├── .github └── workflows │ └── maven.yml ├── .gitignore ├── CITATION.cff ├── LICENSE.txt ├── README.md ├── ReleaseNotes.txt ├── checkstyle.xml ├── oscar4-all ├── pom.xml └── src │ └── main │ └── java │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── all │ └── package-info.java ├── oscar4-api ├── pom.xml └── src │ ├── main │ └── java │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── Oscar.java │ └── test │ └── java │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── OscarTest.java ├── oscar4-chemnamedict ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscar │ │ │ └── chemnamedict │ │ │ ├── core │ │ │ ├── ChemNameDictIO.java │ │ │ ├── ChemNameDictRegistry.java │ │ │ ├── ICMLProvider.java │ │ │ ├── IChemNameDict.java │ │ │ ├── IInChIProvider.java │ │ │ ├── IMutableChemNameDict.java │ │ │ ├── ISMILESProvider.java │ │ │ ├── IStdInChIKeyProvider.java │ │ │ ├── IStdInChIProvider.java │ │ │ ├── ImmutableChemNameDict.java │ │ │ └── MutableChemNameDict.java │ │ │ ├── dictionaries │ │ │ ├── ChEBIDictionary.java │ │ │ ├── DefaultDictionary.java │ │ │ └── PolymerDictionary.java │ │ │ ├── entities │ │ │ ├── ChemicalStructure.java │ │ │ ├── FormatType.java │ │ │ └── ResolvedNamedEntity.java │ │ │ └── records │ │ │ ├── ChemRecord.java │ │ │ ├── ChemRecordIO.java │ │ │ ├── IChemRecord.java │ │ │ ├── IInChIChemRecord.java │ │ │ ├── IOntologyChemRecord.java │ │ │ ├── ISMILESChemRecord.java │ │ │ ├── IStdInChIChemRecord.java │ │ │ ├── IStdInChIKeyChemRecord.java │ │ │ └── NameOnlyChemRecord.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── chemnamedict │ │ ├── chemnamedict.xml │ │ ├── defaultCompounds.xml │ │ └── polymerCompounds.xml │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── chemnamedict │ │ ├── core │ │ ├── ChemNameDictRegistryTest.java │ │ ├── ImmutableChemNameDictTest.java │ │ └── MutableChemNameDictTest.java │ │ ├── dictionaries │ │ ├── AbstractDictionaryTest.java │ │ ├── ChEBIDictionaryTest.java │ │ ├── DefaultDictionaryTest.java │ │ └── PolymerDictionaryTest.java │ │ ├── entities │ │ ├── ChemicalStructureTest.java │ │ └── ResolvedNamedEntityTest.java │ │ └── tools │ │ └── ResourceGetterTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── core │ └── testDict.xml ├── oscar4-core ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscar │ │ │ ├── document │ │ │ ├── Annotation.java │ │ │ ├── IProcessingDocument.java │ │ │ ├── ITokeniser.java │ │ │ ├── NamedEntity.java │ │ │ ├── ProcessingDocument.java │ │ │ ├── ProcessingDocumentFactory.java │ │ │ ├── SafTools.java │ │ │ ├── Token.java │ │ │ └── TokenSequence.java │ │ │ ├── exceptions │ │ │ ├── DataFormatException.java │ │ │ ├── OscarException.java │ │ │ └── OscarInitialisationException.java │ │ │ ├── normalize │ │ │ ├── ITextNormalizer.java │ │ │ ├── Normalizer.java │ │ │ └── NormalizingReader.java │ │ │ ├── scixml │ │ │ ├── SciXMLDocument.java │ │ │ ├── TextToSciXML.java │ │ │ └── XMLStrings.java │ │ │ ├── terms │ │ │ └── TermSets.java │ │ │ ├── tools │ │ │ ├── InlineToSAF.java │ │ │ ├── ResourceGetter.java │ │ │ ├── StandoffTable.java │ │ │ └── StringTools.java │ │ │ ├── types │ │ │ ├── BioTag.java │ │ │ ├── BioType.java │ │ │ └── NamedEntityType.java │ │ │ ├── util │ │ │ └── CacheMap.java │ │ │ └── xmltools │ │ │ ├── XMLSpanTagger.java │ │ │ └── XOMTools.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── terms │ │ ├── abbreviations.txt │ │ ├── chemAses.txt │ │ ├── closedClass.txt │ │ ├── elements.txt │ │ ├── ligands.txt │ │ ├── noSplitPrefixes.txt │ │ ├── nonChemAses.txt │ │ ├── reactWords.txt │ │ ├── splitSuffixes.txt │ │ ├── stopwords.txt │ │ └── usrDictWords.txt │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ ├── document │ │ ├── NamedEntitityTest.java │ │ ├── TokenSequenceTest.java │ │ └── TokenTest.java │ │ ├── normalize │ │ ├── NormalizerTest.java │ │ └── NormalizingReaderTest.java │ │ ├── terms │ │ └── TermSetsTest.java │ │ ├── tools │ │ ├── ResourceGetterTest.java │ │ ├── StandoffTableTest.java │ │ └── StringToolsTest.java │ │ ├── types │ │ ├── BioTagTest.java │ │ ├── BioTypeTest.java │ │ └── NamedEntityTypeTest.java │ │ ├── util │ │ └── CacheMapTest.java │ │ └── xmltools │ │ └── XOMToolsTest.java │ └── resources │ ├── multiline.txt │ ├── test.txt │ ├── tools │ ├── docWithDtd.xml │ ├── dtd.dtd │ └── simple.xml │ └── utf-8.txt ├── oscar4-data ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscardata │ │ │ ├── DataAnnotation.java │ │ │ ├── DataParser.java │ │ │ ├── OscarData.java │ │ │ ├── RPNode.java │ │ │ └── RParser.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscardata │ │ └── regexes.xml │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscardata │ │ ├── DataAnnotationTest.java │ │ ├── DataParserTest.java │ │ ├── OscarDataTest.java │ │ ├── RPNodeTest.java │ │ └── RegexValidationTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscardata │ ├── dataNode.xml │ └── dataNodeWithChild.xml ├── oscar4-formatter ├── pom.xml └── src │ └── main │ └── java │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── formatter │ ├── IOutputFormatter.java │ ├── STDOUTFormatter.java │ └── rdf │ └── CHEMINFFormatter.java ├── oscar4-memmrecogniser-train ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ ├── oscar │ │ │ └── document │ │ │ │ ├── XOMBasedProcessingDocument.java │ │ │ │ └── XOMBasedProcessingDocumentFactory.java │ │ │ └── oscarMEMM │ │ │ ├── memm │ │ │ ├── MEMMTrainer.java │ │ │ ├── data │ │ │ │ └── MutableMEMMModel.java │ │ │ └── rescorer │ │ │ │ └── MEMMOutputRescorerTrainer.java │ │ │ └── models │ │ │ └── TrainingDataExtractor.java │ └── resources │ │ └── log4j.properties │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ ├── oscar │ │ └── document │ │ │ └── XOMBasedProcessingDocumentFactoryTest.java │ │ └── oscarMEMM │ │ ├── memm │ │ ├── MEMMTrainerTest.java │ │ └── data │ │ │ └── MutableMEMMModelTest.java │ │ └── models │ │ └── TrainingDataExtractorTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ ├── oscar │ └── document │ │ ├── learningSpecificTokenisation.xml │ │ └── sciXmlPaper.xml │ └── oscarMEMM │ ├── memm │ ├── eventCollectionTest.xml │ └── paper.xml │ └── models │ ├── scrapbook1.xml │ ├── scrapbook2.xml │ └── scrapbook3.xml ├── oscar4-memmrecogniser ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscarMEMM │ │ │ ├── FeatureSet.java │ │ │ ├── MEMMRecogniser.java │ │ │ ├── memm │ │ │ ├── EntityTokeniser.java │ │ │ ├── FeatureExtractor.java │ │ │ ├── FeatureList.java │ │ │ ├── FeatureSelector.java │ │ │ ├── MEMMModel.java │ │ │ ├── PostProcessor.java │ │ │ ├── gis │ │ │ │ ├── DummyDataReader.java │ │ │ │ ├── SimpleEventCollector.java │ │ │ │ ├── SimpleEventStream.java │ │ │ │ ├── StringGISModelReader.java │ │ │ │ └── StringGISModelWriter.java │ │ │ └── rescorer │ │ │ │ ├── FeatureExtractor.java │ │ │ │ ├── MEMMOutputRescorer.java │ │ │ │ └── ProbabilityConvertor.java │ │ │ └── models │ │ │ ├── ChemPapersModel.java │ │ │ └── PubMedModel.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarMEMM │ │ ├── chemnamedict │ │ └── ChEBIStop.txt │ │ └── models │ │ ├── chempapers.xml │ │ └── pubmed.xml │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarMEMM │ │ ├── MEMMRecogniserTest.java │ │ ├── Oscar4RegressionTest.java │ │ ├── ResourceGetterTest.java │ │ ├── memm │ │ ├── FeatureExtractorTest.java │ │ └── MEMMModelTest.java │ │ ├── models │ │ ├── ChemPapersModelTest.java │ │ └── PubMedModelTest.java │ │ └── rescorer │ │ └── ProbabilityConvertorTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ ├── oscar3 │ └── test │ │ ├── regressionTest │ │ ├── Sentence1.txt │ │ ├── Sentence2.txt │ │ ├── Sentence3.txt │ │ ├── Sentence4.txt │ │ ├── Sentence5.txt │ │ └── Sentence6.txt │ │ └── testcard │ │ └── resources │ │ └── testcard.txt │ └── oscarMEMM │ └── tools │ └── DefaultProperties.dat ├── oscar4-obo ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscar │ │ │ ├── obo │ │ │ ├── OBOOntology.java │ │ │ ├── OntologyTerm.java │ │ │ ├── Synonym.java │ │ │ └── dso │ │ │ │ └── DSOtoOBO.java │ │ │ └── ont │ │ │ ├── EquivalentTermSet.java │ │ │ ├── OntologyTerms.java │ │ │ └── TermsFileReader.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── obo │ │ └── terms │ │ ├── chebi.obo │ │ ├── chebiDDI.obo │ │ ├── fix.obo │ │ ├── ontology.txt │ │ ├── ptcontology.dso │ │ └── rex.obo │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ ├── obo │ │ ├── OBOOntologyTest.java │ │ └── dso │ │ │ └── DSOtoOBOTest.java │ │ └── ont │ │ ├── EquivalentTermSetTest.java │ │ ├── OntologyTermsTest.java │ │ └── TermsFileReaderTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── obo │ ├── brokenTestTerms.txt │ ├── testOntology.obo │ ├── testTerms.txt │ └── testTermsForConcatenation.txt ├── oscar4-opsin ├── pom.xml └── src │ ├── main │ └── java │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscar │ │ └── opsin │ │ └── OpsinDictionary.java │ └── test │ └── java │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscar │ └── opsin │ ├── OpsinDictionaryTest.java │ └── OpsinResolutionTest.java ├── oscar4-patternrecogniser ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscarpattern │ │ │ └── PatternRecogniser.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarpattern │ │ └── terms │ │ └── polyNeTerms.txt │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarpattern │ │ └── PatternRecogniserTest.java │ └── resources │ └── uk │ └── ac │ ├── cam │ └── ch │ │ └── wwmm │ │ ├── oscar │ │ └── test │ │ │ └── testcard │ │ │ └── testcard.txt │ │ └── oscarpattern │ │ └── testNeTerms.txt │ └── nactem │ └── cheta │ ├── conversionTest │ ├── sciborgFile.xml │ └── test1.xml │ └── tokenTest │ ├── source.xml │ ├── source1.xml │ ├── syntax │ ├── tokenisedSentenceTest │ └── tokenisedSentenceTest1 ├── oscar4-preprocessor ├── pom.xml └── src │ ├── main │ └── java │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarpreprocessor │ │ ├── IFormatPreprocessor.java │ │ └── InputAnalyzer.java │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarpreprocessor │ │ └── InputAnalyzerTest.java │ └── resources │ ├── iso8859-1.txt │ ├── utf16.txt │ └── utf8.txt ├── oscar4-recogniser-core ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscarrecogniser │ │ │ ├── extractedtrainingdata │ │ │ └── ExtractedTrainingData.java │ │ │ ├── finder │ │ │ ├── AutomatonState.java │ │ │ ├── DFAFinder.java │ │ │ ├── DFANEFinder.java │ │ │ ├── DFAONTCPRFinder.java │ │ │ ├── DFASupplementaryTermFinder.java │ │ │ ├── NECollector.java │ │ │ ├── RepresentationList.java │ │ │ ├── ResultsCollector.java │ │ │ ├── SuffixTree.java │ │ │ └── TermMaps.java │ │ │ ├── interfaces │ │ │ └── ChemicalEntityRecogniser.java │ │ │ ├── ptcDataStruct │ │ │ └── Bag.java │ │ │ ├── regex │ │ │ └── RegexRecogniser.java │ │ │ ├── saf │ │ │ └── StandoffResolver.java │ │ │ └── tokenanalysis │ │ │ ├── BiooligomerScorer.java │ │ │ ├── NGram.java │ │ │ ├── NGramBuilder.java │ │ │ ├── PrefixFinder.java │ │ │ ├── SuffixClassifier.java │ │ │ └── TokenSuffixClassifier.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarrecogniser │ │ ├── finder │ │ ├── dfa_ontcpr.dat.gz │ │ └── terms │ │ │ ├── custEnt.txt │ │ │ ├── neTerms.txt │ │ │ └── polyOntology.txt │ │ ├── models │ │ ├── chempapers.xml │ │ └── pubmed.xml │ │ └── tokenanalysis │ │ ├── ngram-model-1530351975_-760934510.dat.gz │ │ ├── ngram-model-549922527_-1841482717.dat.gz │ │ ├── ngram-model.dat.gz │ │ └── ngram-model242917507_1140183201.dat.gz │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscarrecogniser │ │ ├── extractedtrainingdata │ │ └── ExtractedTrainingDataTest.java │ │ ├── finder │ │ ├── AutomatonStateTest.java │ │ ├── DFAFinderTest.java │ │ ├── DFANEFinderTest.java │ │ ├── DFAONTCPRFinderTest.java │ │ ├── DFASupplementaryTermFinderTest.java │ │ └── TermMapsTest.java │ │ ├── regex │ │ └── RegexRecogniserTest.java │ │ ├── saf │ │ └── StandoffResolverTest.java │ │ └── tokenanalysis │ │ ├── NGramBuilderTest.java │ │ └── PrefixFinderTest.java │ └── resources │ └── uk │ └── ac │ └── cam │ └── ch │ └── wwmm │ └── oscarrecogniser │ └── finder │ └── testNeTerms.txt ├── oscar4-tokeniser ├── pom.xml └── src │ ├── main │ ├── java │ │ └── uk │ │ │ └── ac │ │ │ └── cam │ │ │ └── ch │ │ │ └── wwmm │ │ │ └── oscartokeniser │ │ │ ├── HyphenTokeniser.java │ │ │ ├── TokenClass.java │ │ │ ├── TokenClassifier.java │ │ │ ├── TokenSequenceSource.java │ │ │ └── Tokeniser.java │ └── resources │ │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ └── oscartokeniser │ │ ├── tlrs.dtd │ │ └── tokenLevelRegularExpressions.xml │ └── test │ ├── java │ └── uk │ │ └── ac │ │ └── cam │ │ └── ch │ │ └── wwmm │ │ ├── oscar │ │ └── document │ │ │ ├── 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