwise_DAG.java │ │ │ │ │ │ │ ├── IDist_Pairwise_DAG.java │ │ │ │ │ │ │ ├── ISim_Pairwise_DAG.java │ │ │ │ │ │ │ ├── Sim_Pairwise_DAG.java │ │ │ │ │ │ │ ├── edge_based │ │ │ │ │ │ │ ├── Dist_DAG_edge_abstract.java │ │ │ │ │ │ │ ├── Dist_pairwise_DAG_edge_Rada_1989.java │ │ │ │ │ │ │ ├── Dist_pairwise_DAG_edge_Rada_LCA_1989.java │ │ │ │ │ │ │ ├── Sim_DAG_edge_abstract.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Kyogoku_basic_2011.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Leacock_Chodorow_1998.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Pekar_Staab_2002.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Rada_1989.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Rada_LCA_1989.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Stojanovic_2001.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Wu_Palmer_1994.java │ │ │ │ │ │ │ ├── experimental │ │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Al_Mubaid_2006.java │ │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_G_SESAME_2007.java │ │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Resnik_1995.java │ │ │ │ │ │ │ │ └── Sim_pairwise_DAG_edge_Slimani_2006.java │ │ │ │ │ │ │ └── utils │ │ │ │ │ │ │ │ └── SimDagEdgeUtils.java │ │ │ │ │ │ │ ├── hybrid │ │ │ │ │ │ │ ├── Sim_DAG_hybrid_abstract.java │ │ │ │ │ │ │ ├── experimental │ │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_edge_Li_2003.java │ │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_hybrid_Ranwez_2006.java │ │ │ │ │ │ │ │ └── Sim_pairwise_DAG_hybrid_Wang_2007.java │ │ │ │ │ │ │ └── utils │ │ │ │ │ │ │ │ └── SimDagHybridUtils.java │ │ │ │ │ │ │ └── node_based │ │ │ │ │ │ │ ├── Sim_DAG_node_abstract.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Constants.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Feature_Tversky_Contrast_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Feature_Tversky_Ratio_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_GL.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_IC_Prop_Tversky_Contrast_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_IC_Prop_Tversky_Ratio_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_IC_Tversky_Contrast_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_IC_Tversky_Ratio_Model.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Jaccard_3W_IC.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Jaccard_IC.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Jiang_Conrath_1997.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Jiang_Conrath_1997_Norm.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Lin_1998.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Resnik_1995.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Schlicker_2006_SimRel.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Sim_IC_2010.java │ │ │ │ │ │ │ └── experimental │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_GL_GraSM.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Harispe_2013.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Lin_1998_GraSM.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Mazandu_2012.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Resnik_1995_Ancestors.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Resnik_1995_Descendants.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Resnik_1995_GraSM.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Schlicker_3WJaccard_SimRel.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Schlicker_GL_SimRel.java │ │ │ │ │ │ │ ├── Sim_pairwise_DAG_node_Schlicker_Jaccard_SimRel.java │ │ │ │ │ │ │ └── Sim_pairwise_DAG_node_Schlicker_Tversky_SimRel.java │ │ │ │ │ ├── others │ │ │ │ │ │ ├── groupwise │ │ │ │ │ │ │ ├── direct │ │ │ │ │ │ │ │ ├── Sim_groupwise_Random.java │ │ │ │ │ │ │ │ └── vector │ │ │ │ │ │ │ │ │ └── VectorSpaceModel.java │ │ │ │ │ │ │ └── indirect │ │ │ │ │ │ │ │ ├── Sim_groupwise_Average.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_BestMatchAverage.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_BestMatchMax.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_Lord_2003.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_Max.java │ │ │ │ │ │ │ │ ├── Sim_groupwise_Min.java │ │ │ │ │ │ │ │ └── experimental │ │ │ │ │ │ │ │ ├── Sim_groupwise_AVERAGE_NORMALIZED_GOSIM.java │ │ │ │ │ │ │ │ └── Sim_groupwise_MAX_NORMALIZED_GOSIM.java │ │ │ │ │ │ └── pairwise │ │ │ │ │ │ │ └── Sim_pairwise_Random.java │ │ │ │ │ ├── string │ │ │ │ │ │ ├── LevenshteinDistance.java │ │ │ │ │ │ └── LevenshteinSimilarity.java │ │ │ │ │ └── vector │ │ │ │ │ │ └── CosineSimilarity.java │ │ │ │ ├── metrics │ │ │ │ │ ├── ic │ │ │ │ │ │ ├── IC.java │ │ │ │ │ │ ├── annot │ │ │ │ │ │ │ ├── IC_annot_resnik_1995.java │ │ │ │ │ │ │ ├── IC_annot_resnik_1995_Normalized.java │ │ │ │ │ │ │ ├── IC_probOccurence_propagatted.java │ │ │ │ │ │ │ └── ICcorpus.java │ │ │ │ │ │ ├── topo │ │ │ │ │ │ │ ├── ICi_ancestors_norm.java │ │ │ │ │ │ │ ├── ICi_depth_max_linear.java │ │ │ │ │ │ │ ├── ICi_depth_max_nonlinear.java │ │ │ │ │ │ │ ├── ICi_depth_min_nonlinear.java │ │ │ │ │ │ │ ├── ICi_harispe_2012.java │ │ │ │ │ │ │ ├── ICi_probOccurence.java │ │ │ │ │ │ │ ├── ICi_probOccurence_propagatted.java │ │ │ │ │ │ │ ├── ICi_resnik_1995.java │ │ │ │ │ │ │ ├── ICi_resnik_unpropagatted_1995.java │ │ │ │ │ │ │ ├── ICi_sanchez_2011.java │ │ │ │ │ │ │ ├── ICi_sanchez_2011_b_adapted.java │ │ │ │ │ │ │ ├── ICi_seco_2004.java │ │ │ │ │ │ │ ├── ICi_zhou_2008.java │ │ │ │ │ │ │ └── ICtopo.java │ │ │ │ │ │ └── utils │ │ │ │ │ │ │ ├── IC_Conf_Corpus.java │ │ │ │ │ │ │ ├── IC_Conf_Topo.java │ │ │ │ │ │ │ ├── ICconf.java │ │ │ │ │ │ │ ├── IcUtils.java │ │ │ │ │ │ │ └── ProbOccurence.java │ │ │ │ │ ├── utils │ │ │ │ │ │ ├── LogBasedMetric.java │ │ │ │ │ │ └── LogBasedMetricInterface.java │ │ │ │ │ └── vector │ │ │ │ │ │ ├── VectorWeight_Chabalier_2007.java │ │ │ │ │ │ └── VectorWeight_Chabalier_Propaggated.java │ │ │ │ └── utils │ │ │ │ │ ├── LCAFinder.java │ │ │ │ │ ├── LCAFinderImpl.java │ │ │ │ │ ├── MathSML.java │ │ │ │ │ ├── OperatorConf.java │ │ │ │ │ ├── SMConstants.java │ │ │ │ │ ├── SMParams.java │ │ │ │ │ ├── SMconf.java │ │ │ │ │ └── SMutils.java │ │ │ └── package-info.java │ │ │ └── smutils │ │ │ ├── ResultsMerger.java │ │ │ └── SQLiteUtils.java │ └── resources │ │ └── scripts │ │ ├── R │ │ ├── cor.R │ │ ├── cor.py │ │ ├── discriminative_power │ │ │ └── plotDiscriminativePower.R │ │ ├── heatmap │ │ │ └── heatmap.R │ │ ├── others │ │ │ ├── plotDepthDistribution.R │ │ │ └── plotICDistribution.R │ │ └── roc │ │ │ └── rocr.R │ │ └── python │ │ ├── html_result.py │ │ ├── kegg_trembl_mapping │ │ ├── human_pathways_prots_kegg_mapping │ │ ├── keggToUniprot.py │ │ ├── pathways_prots │ │ └── yeast_pathways_prots │ │ └── pfam_uniprot_kb │ │ └── buildUniprotKB_pfam_Mapping.py │ └── test │ ├── java │ └── test │ │ ├── TestGraphEngine.java │ │ └── TestGroupwiseIndirectMeasures.java │ └── resources │ ├── graph_test.dot │ ├── graph_test.pdf │ ├── graph_test.slib │ ├── graph_test_expected_values.csv │ ├── log4j.xml │ └── unit_test.zip ├── slib-tools ├── pom.xml ├── slib-tools-module │ ├── pom.xml │ └── src │ │ └── main │ │ └── java │ │ └── slib │ │ └── tools │ │ └── module │ │ ├── CmdHandler.java │ │ ├── FilterBuilderGeneric.java │ │ ├── GenericConfBuilder.java │ │ ├── GlobalConfPattern.java │ │ ├── ModuleConf.java │ │ ├── ModuleCst.java │ │ ├── OptionComparator.java │ │ ├── ToolCmdHandlerCst.java │ │ ├── XMLConfLoaderGeneric.java │ │ ├── XMLConstUtils.java │ │ ├── XML_ModuleConfLoader.java │ │ └── XmlTags.java ├── slib-tools-ontofocus │ ├── Readme.md │ ├── _ENSG00000001084.dot │ ├── pom.xml │ └── src │ │ ├── main │ │ ├── java │ │ │ └── slib │ │ │ │ └── tools │ │ │ │ └── ontofocus │ │ │ │ ├── cli │ │ │ │ ├── OntoFocusCmdHandler.java │ │ │ │ ├── debug │ │ │ │ │ └── App.java │ │ │ │ └── utils │ │ │ │ │ └── OntoFocusCmdHandlerCst.java │ │ │ │ └── core │ │ │ │ ├── OntoFocus.java │ │ │ │ └── utils │ │ │ │ ├── OntoFocusCst.java │ │ │ │ └── QueryEntryURI.java │ │ └── resources │ │ │ ├── log4j.xml │ │ │ └── ontofocus-constants.properties │ │ └── test │ │ ├── java │ │ └── slib │ │ │ └── tools │ │ │ └── ontofocus │ │ │ └── TestOntoFocusReduction.java │ │ └── resources │ │ ├── graph_test.dot │ │ └── graph_test.pdf └── slib-tools-sml-toolkit │ ├── README.md │ ├── nb-configuration.xml │ ├── nbactions-SML Toolkit.xml │ ├── pom.xml │ ├── sml-xmlconf.xml │ └── src │ ├── main │ ├── java │ │ └── slib │ │ │ └── tools │ │ │ └── smltoolkit │ │ │ ├── SmlModuleCLI.java │ │ │ ├── SmlToolKitCli.java │ │ │ ├── SmlToolKitCliCst.java │ │ │ ├── SmlToolKitCst.java │ │ │ └── sm │ │ │ └── cli │ │ │ ├── conf │ │ │ └── xml │ │ │ │ ├── loader │ │ │ │ └── Sm_XMLConfLoader.java │ │ │ │ └── utils │ │ │ │ └── Sm_XML_Cst.java │ │ │ ├── core │ │ │ ├── SmCli.java │ │ │ ├── cmd │ │ │ │ ├── SmCmdHandler.java │ │ │ │ └── SmCmdHandlerCst.java │ │ │ └── utils │ │ │ │ ├── ActionParamsUtils.java │ │ │ │ ├── ActionsParams.java │ │ │ │ ├── FileWriterUtil.java │ │ │ │ ├── QueryConceptsIterator.java │ │ │ │ ├── SML_SM_module_XML_block_conf.java │ │ │ │ ├── SMQueryParam.java │ │ │ │ ├── SMutils.java │ │ │ │ ├── SmToolkitCst.java │ │ │ │ ├── XMLConfUtils.java │ │ │ │ └── calc │ │ │ │ ├── ConceptToConcept_Thread.java │ │ │ │ ├── EntityToEntity_Thread.java │ │ │ │ └── ThreadResultsQueryLoader.java │ │ │ └── profile │ │ │ ├── go │ │ │ ├── SmProfileGOCst.java │ │ │ ├── SmProfileGOHandler.java │ │ │ ├── SmProfile_GO.java │ │ │ └── SmToolkitGOCst.java │ │ │ └── mesh │ │ │ ├── SmProfileMeSHCst.java │ │ │ ├── SmProfileMeSHHandler.java │ │ │ ├── SmProfile_MeSH.java │ │ │ └── SmToolkitMeSHCst.java │ └── resources │ │ ├── log4j.debug.xml │ │ ├── log4j.deploy.xml │ │ ├── log4j.xml │ │ └── sml-toolkit-constants.properties │ └── test │ └── resources │ └── log4j.xml ├── slib-utils ├── pom.xml └── src │ ├── main │ ├── java │ │ └── slib │ │ │ └── utils │ │ │ ├── FileUtils.java │ │ │ ├── Pair.java │ │ │ ├── ex │ │ │ ├── SLIB_Ex_Critic.java │ │ │ ├── SLIB_Ex_Warning.java │ │ │ └── SLIB_Exception.java │ │ │ ├── i │ │ │ ├── CheckableValidity.java │ │ │ ├── Conf.java │ │ │ └── Parametrable.java │ │ │ ├── impl │ │ │ ├── BigFileReader.java │ │ │ ├── IO_RuntimeException.java │ │ │ ├── MapUtils.java │ │ │ ├── MatrixDouble.java │ │ │ ├── MatrixDynamic.java │ │ │ ├── OBOconstants.java │ │ │ ├── OProperty.java │ │ 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