- Acronym
- AcronymLongform
- AhoCorasickLongestMatchCallback
- AhoCorasickOptimized
- AhoCorasickOptimized.MatchCallback
- AhoCorasickOptimized.Util
- BioThesaurusIproClassMerger
- CandidateCacheKey
- CandidateFilter
- CandidateRetrieval
- Column
- ContextGenerator
- ContextIndexFieldNames
- ContextItemsCacheKey
- ContextItemsIndex
- ContextUtils
- DocumentDisambiguationData
- DocumentMappingResult
- ExtensionFileFilter
- GeneCandidateRetrievalException
- GeneDocument
- GeneDocumentFactory
- GeneIdCandidate
- GeneMapperRuntimeException
- GeneMapping
- GeneMappingAnnotator
- GeneMappingConfiguration
- GeneMappingException
- GeneMention
- GeneMention.GeneTagger
- GeneMention.SpecificType
- GeneName
- GeneSet
- GeneSets
- GeneSpeciesOccurrence
- IOUtils
- JaroWinklerScorer
- LevenshteinScorer
- LuceneCandidateRetrieval
- LuceneScorer
- MappingCore
- MaxEntScorer
- MaxEntScorerFeaturePipe
- MaxEntScorerML
- MaxEntScorerPairExtractor
- MentionDisambiguationData
- MentionMappingResult
- MentionMappingResult.MatchType
- MentionMappingResult.RejectionSynHit
- MeshHeading
- PosTag
- QueryGenerator
- ReaderInputStream
- Scorer
- SemanticContextIndex
- SemanticDisambiguation
- SemanticIndex
- SimpleScorer
- SpeciesCandidates
- SpeciesMention
- SynHit
- SynHit.CompareType
- SynHitUtils
- SynonymIndexFieldNames
- TermNormalizer
- TokenJaroSimilarity
- TokenJaroSimilarityScorer
- UIMAUtils
- Utils
- WeepingTreeDisambiguation
- WeepingTreeDocumentDisambiguationData
- WeepingTreeMappingCore
- WeepingTreeMentionDisambiguationData