medaCy
latest
medacy package
medacy.data package
medacy.data.dataset module
medacy.model package
medacy.model.feature_extractor module
medacy.model.model module
medacy.model.stratified_k_fold module
medacy.pipeline_components package
medacy.pipeline_components.annotation package
medacy.pipeline_components.annotation.gold_annotator_component module
medacy.pipeline_components.base package
medacy.pipeline_components.base.base_component module
medacy.pipeline_components.lexicon package
medacy.pipeline_components.lexicon.lexicon_component module
medacy.pipeline_components.metamap package
medacy.pipeline_components.metamap.metamap module
medacy.pipeline_components.metamap.metamap_component module
medacy.pipeline_components.tokenization package
medacy.pipeline_components.tokenization.character_tokenizer module
medacy.pipeline_components.tokenization.clinical_tokenizer module
medacy.pipeline_components.tokenization.systematic_review_tokenizer module
medacy.pipeline_components.units package
medacy.pipeline_components.units.frequency_unit_component module
medacy.pipeline_components.units.mass_unit_component module
medacy.pipeline_components.units.measurement_unit_component module
medacy.pipeline_components.units.route_unit_component module
medacy.pipeline_components.units.time_unit_component module
medacy.pipeline_components.units.unit_component module
medacy.pipeline_components.units.volume_unit_component module
medacy.pipelines package
medacy.pipelines.base package
medacy.pipelines.base.base_pipeline module
medacy.pipelines.clinical_pipeline module
medacy.pipelines.drug_event_pipeline module
medacy.pipelines.fda_nano_drug_label_pipeline module
medacy.pipelines.systematic_review_pipeline module
medacy.pipelines.testing_pipeline module
medacy.tools package
medacy.tools.con package
medacy.tools.con.brat_to_con module
medacy.tools.con.con_to_brat module
medacy.tools.ade_to_brat module
medacy.tools.annotations module
medacy.tools.data_file module
medacy.tools.unicode_to_ascii module
medaCy
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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I
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L
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M
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N
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P
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S
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T
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U
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V
_
_abc_impl (medacy.pipeline_components.annotation.gold_annotator_component.GoldAnnotatorComponent attribute)
(medacy.pipeline_components.base.base_component.BaseComponent attribute)
(medacy.pipeline_components.lexicon.lexicon_component.LexiconComponent attribute)
(medacy.pipeline_components.metamap.metamap_component.MetaMapComponent attribute)
(medacy.pipeline_components.units.frequency_unit_component.FrequencyUnitComponent attribute)
(medacy.pipeline_components.units.mass_unit_component.MassUnitComponent attribute)
(medacy.pipeline_components.units.measurement_unit_component.MeasurementUnitComponent attribute)
(medacy.pipeline_components.units.time_unit_component.TimeUnitComponent attribute)
(medacy.pipeline_components.units.unit_component.UnitComponent attribute)
(medacy.pipeline_components.units.volume_unit_component.VolumeUnitComponent attribute)
(medacy.pipelines.base.base_pipeline.BasePipeline attribute)
(medacy.pipelines.clinical_pipeline.ClinicalPipeline attribute)
(medacy.pipelines.drug_event_pipeline.DrugEventPipeline attribute)
(medacy.pipelines.fda_nano_drug_label_pipeline.FDANanoDrugLabelPipeline attribute)
(medacy.pipelines.systematic_review_pipeline.SystematicReviewPipeline attribute)
(medacy.pipelines.testing_pipeline.TestingPipeline attribute)
_Annotations__default_strict (medacy.tools.annotations.Annotations attribute)
_convert_to_ascii() (medacy.pipeline_components.metamap.metamap.MetaMap method)
_extract_features() (medacy.model.model.Model method)
_get_infix_regex() (medacy.pipeline_components.tokenization.character_tokenizer.CharacterTokenizer method)
(medacy.pipeline_components.tokenization.clinical_tokenizer.ClinicalTokenizer method)
(medacy.pipeline_components.tokenization.systematic_review_tokenizer.SystematicReviewTokenizer method)
_get_prefix_regex() (medacy.pipeline_components.tokenization.character_tokenizer.CharacterTokenizer method)
(medacy.pipeline_components.tokenization.clinical_tokenizer.ClinicalTokenizer method)
(medacy.pipeline_components.tokenization.systematic_review_tokenizer.SystematicReviewTokenizer method)
_get_suffix_regex() (medacy.pipeline_components.tokenization.character_tokenizer.CharacterTokenizer method)
(medacy.pipeline_components.tokenization.clinical_tokenizer.ClinicalTokenizer method)
(medacy.pipeline_components.tokenization.systematic_review_tokenizer.SystematicReviewTokenizer method)
_item_generator() (medacy.pipeline_components.metamap.metamap.MetaMap method)
_parallel_metamap() (medacy.data.dataset.Dataset method)
_restore_from_ascii() (medacy.pipeline_components.metamap.metamap.MetaMap method)
_run_metamap() (medacy.pipeline_components.metamap.metamap.MetaMap method)
_sent_to_feature_dicts() (medacy.model.feature_extractor.FeatureExtractor method)
_sent_to_labels() (medacy.model.feature_extractor.FeatureExtractor method)
_token_to_feature_dict() (medacy.model.feature_extractor.FeatureExtractor method)
A
add_component() (medacy.pipelines.base.base_pipeline.BasePipeline method)
add_exceptions() (medacy.pipeline_components.tokenization.character_tokenizer.CharacterTokenizer method)
(medacy.pipeline_components.tokenization.clinical_tokenizer.ClinicalTokenizer method)
(medacy.pipeline_components.tokenization.systematic_review_tokenizer.SystematicReviewTokenizer method)
Annotations (class in medacy.tools.annotations)
B
BaseComponent (class in medacy.pipeline_components.base.base_component)
BasePipeline (class in medacy.pipelines.base.base_pipeline)
C
CharacterTokenizer (class in medacy.pipeline_components.tokenization.character_tokenizer)
check_valid_line() (in module medacy.tools.con.brat_to_con)
(in module medacy.tools.con.con_to_brat)
ClinicalPipeline (class in medacy.pipelines.clinical_pipeline)
ClinicalTokenizer (class in medacy.pipeline_components.tokenization.clinical_tokenizer)
compare_by_entity() (medacy.tools.annotations.Annotations method)
compare_by_index() (medacy.tools.annotations.Annotations method)
compare_by_index_stats() (medacy.tools.annotations.Annotations method)
convert_brat_to_con() (in module medacy.tools.con.brat_to_con)
convert_con_to_brat() (in module medacy.tools.con.con_to_brat)
cross_validate() (medacy.model.model.Model method)
D
DataFile (class in medacy.tools.data_file)
Dataset (class in medacy.data.dataset)
dependencies (medacy.pipeline_components.annotation.gold_annotator_component.GoldAnnotatorComponent attribute)
(medacy.pipeline_components.lexicon.lexicon_component.LexiconComponent attribute)
(medacy.pipeline_components.metamap.metamap_component.MetaMapComponent attribute)
(medacy.pipeline_components.units.frequency_unit_component.FrequencyUnitComponent attribute)
(medacy.pipeline_components.units.mass_unit_component.MassUnitComponent attribute)
(medacy.pipeline_components.units.measurement_unit_component.MeasurementUnitComponent attribute)
(medacy.pipeline_components.units.time_unit_component.TimeUnitComponent attribute)
(medacy.pipeline_components.units.unit_component.UnitComponent attribute)
(medacy.pipeline_components.units.volume_unit_component.VolumeUnitComponent attribute)
diff() (medacy.tools.annotations.Annotations method)
DrugEventPipeline (class in medacy.pipelines.drug_event_pipeline)
dump() (medacy.model.model.Model method)
E
extract_mapped_terms() (medacy.pipeline_components.metamap.metamap.MetaMap method)
F
FDANanoDrugLabelPipeline (class in medacy.pipelines.fda_nano_drug_label_pipeline)
FeatureExtractor (class in medacy.model.feature_extractor)
find_line_num() (in module medacy.tools.con.brat_to_con)
find_span() (medacy.pipeline_components.annotation.gold_annotator_component.GoldAnnotatorComponent method)
fit() (medacy.model.model.Model method)
FrequencyUnitComponent (class in medacy.pipeline_components.units.frequency_unit_component)
from_ann() (medacy.tools.annotations.Annotations method)
from_con() (medacy.tools.annotations.Annotations method)
G
get_absolute_index() (in module medacy.tools.con.con_to_brat)
get_component_dependencies() (medacy.pipeline_components.base.base_component.BaseComponent method)
get_component_name() (medacy.pipeline_components.base.base_component.BaseComponent method)
get_components() (medacy.pipelines.base.base_pipeline.BasePipeline method)
get_data_directory() (medacy.data.dataset.Dataset method)
get_data_files() (medacy.data.dataset.Dataset method)
get_end_word_index() (in module medacy.tools.con.brat_to_con)
get_entity_annotations() (medacy.tools.annotations.Annotations method)
get_entity_count() (medacy.tools.annotations.Annotations method)
get_feature_extractor() (medacy.pipelines.base.base_pipeline.BasePipeline method)
(medacy.pipelines.clinical_pipeline.ClinicalPipeline method)
(medacy.pipelines.drug_event_pipeline.DrugEventPipeline method)
(medacy.pipelines.fda_nano_drug_label_pipeline.FDANanoDrugLabelPipeline method)
(medacy.pipelines.systematic_review_pipeline.SystematicReviewPipeline method)
(medacy.pipelines.testing_pipeline.TestingPipeline method)
get_features_with_span_indices() (medacy.model.feature_extractor.FeatureExtractor method)
get_info() (medacy.model.model.Model method)
get_language_pipeline() (medacy.pipelines.base.base_pipeline.BasePipeline method)
get_learner() (medacy.pipelines.base.base_pipeline.BasePipeline method)
(medacy.pipelines.clinical_pipeline.ClinicalPipeline method)
(medacy.pipelines.drug_event_pipeline.DrugEventPipeline method)
(medacy.pipelines.fda_nano_drug_label_pipeline.FDANanoDrugLabelPipeline method)
(medacy.pipelines.systematic_review_pipeline.SystematicReviewPipeline method)
(medacy.pipelines.testing_pipeline.TestingPipeline method)
get_pipeline_information() (medacy.pipelines.base.base_pipeline.BasePipeline method)
get_relative_index() (in module medacy.tools.con.brat_to_con)
get_semantic_types_by_term() (medacy.pipeline_components.metamap.metamap.MetaMap method)
get_span_by_term() (medacy.pipeline_components.metamap.metamap.MetaMap method)
get_term_by_semantic_type() (medacy.pipeline_components.metamap.metamap.MetaMap method)
get_tokenizer() (medacy.pipelines.base.base_pipeline.BasePipeline method)
(medacy.pipelines.clinical_pipeline.ClinicalPipeline method)
(medacy.pipelines.drug_event_pipeline.DrugEventPipeline method)
(medacy.pipelines.fda_nano_drug_label_pipeline.FDANanoDrugLabelPipeline method)
(medacy.pipelines.systematic_review_pipeline.SystematicReviewPipeline method)
(medacy.pipelines.testing_pipeline.TestingPipeline method)
GoldAnnotatorComponent (class in medacy.pipeline_components.annotation.gold_annotator_component)
I
InvalidAnnotationError
is_metamapped() (medacy.data.dataset.Dataset method)
is_training() (medacy.data.dataset.Dataset method)
L
LexiconComponent (class in medacy.pipeline_components.lexicon.lexicon_component)
line_to_dict() (in module medacy.tools.con.brat_to_con)
(in module medacy.tools.con.con_to_brat)
load() (medacy.model.model.Model method)
(medacy.pipeline_components.metamap.metamap.MetaMap method)
load_external() (medacy.data.dataset.Dataset static method)
(medacy.model.model.Model static method)
M
map_corpus() (medacy.pipeline_components.metamap.metamap.MetaMap method)
map_file() (medacy.pipeline_components.metamap.metamap.MetaMap method)
map_text() (medacy.pipeline_components.metamap.metamap.MetaMap method)
mapped_terms_to_spacy_ann() (medacy.pipeline_components.metamap.metamap.MetaMap method)
mapper_for_crf_wrapper() (medacy.model.feature_extractor.FeatureExtractor method)
MassUnitComponent (class in medacy.pipeline_components.units.mass_unit_component)
MeasurementUnitComponent (class in medacy.pipeline_components.units.measurement_unit_component)
medacy.data.dataset (module)
medacy.model.feature_extractor (module)
medacy.model.model (module)
medacy.model.stratified_k_fold (module)
medacy.pipeline_components.annotation.gold_annotator_component (module)
medacy.pipeline_components.base.base_component (module)
medacy.pipeline_components.lexicon.lexicon_component (module)
medacy.pipeline_components.metamap.metamap (module)
medacy.pipeline_components.metamap.metamap_component (module)
medacy.pipeline_components.tokenization.character_tokenizer (module)
medacy.pipeline_components.tokenization.clinical_tokenizer (module)
medacy.pipeline_components.tokenization.systematic_review_tokenizer (module)
medacy.pipeline_components.units.frequency_unit_component (module)
medacy.pipeline_components.units.mass_unit_component (module)
medacy.pipeline_components.units.measurement_unit_component (module)
medacy.pipeline_components.units.route_unit_component (module)
medacy.pipeline_components.units.time_unit_component (module)
medacy.pipeline_components.units.unit_component (module)
medacy.pipeline_components.units.volume_unit_component (module)
medacy.pipelines.base.base_pipeline (module)
medacy.pipelines.clinical_pipeline (module)
medacy.pipelines.drug_event_pipeline (module)
medacy.pipelines.fda_nano_drug_label_pipeline (module)
medacy.pipelines.systematic_review_pipeline (module)
medacy.pipelines.testing_pipeline (module)
medacy.tools.annotations (module)
medacy.tools.con.brat_to_con (module)
medacy.tools.con.con_to_brat (module)
medacy.tools.data_file (module)
medacy.tools.unicode_to_ascii (module)
MetaMap (class in medacy.pipeline_components.metamap.metamap)
metamap() (medacy.data.dataset.Dataset method)
MetaMapComponent (class in medacy.pipeline_components.metamap.metamap_component)
Model (class in medacy.model.model)
N
name (medacy.pipeline_components.annotation.gold_annotator_component.GoldAnnotatorComponent attribute)
(medacy.pipeline_components.lexicon.lexicon_component.LexiconComponent attribute)
(medacy.pipeline_components.metamap.metamap_component.MetaMapComponent attribute)
(medacy.pipeline_components.units.frequency_unit_component.FrequencyUnitComponent attribute)
(medacy.pipeline_components.units.mass_unit_component.MassUnitComponent attribute)
(medacy.pipeline_components.units.measurement_unit_component.MeasurementUnitComponent attribute)
(medacy.pipeline_components.units.time_unit_component.TimeUnitComponent attribute)
(medacy.pipeline_components.units.unit_component.UnitComponent attribute)
(medacy.pipeline_components.units.volume_unit_component.VolumeUnitComponent attribute)
P
predict() (medacy.model.model.Model method)
S
SequenceStratifiedKFold (class in medacy.model.stratified_k_fold)
set_data_limit() (medacy.data.dataset.Dataset method)
stats() (medacy.tools.annotations.Annotations method)
switch_extension() (in module medacy.tools.con.brat_to_con)
(in module medacy.tools.con.con_to_brat)
SystematicReviewPipeline (class in medacy.pipelines.systematic_review_pipeline)
SystematicReviewTokenizer (class in medacy.pipeline_components.tokenization.systematic_review_tokenizer)
T
TestingPipeline (class in medacy.pipelines.testing_pipeline)
TimeUnitComponent (class in medacy.pipeline_components.units.time_unit_component)
to_ann() (medacy.tools.annotations.Annotations method)
to_con() (medacy.tools.annotations.Annotations method)
to_html() (medacy.tools.annotations.Annotations method)
U
UnitComponent (class in medacy.pipeline_components.units.unit_component)
V
VolumeUnitComponent (class in medacy.pipeline_components.units.volume_unit_component)
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