All Classes Interface Summary Class Summary Enum Summary Exception Summary
| Class |
Description |
| A |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| A_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| ACCollector |
Deprecated.
|
| AcronymPipe |
|
| AcronymTextCoverWriter |
|
| AnchorDisambiguationStep |
|
| AppUtils |
|
| BC2Evaluation |
|
| BC3CorpusEvaluation |
|
| Be |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Be |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Be_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Be_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| BioThesaurusFilterDisambiguationStep |
Removes IDs for which the respective candidate synonym stems from the BioThesaurus as long as other options are available.
|
| BioThesaurusIproClassMerger |
|
| BTMatcher |
|
| CandidateRetrievalOptimizationRoute |
|
| ChemicalSuffix |
Taken from GNormPlus code: Wei, C.
|
| ChunkTypePipe |
|
| ClosedParenthesis |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| ClosedParenthesis_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Column |
|
| CompositeMentionTokenizer |
Special tokenization for composite concept resolution.
|
| CompositePatternResolver |
This is the base class for composite gene name resolution classes.
|
| CompositeToken |
This class represents the individual tokens of the composite gene mention tokenization.
|
| Configuration |
|
| ContextEmbeddingPipe |
|
| ContextGenerator |
|
| ContextIndexFieldNames |
|
| ContextItemRecordsIndex |
Deprecated.
|
| ContextItemsCacheKey |
|
| ContextItemsIndex |
|
| ContextPosPipe |
|
| ContextPosPipe |
|
| ContextRanker |
|
| ContextScoreCacheKey |
|
| ContextUtils |
|
| Dash |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Dash_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Det |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Det |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Det_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Det_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| DictionaryClusterCleaner |
|
| DocResult |
|
| DocumentDisambiguationData |
|
| Domain |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Domain_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| DomainCue |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| DomainCue_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| DypsisCandidateRanker |
Uses machine learning methods to create features for the mapping candidates of a gene mention.
|
| DypsisCandidateRejector |
|
| DypsisCandidateSetter |
|
| DypsisContextRanker |
|
| DypsisDocumentDisambiguationData |
|
| DypsisGeneSelector |
|
| DypsisGeneSetHomogenizator |
|
| DypsisMapLocationDisambiguator |
|
| DypsisMappingCore |
This mapping core is named after the Dypsis lutescens, "Goldfruchtpalme" is
is supposed to augment the older YukkaMappingCore with a document oriented
integrity approach.
|
| DypsisMappingCore.NameLevelUnificationStrategy |
|
| DypsisRankingMerger |
|
| EgSummaryEntity |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| EgSummaryEntity_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| EGSummaryStructureAnnotator |
|
| EmbeddedAcronymPatternResolver |
|
| EmbeddingsWithTokensConnectionAnnotator |
|
| Entity |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Entity_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| EntityChunk |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| EntityChunk_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| EntrezGeneUniProtLexcionCreator |
|
| EnumerationResolver |
For simple enumerations like NK-2, NK-3 and NK-3 receptor (those are three different entities).
|
| ExperimentsPipe |
|
| ExtendedProtein |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| ExtendedProtein_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| ExtendedProteinsMerger |
|
| ExtensionFileFilter |
|
| Family |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Family |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Family_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Family_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyAcronym |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyAcronym |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyAcronym_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyAcronym_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyConfidencePipe |
|
| FamilyCue |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyCue |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyCue |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyCue_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyCue_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyCue_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyGenegroupProbabilityPipe |
|
| FamilyIndicator |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyIndicator_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyMatchPipe |
|
| FamilyStopword |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| FamilyStopword_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| FamilyUtils |
|
| FlairCompositeMentionTagger |
|
| GeneCompositeNameResolver |
|
| GeneConfigurationDependentPipe |
Some pipes access resources whose path are given in the gene configuration and which cannot be stored
on disc when saving the model.
|
| GeneDocumentFactory |
|
| GeneId |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| GeneId_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| GeneIdCorrectnessRenderer |
|
| GenelistByTaxonomyFilter |
Reads a gene list (the second field must be the
gene ID) and writes out the same file but filtered for a specific taxonomy ID.
|
| GenelistIdUpdater |
Reads a gene list and writes the same list where for each gene ID is checked if it has been replaced in NCBI Gene.
|
| GenelistTaxonomyPredictor |
Reads annotation data that includes genes, organisms, sentences, chunks and possibly more and predicts a taxonomy ID
for each gene mention.
|
| GenelistToTaxonomyListConverter |
Reads a gene list (the second field must be the
gene ID) and writes out the same file but with the gene IDs replaced by the taxonomy ID of the respective gene.
|
| GeneMapper |
|
| GeneMapperAnnotator |
|
| GeneMapperException |
|
| GeneMapperInitializationException |
|
| GeneMapperRuntimeException |
|
| GeneMappingModule |
|
| GeneMappingOptimizationRoute |
|
| GeneMention2Token |
|
| GeneMentionFamilyFeatureSetter |
Experimental.
|
| GeneMentionFilter |
|
| GeneMentionTaxIdCountWriter |
|
| GeneNameToAmbiguousIdsMapper |
This class takes a list of gene names and a taxonomy ID.
|
| GeneRecordQueryDisambiguationStep |
|
| GeneSequence2SingleGene |
For non-sequence filtering, we will have a single gene per GeneSet in
the GeneDocument passed to GeneSet2GeneSequence which should
be the very first pipe to be employed in each pipe sequence. |
| GeneSet2GeneSequence |
|
| GeneSet2Token |
|
| GenesetsOptimizationRoute |
|
| GeneSynonymEmbeddingCentroidWriter |
|
| GeneToProteinConverter |
|
| GnHpoServer |
|
| GNormPlusBC2GNTrainEntityFiltering |
|
| GNormPlusBC2TestRoute |
|
| GNormPlusCorpusEvaluation |
|
| Greek |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Greek_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| IndexIdWriter |
|
| InstanceListCreator |
|
| InstanceListCreator |
|
| InteractiveCandidateFinder |
|
| InteractiveNameCentricCandidateFinder |
|
| InteractiveSpellingChecker |
|
| InteractiveWikipediaPageRetrieval |
|
| IOUtils |
|
| IsAPipe |
|
| IsFamilyPipe |
|
| JCasConverter |
|
| JJ |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| JJ_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| LastWordPipe |
|
| Line |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Line_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| LowerCaseBoWPipe |
|
| LowerCasePipe |
|
| MappingCore |
|
| MentionAndDocResult |
|
| MentionDisambiguationData |
|
| MentionEnvironmentPipe |
|
| MentionPrefixPipe |
This pipe adds a feature indicated whether the given gene name is a prefix of
another gene in the same document.
|
| MentionTypeHint |
Taken from GNormPlus code: Wei, C.
|
| MissingConfigurationException |
|
| MLGeneFilter |
|
| MoleculeType |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| MoleculeType_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| NDCG |
|
| NextCharPipe |
|
| NlmGeneCorpusEvaluation |
|
| NoDbHitsPipe |
This pipe adds a feature indicated whether the given gene name is a prefix of
the official symbol of the gene candidate that was retrieved for the gene
name.
|
| NonDescriptivePipe |
|
| NonFamilyIndicator |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| NonFamilyIndicator_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| NonGeneCue |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| NonGeneCue_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| NonGenePhrase |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| NonGenePhrase_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.NonGeneEntityRecognizer
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| NormalizeFeaturesForGeneSetSize |
|
| NounPipe |
|
| NumberClassPipe |
|
| NumberElipseEnumerationPatternResolver |
|
| Of |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Of |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Of_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Of_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| OfficialSymbolPromotionDisambiguationStep |
If there are IDs for which the candidate synonym is the official symbol, remove all other options.
|
| OrganismEnumeration |
Type defined in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| OrganismEnumeration_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.OrganismEnumeration
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| PatternResolutionChain |
|
| Plural |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Plural_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| PluralPipe |
|
| PoSBoWPipe |
|
| PrevCharPipe |
|
| PrintBestSmacConfiguration |
|
| ProteinConsistencyTagger |
|
| ProteinFamilyRulesApplier |
|
| ProteinModifier |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| ProteinModifier_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| ProteinSymbols |
Taken from GNormPlus code: Wei, C.
|
| ProteinToGeneConverter |
|
| ProtEnum |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| ProtEnum_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyResolution
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| QuercusCandidateSetter |
|
| QuercusDisambiguation |
|
| QuercusDisambiguationStep |
|
| QuercusMappingCore |
|
| ReaderInputStream |
This class convert Reader to InputStream.
|
| RefCounter |
|
| RegExPipe |
|
| RejectionConstants |
|
| ResolvedCompositeGeneName |
This class represents a re-assembled gene name from a formerly tokenized and possibly rearranged composite
gene name to identify multiple gene names denoted by one composite expression.
|
| Roman |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Roman_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| RRFSynHitListFusion |
|
| RuleBasedFamilyAssigner |
|
| SemanticContextIndex |
|
| SemanticIndex |
A common interface for all kinds of indices for gene mention disambiguation.
|
| SemanticIndexDisambiguationStep |
|
| SetFeatureVectorToGeneSetPipe |
|
| SetInstanceSourceToGeneSetPipe |
|
| SlashDashAlternativePatternResolver |
|
| SmacRunRepeater |
This class was created for debugging purposes.
|
| SpeciesMultiPatternSearcher |
|
| SpecifiedMoleculeType |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| SpecifiedMoleculeType_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| Specifier |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Specifier_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| SpecifierDetectionPipe |
|
| Stats |
|
| StringHelper |
This class offers some methods useful when working with (arrays of) strings.
|
| SymbolPrefixPipe |
This pipe adds a feature indicated whether the given gene name is a prefix of
the official symbol of the gene candidate that was retrieved for the gene
name.
|
| SynHitListFusion |
|
| SynHitSet |
|
| SynHitUtils |
|
| Synonym |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| Synonym_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| SynonymStopword |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| SynonymStopword_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| TAPEvaluator |
|
| TAPEvaluator.TapInputLine |
|
| TAPEvaluator.TapInputList |
|
| TAPEvaluator.TapResult |
|
| TAPEvaluator.TapResultList |
|
| TAPEvaluator.TapResultRecord |
|
| TaxIdIntegratedTextWriter |
|
| TaxIdSentenceLabelWriter |
|
| TestDisambiguationStep |
|
| ThesaurusCleaner |
|
| TokenPrefixPipe |
|
| TransformerClassifier |
|
| TransformerDisambiguationDataUtils |
|
| TwoPartedRangePatternResolver |
For composites like AKR1C1-AKR1C4.
|
| TypeWord |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| TypeWord_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.ProteinOffsetExpansion
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| UIMAUtils |
copied from Ph.
|
| UnderspecifiedNameDisambiguationStep |
|
| UnspecificNameFilter |
Also known as the CrazyRegExFilter.
|
| UnspecifiedDeterminer |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| UnspecifiedDeterminer_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.FamilyAndSynonymsExtraction
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| UnspecifiedPipe |
|
| UnspecTitle |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
XML source: /Users/faessler/Coding/git/jcore-gene-mapper-ae/gene-id-mapper/target/jcasgen/typesystem.xml
|
| UnspecTitle_Type |
Type defined in de.julielab.jcore.ae.genemapper.desc.WikipediaFamilyParsing
Updated by JCasGen Sat Dec 03 19:46:40 CET 2022
|
| WikipediaCategoryManager |
|
| WikipediaClassLookupDevelopment |
|
| WikipediaEntity |
|
| WikipediaEntityClassDecisionBear |
(()__(()
/ \
( / \ \
\ o o /
(_()_)__/ \
/ _,==.____ \
( |--| )
/\_.|__|'-.__/\_
/ ( / \
\ \ ( /
) '._____) /
(((____.--(((____/mrf
|
| WikipediaIndexFields |
|
| WikipediaIndexReader |
|
| WikipediaModule |
|
| WordClassPipe |
|
| WordEmbeddingPipe |
|