Constant Field Values

Contents

• de.julielab.*

de.julielab.*

de.julielab.genemapper.Configuration

Modifier and Type	Constant Field	Value
public static final String	APPROX_MATCH	"approxmatch"
public static final String	APPROX_SCORER_TYPE	"approx_scorer_type"
public static final String	CONTEXT_INDEX	"semantic_index"
public static final String	CONTEXT_ITEMS_INDEX	"context_items_index"
public static final String	EXACT_MATCH	"exactmatch"
public static final String	EXACT_SCORER_TYPE	"exact_scorer_type"
public static final String	FIXED_TAX_ID	"fixed_tax_id"
public static final String	GENE_RECORD_INDEX	"gene_record_index"
public static final String	GENE_RECORD_ORIGINAL_NAMES_INDEX	"gene_record_original_names_index"
public static final String	KEY_MAX_FAMILY_MATCH_SCORE	"max_family_match_score"
public static final String	KEY_MIN_FAMILY_MATCH_SCORE	"min_family_match_score"
public static final String	MAPPING_CORE	"mapping_core"
public static final String	MENTION_INDEX	"mention_index"
public static final String	PARAM_ADD_CONTEXT_GENES_AS_LUCENE_RELEVANCE_SIGNAL	"add_context_genes_as_lucene_relevance_signal"
public static final String	PARAM_ADD_SPECIES_PREFIX_STRIPPED_VARIANT_AS_GENENAME_ALTERNATIVE	"strip_species_prefix_for_alternative"
public static final String	PARAM_ALTERNATIVE_NAMES_SEARCH_MODE	"alternative_names_search_mode"
public static final String	PARAM_COMPOSITE_FLAIR_MODEL	"composite_flair_model"
public static final String	PARAM_CONTEXT_GENE_FEATURE_GENERATION	"context_gene_feature_generation"
public static final String	PARAM_DISAMBIGUATE_BY_MAP_LOCATION	"disambiguate_by_map_location"
public static final String	PARAM_DISAMBIGUATE_EXACT_HITS_BY_ORIGINAL_NAME	"disambiguate_exact_hits_by_original_name"
public static final String	PARAM_DISMAX_TIE_BREAKER	"dismax_tie_breaker"
public static final String	PARAM_DO_CONTEXTUAL_RANKING	"do_disambiguation"
public static final String	PARAM_DO_FAMILY_REJECTION	"do_family_rejection"
public static final String	PARAM_DO_LOW_SCORE_REJECTION	"do_low_score_rejection"
public static final String	PARAM_DO_RRF_WITH_CANDIDATE_LISTS	"do_rrf_with_candidate_lists"
public static final String	PARAM_EXCLUDE_GENES_FOR_CONTEXT_ITEM_SCORING	"exclude_genes_for_context_item_scoring"
public static final String	PARAM_GENE_RECORDS_FIELD_QUERY_TYPE	"gene_records_field_query_type"
public static final String	PARAM_GPU_COMPOSITE_MENTIONS	"gpu_composite_mentions"
public static final String	PARAM_GPU_TRANSFORMER_CANDIDATE_RANKING	"gpu_transformer_candidate_ranking"
public static final String	PARAM_INTERSECTION_FILTER	"intersection_filter"
public static final String	PARAM_LEX_CONTEXT_FUSE_METHOD	"lex_context_fuse_method"
public static final String	PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_APPROX	"lexical_semantic_balancing_factor_approx"
public static final String	PARAM_LEXICAL_SEMANTIC_BALANCING_FACTOR_EXACT	"lexical_semantic_balancing_factor_exact"
public static final String	PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_EXACT_MATCH_SORTING	"lucene_score_ratio_threshold_for_exact_match_sorting"
public static final String	PARAM_LUCENE_SCORE_RATIO_THRESHOLD_FOR_RERANKING	"lucene_score_threshold_for_reranking"
public static final String	PARAM_MAKE_TOKEN_WINDOW_DISTINCT	"make_token_window_distinct"
public static final String	PARAM_MAPPING_MODE	"mapping_mode"
public static final String	PARAM_MERGE_CONTINUOUS_GENE_ANNOTATIONS	"merge_continuous_gene_annotations"
public static final String	PARAM_NORMALIZE_JARO_WINKLER_SYNONYM_SCORES	"normalize_jaro_winkler_synonym_scores"
public static final String	PARAM_NORMALIZE_LUCENE_SYNONYM_SCORES	"normalize_lucene_synonym_scores"
public static final String	PARAM_RANK_BY_SINGLE_FEATURE_VALUE	"score_by_single_feature_value"
public static final String	PARAM_REMOVE_SPECIES_PREFIXES_FOR_CANDIDATE_RETRIEVAL	"remove_species_prefixes_for_candidate_retrieval"
public static final String	PARAM_REPLACE_ML_MENTIONS_WITH_LONGER_GAZETTEER_MENTIONS	"replace_ml_mentions_with_longer_gazetteer_mentions"
public static final String	PARAM_SCALE_FAMILY_NAME_MATCH_SCORE	"scale_family_name_match_score"
public static final String	PARAM_SCORE_FAMILY_NAMES_WITH_JARO_WINKLER	"score_family_names_with_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_JARO_WINKLER	"score_gscontext_on_descriptions_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_DESCRIPTIONS_LUCENE	"score_gscontext_on_descriptions_lucene"
public static final String	PARAM_SCORE_GSCONTEXT_ON_GENERIFS_JARO_WINKLER	"score_gscontext_on_generifs_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_GENERIFS_LUCENE	"score_gscontext_on_generifs_lucene"
public static final String	PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_JARO_WINKLER	"score_gscontext_on_interactions_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_INTERACTIONS_LUCENE	"score_gscontext_on_interactions_lucene"
public static final String	PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_JARO_WINKLER	"score_gscontext_on_summaries_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_SUMMARIES_LUCENE	"score_gscontext_on_summaries_lucene"
public static final String	PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_JARO_WINKLER	"score_gscontext_on_synonyms_jaro_winkler"
public static final String	PARAM_SCORE_GSCONTEXT_ON_SYNONYMS_LUCENE	"score_gscontext_on_synonyms_lucene"
public static final String	PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_JARO_WINKLER	"score_synonyms_on_descriptions_jaro_winkler"
public static final String	PARAM_SCORE_SYNONYMS_ON_DESCRIPTIONS_LUCENE	"score_synonyms_on_descriptions_lucene"
public static final String	PARAM_SCORE_SYNONYMS_ON_GENERIFS_JARO_WINKLER	"score_synonyms_on_generifs_jaro_winkler"
public static final String	PARAM_SCORE_SYNONYMS_ON_GENERIFS_LUCENE	"score_synonyms_on_generifs_lucene"
public static final String	PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_JARO_WINKLER	"score_synonyms_on_interactions_jaro_winkler"
public static final String	PARAM_SCORE_SYNONYMS_ON_INTERACTIONS_LUCENE	"score_synonyms_on_interactions_lucene"
public static final String	PARAM_SCORE_SYNONYMS_ON_SUMMARIES_JARO_WINKLER	"score_synonyms_on_summaries_jaro_winkler"
public static final String	PARAM_SCORE_SYNONYMS_ON_SUMMARIES_LUCENE	"score_synonyms_on_summaries_lucene"
public static final String	PARAM_SEARCH_GM_NP_MODE	"search_gm_np_mode"
public static final String	PARAM_SEARCH_TAX_SPECIFIC_CANDIDATES_FIRST	"search_tax_specific_candidates_first"
public static final String	PARAM_SORT_CANDIDATES_BY_MATCHED_FIELD	"sort_candidates_by_matched_field"
public static final String	PARAM_SORT_EXACT_MATCHES_BY_ORIGINAL_SIMILARITY	"sort_exact_matches_by_original_similarity"
public static final String	PARAM_SORT_ML_BY_EXACT_MATCH_FIRST	"mlranking.sort_by_exact_match_first"
public static final String	PARAM_SPLIT_AT_SLASH	"split_at_slash"
public static final String	PARAM_STOP_CANDIDATE_SEARCH_ON_EXACT_MATCH	"stop_candidate_search_on_exact_match"
public static final String	PARAM_SYNONYM_SEARCH_MODE	"synonym_search_mode"
public static final String	PARAM_THRESHOLD_APPROX_LENGTH_DIFF_PENALTY_FACTOR	"threshold_approx_length_penalty_factor"
public static final String	PARAM_THRESHOLD_APPROX_MATCHES	"threshold_approx_matches"
public static final String	PARAM_THRESHOLD_EXACT_MATCHES	"threshold_exact_matches"
public static final String	PARAM_TOKEN_WINDOW_GENE_SETS_SIZE	"token_window_gene_sets_size"
public static final String	PARAM_TOP_N_CANDIDATES_RERANKING	"top_n_candidates_for_reranking"
public static final String	PARAM_TRAIN_MODE	"train_mode"
public static final String	PARAM_TRANSFORMER_RANKING_MODEL	"transformer_ranking_model"
public static final String	PARAM_TRY_ORTHOLOGS	"try_orthologs"
public static final String	PARAM_USE_APPOSITIONS_AS_LUCENE_RELEVANCE_SIGNAL	"use_appositions_as_lucene_relevance_signal"
public static final String	PARAM_USE_APPOSITIONS_ON_GENE_CONTEXT_FEATURES	"use_appositions_on_gene_context_features"
public static final String	PARAM_USE_FAMILY_MATCH_EXACT_FEATURE	"use_family_match_exact_feature"
public static final String	PARAM_USE_FAMILY_MATCH_FRACTION_FEATURE	"use_family_match_fraction_feature"
public static final String	PARAM_USE_FAMILY_MATCH_RANK_FEATURE	"use_family_match_rank_feature"
public static final String	PARAM_USE_FAMILY_MATCH_SCORE_FEATURE	"use_family_match_score_feature"
public static final String	PARAM_USE_GENE_FAMILY_SCORE_FEATURE	"use_gene_family_score_feature"
public static final String	PARAM_USE_GENERIF	"use_generif"
public static final String	PARAM_USE_GNORMPLUS_CHEMICAL_SUFFIX_FEATURES	"use_gnormplus_chemical_suffix_features"
public static final String	PARAM_USE_GNORMPLUS_MENTION_TYPE_HINT_FEATURES	"use_gnormplus_mention_type_hint_features"
public static final String	PARAM_USE_GNORMPLUS_PROTEIN_SYMBOLS_FEATURES	"use_gnormplus_protein_symbols_features"
public static final String	PARAM_USE_GODESC	"use_godesc"
public static final String	PARAM_USE_GOLD_TAX	"use_gold_tax"
public static final String	PARAM_USE_INTERACTION	"use_interaction"
public static final String	PARAM_USE_JACCARD_FEATURES	"use_jaccard_features"
public static final String	PARAM_USE_JARO_WINKLER_APPROX_SCORES	"use_jaro_winkler_approx_scores"
public static final String	PARAM_USE_JARO_WINKLER_EXACT_SCORES	"use_jaro_winkler_exact_scores"
public static final String	PARAM_USE_JARO_WINKLER_FEATURES	"use_jarowinkler_features"
public static final String	PARAM_USE_LASTWORD_FEATURE	"use_lastword_feature"
public static final String	PARAM_USE_LEVENSHTEIN_FEATURES	"use_levenshtein_features"
public static final String	PARAM_USE_LUCENE_APPROX_SCORES	"use_lucene_approx_scores"
public static final String	PARAM_USE_LUCENE_EXACT_SCORES	"use_lucene_exact_scores"
public static final String	PARAM_USE_LUCENE_SYNONYM_SET	"use_lucene_synonym_set"
public static final String	PARAM_USE_NEEDLEMANWUNSCH_FEATURES	"use_needlemanwunsch_features"
public static final String	PARAM_USE_OTHER_HAS_SPECIFIER_FEATURE	"use_other_has_specifier"
public static final String	PARAM_USE_QUERY_FIELD_WEIGHTS	"use_query_field_weights"
public static final String	PARAM_USE_SCORER_AVERAGE	"use_scorer_average"
public static final String	PARAM_USE_SMITHWATERMAN_FEATURES	"use_smithwaterman_features"
public static final String	PARAM_USE_SUMMARY	"use_summary"
public static final String	PARAM_USE_TFIDF_FEATURES	"use_tfidf_features"
public static final String	PARAM_USE_TOKEN_FEATURES	"use_token_features"
public static final String	PARAM_USE_TOKEN_JARO_FEATURES	"use_tokenjaro_features"
public static final String	PREFIX_ANCHORING	"anchoring"
public static final String	PREFIX_CANDIDATE_FILTER	"candidate_filter"
public static final String	PREFIX_CANDIDATE_RETRIEVAL	"candidate_retrieval"
public static final String	PREFIX_DISAMBIGUATION	"disambiguation"
public static final String	PREFIX_ID_HOMOGENIZATION	"id_homogenization"
public static final String	PREFIX_RECORD_CONTEXT	"recordcontext"
public static final String	PREFIX_REJECTION	"rejection"
public static final String	PREFIX_REJECTION_HOMOGENIZATION	"rejection_homogenization"
public static final String	SPELLING_INDEX	"spelling_index"
public static final String	SYNONYM_INDEX	"mention_index"
public static final String	USE_LUCENE_CANDIDATES_CACHE	"use_lucene_candidates_cache"
public static final String	VALUE_ADDITIONAL_SEARCH	"additional_search"
public static final String	VALUE_ALL	"all"
public static final String	VALUE_BALANCED_SCORES	"balanced_scores"
public static final String	VALUE_CNF_RELEVANCE_SIGNAL	"cnf_relevance_signal"
public static final String	VALUE_CONTEXT_SCORES	"context_scores"
public static final String	VALUE_DISJUNCTION	"disjunction"
public static final String	VALUE_DISMAX	"dismax"
public static final String	VALUE_GENE_MENTIONS	"gene_mentions"
public static final String	VALUE_GENE_RECORDS	"gene_records"
public static final String	VALUE_GENESETS	"genesets"
public static final String	VALUE_LINEAR_COMBINATION	"linear_combination"
public static final String	VALUE_MAJORITY_VOTE	"majority_vote"
public static final String	VALUE_MAX	"max"
public static final String	VALUE_MAX_BALANCED_SCORE	"max_balanced_score"
public static final String	VALUE_MAX_BALANCED_SCORE_SUM	"max_balanced_score_sum"
public static final String	VALUE_MEAN_SCORE	"mean_score"
public static final String	VALUE_NAME_CENTRIC	"name_centric"
public static final String	VALUE_NO_GS_HOMOGENIZATION	"no_gs_homogenization"
public static final String	VALUE_NONE	"none"
public static final String	VALUE_RANK_FUSION	"rank_fusion"
public static final String	VALUE_SEMANTIC_CONTEXT	"genecontext_semanticcontext_JAROWINKLER"
public static final String	VALUE_SUM	"sum"
public static final String	WIKIPEDIA_INDEX	"wikipedia_index"

de.julielab.genemapper.GeneMapper

Modifier and Type	Constant Field	Value
public static final String	APP_NAME	"GeNo"
public static final boolean	LEGACY_INDEX_SUPPORT	true

de.julielab.genemapper.RejectionConstants

Modifier and Type	Constant Field	Value
public static final String	NER_CONFIDENCE	"ner_confidence"
public static final String	PARAM_APPROX_SINGLE_TOKEN	"approx_single_token"
public static final String	PARAM_CONTRADICTING_GREEK	"contradicting_greek"
public static final String	PARAM_CONTRADICTING_NUMBER	"contradicting_number"
public static final String	PARAM_FILTER_OUT_METHOD	"filter_out_method"
public static final String	PARAM_NO_TOKEN_OVERLAP	"no_token_overlap"
public static final String	RANKING_SCORE	"ranking_score"
public static final String	THRESHOLD	"threshold"

de.julielab.genemapper.classification.TransformerDisambiguationDataUtils

Modifier and Type	Constant Field	Value
public static final boolean	ADD_DESC	false
public static final boolean	ADD_GENERIF	false
public static final boolean	ADD_INTERACTIONS	false
public static final boolean	ADD_NAME_TYPES	true
public static final boolean	ADD_SUMMARY	false
public static final boolean	EXCLUDE_FP_GM	false
public static final int	MAX_DOC_CONTEXT_SIZE	256
public static final boolean	NORMALIZE_CONTEXT_GENES	false
public static final boolean	ONLY_APPROX_MATCHES	true
public static final boolean	ONLY_EXACT_MATCHES	false
public static final boolean	USE_GOLD_TAX_FOR_CANDIDATE_RETRIEVAL	true
public static final boolean	USE_ORIGINAL_QUERY_NAMES	true
public static final int	VERSION	23

de.julielab.genemapper.hpo.CandidateRetrievalOptimizationRoute

Modifier and Type	Constant Field	Value
public static final boolean	EVAL_ON_HUMAN_ONLY	false
public static final String	GET_MENTION_SEARCH_SCORE	"get_mention_score_search"

de.julielab.genemapper.hpo.GeneMappingOptimizationRoute

Modifier and Type	Constant Field	Value
public static final String	GET_GENE_MAPPING_SCORE	"get_gene_mapping_score"

de.julielab.genemapper.hpo.GenesetsOptimizationRoute

Modifier and Type	Constant Field	Value
public static final String	GET_GENESET_SCORE	"get_geneset_score"

de.julielab.genemapper.index.ContextIndexFieldNames

Modifier and Type	Constant Field	Value
public static final String	FIELD_ACTIVITY_REGULATION	"activity_regulation"
public static final String	FIELD_CHROMOSOME	"chromosome"
public static final String	FIELD_CONTEXT_ITEM	"contextitem"
public static final String	FIELD_DESCRIPTION	"description"
public static final String	FIELD_DESIGNATION	"designation"
public static final String	FIELD_DEVELOPMENTAL_STAGE	"developmental_stage"
public static final String	FIELD_DISEASE	"disease"
public static final String	FIELD_DOMAIN	"domain"
public static final String	FIELD_FUNCTION	"function"
public static final String	FIELD_GENERIF	"generif"
public static final String	FIELD_INDUCTION	"induction"
public static final String	FIELD_INTERACTION	"interaction"
public static final String	FIELD_ITEM_TYPE	"itemtype"
public static final String	FIELD_KEYWORD	"keyword"
public static final String	FIELD_MAP_LOCATION	"map_location"
public static final String	FIELD_MISCELLANEOUS	"miscellaneous"
public static final String	FIELD_PATHWAY	"pathway"
public static final String	FIELD_SIMILARITY	"similarity"
public static final String	FIELD_SUBCELLULAR_LOCATION	"subcellular_location"
public static final String	FIELD_SUBUNIT	"subunit"
public static final String	FIELD_SUMMARY	"summary"
public static final String	FIELD_SYNONYMS_BOW	"synonyms_bow"
public static final String	FIELD_SYNONYMS_EXACT	"synonyms_exact"
public static final String	FIELD_TISSUE	"tissue"
public static final String	FIELD_TISSUE_SPECIFICITY	"_tissue_specificity"
public static final String	LOOKUP_CONTEXT_FIELD	"indexed_context"
public static final String	LOOKUP_ID_FIELD	"indexed_id"

de.julielab.genemapper.index.WikipediaIndexFields

Modifier and Type	Constant Field	Value
public static final String	ENTITIES	"entities"
public static final String	ENTITYCHUNKS	"entitychunks"
public static final String	HASUNSPECTITLE	"hasunspectitle"
public static final String	MENTIONED_PAGE_TITLES	"mentionedpagetitles"
public static final String	MOLECULAR_BIOLOGY_PATH	"molecularbiologypath"
public static final String	MOLECULAR_BIOLOGY_PATH_LENGTH	"molecularbiologypathlength"
public static final String	PAGE_ID	"pageid"
public static final String	TITLE	"title"
public static final String	TITLEISINPLURAL	"titleisinplural"

de.julielab.genemapper.mappingcores.DypsisCandidateSetter

Modifier and Type	Constant Field	Value
public static final boolean	recordStats	false

de.julielab.genemapper.uima.GeneMapperAnnotator

Modifier and Type	Constant Field	Value
public static final String	CONTEXT_WINDOW_SIZE	"ContextWindowSize"
public static final String	ENTITY_MAPPING_TYPES	"EntityMappingTypes"
public static final String	MAPPER_CONFIG_FILE	"MapperConfigFile"
public static final String	REMOVE_EXISTING_RESOURCE_ENTRIES	"RemoveExistingResourceEntries"
public static final String	TOKEN_CONTEXT	"TokenContext"

de.julielab.genemapper.uima.GeneMentionTaxIdCountWriter

Modifier and Type	Constant Field	Value
public static final String	PARAM_OUTPUT_PATH	"OutputPath"

de.julielab.genemapper.uima.GeneSynonymEmbeddingCentroidWriter

Modifier and Type	Constant Field	Value
public static final String	PARAM_DB_DIR	"EmbeddingDbDir"

de.julielab.genemapper.uima.ProteinConsistencyTagger

Modifier and Type	Constant Field	Value
public static final String	PARAM_OFFSET_EXPANSION_TYPE	"OffsetExpansionType"
public static final String	PARAMETER_PROTEIN_TYPE	"ProteinType"

de.julielab.genemapper.uima.TaxIdIntegratedTextWriter

Modifier and Type	Constant Field	Value
public static final String	PARAM_BASE_PATH	"OutputBasePath"
public static final String	PARAM_LEMMAS	"UseLemmas"
public static final String	PARAM_LOWERCASING	"DoLowercase"
public static final String	PARAM_MODE	"TaxIdInsertionMode"
public static final String	PARAM_TOKENIZATION	"UseTokenization"

de.julielab.genemapper.uima.TaxIdSentenceLabelWriter

Modifier and Type	Constant Field	Value
public static final String	PARAM_BASE_PATH	"OutputBasePath"
public static final String	PARAM_LEMMAS	"UseLemmas"
public static final String	PARAM_LOWERCASING	"DoLowercase"
public static final String	PARAM_MASK_ORGANISM_NAMES	"MaskOrganismNames"
public static final String	PARAM_TOKENIZATION	"UseTokenization"