Index

A

add_child() (pymedextcore.annotators.Annotation method) add_property() (pymedextcore.annotators.Annotation method) annotate() (pymedextcore.document.Document method) annotate_function() (pymedextcore.annotators.Annotator method) Annotation (class in pymedextcore.annotators)

Annotator (class in pymedextcore.annotators) APIConnector (class in pymedextcore.connector) Attribute (class in pymedextcore.brat_parser) attributes (pymedextcore.brat_parser.AugmentedEntity attribute) (pymedextcore.brat_parser.Document attribute) AugmentedEntity (class in pymedextcore.brat_parser)

B

BioC (class in pymedextcore.bioctransform)

brat (class in pymedextcore.brattransform) buildNoteNlP() (pymedextcore.omoptransform.omop method)

C

clean_csv_value() (in module pymedextcore.omopsource) Connector (class in pymedextcore.connector)

create_label() (pymedextcore.doccanosource.DoccanoSource method) create_project() (pymedextcore.doccanosource.DoccanoSource method) cxORacleConnector (class in pymedextcore.connector)

D

DatabaseConnector (class in pymedextcore.connector) DataTransform (class in pymedextcore.datatransform) Doccano (class in pymedextcore.doccanotransform) DoccanoAnnotation (class in pymedextcore.doccanoannotator) DoccanoDocument (class in pymedextcore.doccanodocument) DoccanoEvalClass() (pymedextcore.doccanotransform.Doccano method)

DoccanoEvalN() (pymedextcore.doccanotransform.Doccano method) DoccanoEvalRappel() (pymedextcore.doccanotransform.Doccano method) DoccanoSource (class in pymedextcore.doccanosource) docForDoccano() (pymedextcore.doccanotransform.Doccano method) Document (class in pymedextcore.brat_parser) (class in pymedextcore.document)

E

end (pymedextcore.brat_parser.AugmentedEntity property) (pymedextcore.brat_parser.Entity property) entities (pymedextcore.brat_parser.Document attribute)

Entity (class in pymedextcore.brat_parser) exp_get_doc_list() (pymedextcore.doccanosource.DoccanoSource method) export() (in module pymedextcore.pymedext_cmdline)

F

FHIR (class in pymedextcore.fhirtransform)

find_project_id() (pymedextcore.doccanosource.DoccanoSource method) from_dict() (pymedextcore.document.Document static method)

G

generateNote() (pymedextcore.omoptransform.omop method) generateNoteNLP() (pymedextcore.omoptransform.omop method) generatePerson() (pymedextcore.omoptransform.omop method) get_all_key_input() (pymedextcore.annotators.Annotator method) get_annotation_by_id() (pymedextcore.document.Document method) get_annotation_detail() (pymedextcore.doccanosource.DoccanoSource method) get_annotation_list() (pymedextcore.doccanosource.DoccanoSource method) get_annotations() (pymedextcore.document.Document method) get_attributes() (pymedextcore.annotators.Annotation method) get_augmented_entities() (in module pymedextcore.brat_parser) get_children_span() (pymedextcore.annotators.Annotation method) get_doc_download() (pymedextcore.doccanosource.DoccanoSource method) get_document_detail() (pymedextcore.doccanosource.DoccanoSource method) get_document_list() (pymedextcore.doccanosource.DoccanoSource method) get_entities_children() (pymedextcore.annotators.Annotation method) get_entities_relations_attributes_groups() (in module pymedextcore.brat_parser) get_features() (pymedextcore.doccanosource.DoccanoSource method) get_first_key_input() (pymedextcore.annotators.Annotator method) get_graph() (pymedextcore.document.Document method) get_key_input() (pymedextcore.annotators.Annotator method) get_label_detail() (pymedextcore.doccanosource.DoccanoSource method)

get_label_id() (pymedextcore.doccanosource.DoccanoSource method) get_label_list() (pymedextcore.doccanosource.DoccanoSource method) get_me() (pymedextcore.doccanosource.DoccanoSource method) get_ngram() (pymedextcore.annotators.Annotation method) get_parent() (pymedextcore.annotators.Annotation method) get_parents_properties() (pymedextcore.annotators.Annotation method) get_pmids_annotations() (pymedextcore.ncbisource.PubTatorSource method) get_project_detail() (pymedextcore.doccanosource.DoccanoSource method) get_project_id() (pymedextcore.doccanosource.DoccanoSource method) get_project_list() (pymedextcore.doccanosource.DoccanoSource method) get_project_statistics() (pymedextcore.doccanosource.DoccanoSource method) get_properties() (pymedextcore.annotators.Annotation method) get_relation_by_id() (pymedextcore.document.Document method) get_relations() (pymedextcore.document.Document method) get_rolemapping_detail() (pymedextcore.doccanosource.DoccanoSource method) get_rolemapping_list() (pymedextcore.doccanosource.DoccanoSource method) get_roles() (pymedextcore.doccanosource.DoccanoSource method) get_span() (pymedextcore.annotators.Annotation method) get_user_id() (pymedextcore.doccanosource.DoccanoSource method) get_user_list() (pymedextcore.doccanosource.DoccanoSource method) getLastNotenlpid() (pymedextcore.omopsource.OmopSource method) Grouping (class in pymedextcore.brat_parser)

I

id (pymedextcore.brat_parser.Attribute attribute) (pymedextcore.brat_parser.AugmentedEntity attribute) (pymedextcore.brat_parser.Entity attribute) (pymedextcore.brat_parser.Grouping attribute) (pymedextcore.brat_parser.Relation attribute)

items (pymedextcore.brat_parser.Grouping attribute)

L

list_to_dict() (in module pymedextcore.brat_parser) load() (pymedextcore.datatransform.DataTransform static method) (pymedextcore.omoptransform.omop method) load_annotations_files() (pymedextcore.document.Document method)

load_collection() (pymedextcore.bioctransform.BioC static method) load_from_brat() (pymedextcore.brattransform.brat static method) load_xml() (pymedextcore.fhirtransform.FHIR method) loadFile() (in module pymedextcore.pymedext_cmdline) loadFromSource() (pymedextcore.source.Source static method)

M

main() (in module pymedextcore.pymedext_cmdline) module pymedextcore pymedextcore.annotators pymedextcore.bioctransform pymedextcore.brat_parser pymedextcore.brattransform pymedextcore.connector pymedextcore.datatransform pymedextcore.doccanoannotator pymedextcore.doccanodocument pymedextcore.doccanosource pymedextcore.doccanotransform pymedextcore.document pymedextcore.fhirtransform pymedextcore.ncbisource pymedextcore.normalize pymedextcore.omopsource pymedextcore.omoptransform pymedextcore.pymedext pymedextcore.pymedext_cmdline pymedextcore.source

N

normalize (class in pymedextcore.normalize)

O

obj (pymedextcore.brat_parser.Relation attribute)

omop (class in pymedextcore.omoptransform) OmopSource (class in pymedextcore.omopsource)

P

parse() (in module pymedextcore.brat_parser) parse_attribute() (in module pymedextcore.brat_parser) parse_entity() (in module pymedextcore.brat_parser) parse_relation() (in module pymedextcore.brat_parser) parse_string() (in module pymedextcore.brat_parser) parse_string_to_augmented_entities() (in module pymedextcore.brat_parser) post_approve_labels() (pymedextcore.doccanosource.DoccanoSource method) post_doc_upload() (pymedextcore.doccanosource.DoccanoSource method) PostGresConnector (class in pymedextcore.connector) PubTatorSource (class in pymedextcore.ncbisource) pymedextcore module pymedextcore.annotators module pymedextcore.bioctransform module pymedextcore.brat_parser module pymedextcore.brattransform module pymedextcore.connector module pymedextcore.datatransform module pymedextcore.doccanoannotator module

pymedextcore.doccanodocument module pymedextcore.doccanosource module pymedextcore.doccanotransform module pymedextcore.document module pymedextcore.fhirtransform module pymedextcore.ncbisource module pymedextcore.normalize module pymedextcore.omopsource module pymedextcore.omoptransform module pymedextcore.pymedext module pymedextcore.pymedext_cmdline module pymedextcore.source module

R

raw_text() (pymedextcore.document.Document method) read() (pymedextcore.omopsource.StringIteratorIO method) read_file_annotations() (in module pymedextcore.brat_parser) readable() (pymedextcore.omopsource.StringIteratorIO method) Relation (class in pymedextcore.annotators) (class in pymedextcore.brat_parser)

relations (pymedextcore.brat_parser.Document attribute) relations_from_me (pymedextcore.brat_parser.AugmentedEntity attribute) relations_to_me (pymedextcore.brat_parser.AugmentedEntity attribute) remove_empty() (in module pymedextcore.brat_parser)

S

sanitize_tabs() (in module pymedextcore.brat_parser) save() (pymedextcore.datatransform.DataTransform static method) save_as_collection() (pymedextcore.bioctransform.BioC static method) save_to_brat() (pymedextcore.brattransform.brat method) saveToSource() (pymedextcore.omopsource.OmopSource method) (pymedextcore.source.Source static method) select_all_inputs() (pymedextcore.annotators.Annotator method) select_first_input() (pymedextcore.annotators.Annotator method) set_ngram() (pymedextcore.annotators.Annotation method) set_parent() (pymedextcore.annotators.Annotation method) set_rolemapping_list() (pymedextcore.doccanosource.DoccanoSource method) set_root() (pymedextcore.annotators.Annotation method)

SimpleAPIConnector (class in pymedextcore.connector) Source (class in pymedextcore.source) span (pymedextcore.brat_parser.AugmentedEntity attribute) (pymedextcore.brat_parser.Entity attribute) SSHConnector (class in pymedextcore.connector) start (pymedextcore.brat_parser.AugmentedEntity property) (pymedextcore.brat_parser.Entity property) start_connection() (pymedextcore.connector.DatabaseConnector method) (pymedextcore.connector.PostGresConnector method) (pymedextcore.connector.SimpleAPIConnector method) StringIteratorIO (class in pymedextcore.omopsource) subj (pymedextcore.brat_parser.Relation attribute)

T

target (pymedextcore.brat_parser.Attribute attribute) text (pymedextcore.brat_parser.AugmentedEntity attribute) (pymedextcore.brat_parser.Entity attribute) (pymedextcore.brat_parser.Grouping property) to_dict() (pymedextcore.annotators.Annotation method) (pymedextcore.annotators.Relation method) (pymedextcore.doccanoannotator.DoccanoAnnotation method) (pymedextcore.document.Document method) to_json() (pymedextcore.annotators.Annotation method) (pymedextcore.annotators.Relation method) (pymedextcore.doccanoannotator.DoccanoAnnotation method) (pymedextcore.document.Document method)

toDictDoccano() (pymedextcore.doccanodocument.DoccanoDocument method) toDoccanoDrWH() (pymedextcore.doccanotransform.Doccano method) toDoccanoImaPrecision() (pymedextcore.doccanotransform.Doccano method) toDoccanoImaRappel() (pymedextcore.doccanotransform.Doccano method) toDoccanoPb() (pymedextcore.doccanotransform.Doccano method) toJsonDoccano() (pymedextcore.doccanodocument.DoccanoDocument method) type (pymedextcore.brat_parser.Attribute attribute) (pymedextcore.brat_parser.AugmentedEntity attribute) (pymedextcore.brat_parser.Entity attribute) (pymedextcore.brat_parser.Grouping attribute) (pymedextcore.brat_parser.Relation attribute)

U

uri() (pymedextcore.normalize.normalize static method)

V

values (pymedextcore.brat_parser.Attribute attribute)

W

write_bioc_collection() (pymedextcore.bioctransform.BioC static method)

write_json() (pymedextcore.document.Document method) writeJsonDoccano() (pymedextcore.doccanodocument.DoccanoDocument method)