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db.schemas.legacy.models

emtellipro.db.schemas.legacy.models

This module contains all the ORM models, implemented using SQLAlchemy.

The attributes of each object are documented as being either ‘column’ or ‘dynamic’; ‘column’ means they’re actual columns in the database table, and ‘dynamic’ means they’re only convenience attributes created by the ORM to handle relationships.

Note that the actual data types used when creating tables depends on the SQL dialect used (i.e. which database it’s connected to). To check the exact data types, one can refer to SQLAlchemy’s documentation, or inspect the schema of the tables that were created using this tool.

NOTE: back-references may not always be documented.

Module Contents

Classes

NameDescription
BaseThe base of all tables.
AlembicVersionTable containg the alembic version. It’s defined here so that we can easily create and drop it along with all the other tables.
ProcessingDetailsTable containing details about the job submitted for processing.
DocumentMetadataTable containing arbitrary metadata for each document.
DocumentStructuredMetadataTable containing arbitrary metadata for each document.
DocumentTable containing details specific the the overall document that was processed.
DocumentSourceChunkTable containing chunks of source data.
OntologyVersionTable of ontology versions for each document.
EntityTable of entities stored in a specific document. The entity information is stored in different tables depending on entity type. The “type_column can be used along with theentity_id` to determine which exact entity is referred to.
AssumedEntityTable containing assumed entities.
FoundEntityTable containing found entities.
FoundEntityMeasurementUnitTable containing the measurement units for a found entity
FoundEntityTypeTable containing the type_name information from found entities.
ConceptTable containing information about a specific column, with the primary keys being the concept_id and ontology.
FoundEntitySpanTable containging spans contained in found entities.
SentenceLocationTable containing sentence locations. It exists mainly as a link between the locations table and the spans.
SentenceLocationSpanTable containing sentence location spans
HeadingLocationTable containing heading locations. It exists mainly as a link between the locations table and the spans.
HeadingLocationSpanTable containing heading location spans
PageLocationTable containing page locations. It exists mainly as a link between the locations table and the spans.
PageLocationSpanTable containing page location spans
PageSectionTable containing links between pages and section, with a composite primary key of page_id and section_id.
RelationTable containing links to all the different kinds of relations. Use the type_ and relation_id fields to find the actual relation in one of the other *Relation tables.
LocationTable containing links to all the different kinds of locations. Use the type_ and location_id fields to find the actual location in one of the other *Location tables.
SectionLocationSpanTable containing sentence location span information.
ImageLinkRelationTable containing image link relation information.
FollowupRelationTable containign follow-up relation information.
ExperiencerRelationTable containing experience relation information.
MeasurementRelationTable containing measurement relations.
QualifierRelationTable containing qualifier relations.
MedicationRelationTable containing medication relations.
TemporalityRelationTable containing temporality relations.
ReportedEventRelationTable containing reported event relations.
AnatomicSiteRelationTable containing anatomic site relations.
SectionLocationTable containg section locations.
SentenceSectionTable containing links between sentences and section, with a composite primary key of sentence_id and section_id.
DocumentConceptAssociation table linking documents to concepts.
FoundEntityConceptAssociation table linking found entities to concepts.
FoundEntityLocationAssociation table linking found entities to locations.
ImageLinkRelationImageFindingAssociation table linking image link relations to entities specified as image findings.
ImageLinkRelationReferenceAssociation table linking image link relations to entities specified as references.
FollowupRelationProcedureAssociation table linking followup relations to entities specified as procedures.
FollowupRelationReasonAssociation table linking followup relations to entities specified as reasons.
MedicationRelationDosageAssociation table linking medication relations to entities specified as dosage
MedicationRelationFrequencyAssociation table linking medication relations to entities specified as frequency
MedicationRelationModeAssociation table linking medication relations to entities specified as mode
MedicationRelationQuantityAssociation table linking medication relations to entities specified as quantity
MedicationRelationRouteAssociation table linking medication relations to entities specified as route
MedicationRelationNecessityAssociation table linking medication relations to entities specified as route
MedicationRelationModifierAssociation table linking medication relations to entities specified as route
MedicationRelationDurationAssociation table linking medication relations to entities specified as duration
MedicationRelationIndicationAssociation table linking medication relations to entities specified as indication
MedicationRelationDatetimeAssociation table linking medication relations to entities specified as datetimes.
TemporalityRelationModifierAssociation table linking temporality relations to entities specified as modifiers
ReportedEventRelationToEntityAssociation table linking reported-event relations to entities which were recipients of the communication.
ReportedEventRelationFromEntityAssociation table linking reported-event relations to entities which were sources of the communication.
ReportedEventRelationMethodAssociation table linking reported-event relations to entities which were the methods of communication
ReportedEventRelationTimeExpressionAssociation table linking reported-event relations to entities which were the time expressions that indicate when the communication took place

Functions

NameDescription
recreate_indexesRe-create all the full text search indexes.

Data

_supported_indexes_for _model_type_registry

API

emtellipro.db.schemas.legacy.models.Base

1class emtellipro.db.schemas.legacy.models.Base

Bases: sqlalchemy.orm.DeclarativeBase

The base of all tables.

Base.metadata
1metadata

Value: create_metadata(...)

Base.__tablename__
1__tablename__()

emtellipro.db.schemas.legacy.models.AlembicVersion

1class emtellipro.db.schemas.legacy.models.AlembicVersion

Bases: emtellipro.db.schemas.legacy.models.Base

Table containg the alembic version. It’s defined here so that we can easily create and drop it along with all the other tables.

AlembicVersion.__tablename__
1__tablename__

Value: alembic_version

AlembicVersion.version_num
1version_num

Value: Column(...)

AlembicVersion.__table_args__
1__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.ProcessingDetails

1class emtellipro.db.schemas.legacy.models.ProcessingDetails

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing details about the job submitted for processing.

ProcessingDetails.id
1id

Value: Column(...)

ProcessingDetails.job_id
1job_id

Value: Column(...)

ProcessingDetails.submit_timestamp
1submit_timestamp

Value: Column(...)

ProcessingDetails.task_id
1task_id

Value: Column(...)

ProcessingDetails.engine_version
1engine_version

Value: Column(...)

ProcessingDetails.sdk_version
1sdk_version

Value: Column(...)

ProcessingDetails.sql_query
1sql_query

Value: Column(...)

emtellipro.db.schemas.legacy.models.DocumentMetadata

1class emtellipro.db.schemas.legacy.models.DocumentMetadata

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing arbitrary metadata for each document.

DocumentMetadata.id
1id

Value: Column(...)

DocumentMetadata.document_id
1document_id

Value: Column(...)

DocumentMetadata.document
1document

Value: relationship(...)

DocumentMetadata.source_document_id
1source_document_id

Value: Column(...)

DocumentMetadata.source_document_id_2
1source_document_id_2

Value: Column(...)

DocumentMetadata.source_document_id_3
1source_document_id_3

Value: Column(...)

DocumentMetadata.original_category
1original_category

Value: Column(...)

DocumentMetadata.original_subcategory
1original_subcategory

Value: Column(...)

DocumentMetadata.clinical_domain
1clinical_domain

Value: Column(...)

DocumentMetadata.institution
1institution

Value: Column(...)

DocumentMetadata.subject_id
1subject_id

Value: Column(...)

DocumentMetadata.subject_id_2
1subject_id_2

Value: Column(...)

DocumentMetadata.description
1description

Value: Column(...)

DocumentMetadata.hadm_id
1hadm_id

Value: Column(...)

DocumentMetadata.chartdate
1chartdate

Value: Column(...)

DocumentMetadata.encounterdate
1encounterdate

Value: Column(...)

DocumentMetadata.author_name
1author_name

Value: Column(...)

DocumentMetadata.subject_name
1subject_name

Value: Column(...)

DocumentMetadata.subject_dob
1subject_dob

Value: Column(...)

DocumentMetadata.subject_gender
1subject_gender

Value: Column(...)

DocumentMetadata.subject_address
1subject_address

Value: Column(...)

DocumentMetadata.requestor
1requestor

Value: Column(...)

DocumentMetadata.document_summary
1document_summary

Value: Column(...)

DocumentMetadata.predefined_names
1predefined_names

Value: ['author_name', 'chartdate', 'encounterdate', 'clinical_domain', 'description', 'document_summary', 'hadm_id', 'institution', 'original_category', 'original_subcategory', 'requestor', 'source_document_id', 'source_document_id_2', 'source_document_id_3', 'subject_address', 'subject_dob', 'subject_gender', 'subject_id', 'subject_id_2', 'subject_name']

DocumentMetadata.__table_args__
1__table_args__

Value: ()

DocumentMetadata.parse_dates
1parse_dates(
2    metadata, parse_dates = False
3)

Optionally parse dates in the metadata. This also converts empty strings to None.

emtellipro.db.schemas.legacy.models.DocumentStructuredMetadata

1class emtellipro.db.schemas.legacy.models.DocumentStructuredMetadata

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing arbitrary metadata for each document.

DocumentStructuredMetadata.id
1id

Value: Column(...)

DocumentStructuredMetadata.document_id
1document_id

Value: Column(...)

DocumentStructuredMetadata.document
1document

Value: relationship(...)

DocumentStructuredMetadata.key
1key

Value: Column(...)

DocumentStructuredMetadata.value
1value

Value: Column(...)

emtellipro.db.schemas.legacy.models.Document

1class emtellipro.db.schemas.legacy.models.Document

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing details specific the the overall document that was processed.

Document.id
1id

Value: Column(...)

Document.category
1category

Value: Column(...)

Document.subcategory
1subcategory

Value: Column(...)

Document.filename
1filename

Value: Column(...)

Document.section_label
1section_label

Value: Column(...)

Document.text
1text

Value: Column(...)

Document.json_representation
1json_representation

Value: Column(...)

Document.processing_status
1processing_status

Value: Column(...)

Document.processing_details_id
1processing_details_id

Value: Column(...)

Document.source_type
1source_type

Value: Column(...)

Document.source_path
1source_path

Value: Column(...)

Document.source_size
1source_size

Value: Column(...)

Document.processing_details
1processing_details

Value: relationship(...)

Document.concepts
1concepts

Value: relationship(...)

Document.entities
1entities

Value: relationship(...)

Document.relations
1relations

Value: relationship(...)

Document.locations
1locations

Value: relationship(...)

Document.ontology_versions
1ontology_versions

Value: relationship(...)

emtellipro.db.schemas.legacy.models.DocumentSourceChunk

1class emtellipro.db.schemas.legacy.models.DocumentSourceChunk

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing chunks of source data.

This is useful for storing the original PDF data if you’ve extracted the text from it and have used the plaintext for processing.

DocumentSourceChunk.document_id
1document_id

Value: Column(...)

DocumentSourceChunk.offset
1offset

Value: Column(...)

DocumentSourceChunk.data
1data

Value: Column(...)

emtellipro.db.schemas.legacy.models.OntologyVersion

1class emtellipro.db.schemas.legacy.models.OntologyVersion

Bases: emtellipro.db.schemas.legacy.models.Base

Table of ontology versions for each document.

OntologyVersion.document_id
1document_id

Value: Column(...)

OntologyVersion.ontology
1ontology

Value: Column(...)

OntologyVersion.release_version
1release_version

Value: Column(...)

OntologyVersion.document
1document

Value: relationship(...)

emtellipro.db.schemas.legacy.models.Entity

1class emtellipro.db.schemas.legacy.models.Entity

Bases: emtellipro.db.schemas.legacy.models.Base

Table of entities stored in a specific document. The entity information is stored in different tables depending on entity type. The “type_column can be used along with theentity_id` to determine which exact entity is referred to.

Entity.id
1id

Value: Column(...)

Entity.type_
1type_

Value: Column(...)

Entity.document_id
1document_id

Value: Column(...)

Entity.entity_id
1entity_id

Value: Column(...)

Entity.entity
1entity

The actual *Entity instance this relation references.

emtellipro.db.schemas.legacy.models.AssumedEntity

1class emtellipro.db.schemas.legacy.models.AssumedEntity

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing assumed entities.

AssumedEntity.id
1id

Value: Column(...)

AssumedEntity.value
1value

Value: Column(...)

AssumedEntity.document_id
1document_id

Value: Column(...)

AssumedEntity.document
1document

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntity

1class emtellipro.db.schemas.legacy.models.FoundEntity

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing found entities.

FoundEntity.id
1id

Value: Column(...)

FoundEntity.polarity
1polarity

Value: Column(...)

FoundEntity.section_name
1section_name

Value: Column(...)

FoundEntity.uncertainty
1uncertainty

Value: Column(...)

FoundEntity.known_ambiguity
1known_ambiguity

Value: Column(...)

FoundEntity.question_status
1question_status

Value: Column(...)

FoundEntity.guidance
1guidance

Value: Column(...)

FoundEntity.experiencer
1experiencer

Value: Column(...)

FoundEntity.factuality
1factuality

Value: Column(...)

FoundEntity.heading_status
1heading_status

Value: Column(...)

FoundEntity.text
1text

Value: Column(...)

FoundEntity.start
1start

Value: Column(...)

FoundEntity.document_id
1document_id

Value: Column(...)

FoundEntity.document
1document

Value: relationship(...)

FoundEntity.concepts
1concepts

Value: relationship(...)

FoundEntity.locations
1locations

Value: relationship(...)

FoundEntity.spans
1spans

Value: relationship(...)

FoundEntity.type_names
1type_names

Value: relationship(...)

FoundEntity.measurement_units
1measurement_units

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntityMeasurementUnit

1class emtellipro.db.schemas.legacy.models.FoundEntityMeasurementUnit

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing the measurement units for a found entity

FoundEntityMeasurementUnit.id
1id

Value: Column(...)

FoundEntityMeasurementUnit.found_entity_id
1found_entity_id

Value: Column(...)

FoundEntityMeasurementUnit.text
1text

Value: Column(...)

emtellipro.db.schemas.legacy.models.FoundEntityType

1class emtellipro.db.schemas.legacy.models.FoundEntityType

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing the type_name information from found entities.

Note that all 3 columns form the primary key since there is a unique type name per ontology per found entity.

FoundEntityType.found_entity_id
1found_entity_id

Value: Column(...)

FoundEntityType.ontology
1ontology

Value: Column(...)

FoundEntityType.type_name
1type_name

Value: Column(...)

emtellipro.db.schemas.legacy.models.Concept

1class emtellipro.db.schemas.legacy.models.Concept

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing information about a specific column, with the primary keys being the concept_id and ontology.

Concept.concept_id
1concept_id

Value: Column(...)

Concept.ontology
1ontology

Value: Column(...)

Concept.description
1description

Value: Column(...)

Concept.documents
1documents

Value: relationship(...)

Concept.found_entities
1found_entities

Value: relationship(...)

emtellipro.db.schemas.legacy.models.FoundEntitySpan

1class emtellipro.db.schemas.legacy.models.FoundEntitySpan

Bases: emtellipro.db.schemas.legacy.models.Base

Table containging spans contained in found entities.

FoundEntitySpan.id
1id

Value: Column(...)

FoundEntitySpan.start
1start

Value: Column(...)

FoundEntitySpan.end
1end

Value: Column(...)

FoundEntitySpan.text
1text

Value: Column(...)

FoundEntitySpan.found_entity_id
1found_entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.SentenceLocation

1class emtellipro.db.schemas.legacy.models.SentenceLocation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence locations. It exists mainly as a link between the locations table and the spans.

SentenceLocation.id
1id

Value: Column(...)

SentenceLocation.text
1text

Value: Column(...)

SentenceLocation.spans
1spans

Value: relationship(...)

SentenceLocation.sections
1sections

Value: relationship(...)

emtellipro.db.schemas.legacy.models.SentenceLocationSpan

1class emtellipro.db.schemas.legacy.models.SentenceLocationSpan

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence location spans

SentenceLocationSpan.id
1id

Value: Column(...)

SentenceLocationSpan.start
1start

Value: Column(...)

SentenceLocationSpan.end
1end

Value: Column(...)

SentenceLocationSpan.sentence_location_id
1sentence_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.HeadingLocation

1class emtellipro.db.schemas.legacy.models.HeadingLocation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing heading locations. It exists mainly as a link between the locations table and the spans.

HeadingLocation.id
1id

Value: Column(...)

HeadingLocation.text
1text

Value: Column(...)

HeadingLocation.section_location_id
1section_location_id

Value: Column(...)

HeadingLocation.spans
1spans

Value: relationship(...)

HeadingLocation.section
1section

Value: relationship(...)

emtellipro.db.schemas.legacy.models.HeadingLocationSpan

1class emtellipro.db.schemas.legacy.models.HeadingLocationSpan

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing heading location spans

HeadingLocationSpan.id
1id

Value: Column(...)

HeadingLocationSpan.start
1start

Value: Column(...)

HeadingLocationSpan.end
1end

Value: Column(...)

HeadingLocationSpan.heading_location_id
1heading_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.PageLocation

1class emtellipro.db.schemas.legacy.models.PageLocation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing page locations. It exists mainly as a link between the locations table and the spans.

PageLocation.id
1id

Value: Column(...)

PageLocation.text
1text

Value: Column(...)

PageLocation.page_index
1page_index

Value: Column(...)

PageLocation.spans
1spans

Value: relationship(...)

PageLocation.sections
1sections

Value: relationship(...)

emtellipro.db.schemas.legacy.models.PageLocationSpan

1class emtellipro.db.schemas.legacy.models.PageLocationSpan

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing page location spans

PageLocationSpan.id
1id

Value: Column(...)

PageLocationSpan.start
1start

Value: Column(...)

PageLocationSpan.end
1end

Value: Column(...)

PageLocationSpan.page_location_id
1page_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.PageSection

1class emtellipro.db.schemas.legacy.models.PageSection

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links between pages and section, with a composite primary key of page_id and section_id.

PageSection.page_id
1page_id

Value: Column(...)

PageSection.section_id
1section_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.Relation

1class emtellipro.db.schemas.legacy.models.Relation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links to all the different kinds of relations. Use the type_ and relation_id fields to find the actual relation in one of the other *Relation tables.

Relation.id
1id

Value: Column(...)

Relation.type_
1type_

Value: Column(...)

Relation.document_id
1document_id

Value: Column(...)

Relation.relation_id
1relation_id

Value: Column(...)

Relation.relation
1relation

The actual *Relation instance this relation references.

emtellipro.db.schemas.legacy.models.Location

1class emtellipro.db.schemas.legacy.models.Location

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links to all the different kinds of locations. Use the type_ and location_id fields to find the actual location in one of the other *Location tables.

Location.id
1id

Value: Column(...)

Location.type_
1type_

Value: Column(...)

Location.document_id
1document_id

Value: Column(...)

Location.location_id
1location_id

Value: Column(...)

Location.location
1location

The actual *Location instance this relation references.

emtellipro.db.schemas.legacy.models.SectionLocationSpan

1class emtellipro.db.schemas.legacy.models.SectionLocationSpan

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing sentence location span information.

SectionLocationSpan.id
1id

Value: Column(...)

SectionLocationSpan.start
1start

Value: Column(...)

SectionLocationSpan.end
1end

Value: Column(...)

SectionLocationSpan.section_location_id
1section_location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelation

1class emtellipro.db.schemas.legacy.models.ImageLinkRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing image link relation information.

ImageLinkRelation.id
1id

Value: Column(...)

ImageLinkRelation.image_findings
1image_findings

Value: relationship(...)

ImageLinkRelation.references
1references

Value: relationship(...)

ImageLinkRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelation

1class emtellipro.db.schemas.legacy.models.FollowupRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containign follow-up relation information.

FollowupRelation.id
1id

Value: Column(...)

FollowupRelation.polarity
1polarity

Value: Column(...)

FollowupRelation.time_expression_id
1time_expression_id

Value: Column(...)

FollowupRelation.time_expression
1time_expression

Value: relationship(...)

FollowupRelation.procedures
1procedures

Value: relationship(...)

FollowupRelation.reasons
1reasons

Value: relationship(...)

FollowupRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.ExperiencerRelation

1class emtellipro.db.schemas.legacy.models.ExperiencerRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing experience relation information.

ExperiencerRelation.id
1id

Value: Column(...)

ExperiencerRelation.polarity
1polarity

Value: Column(...)

ExperiencerRelation.experiencer_id
1experiencer_id

Value: Column(...)

ExperiencerRelation.experienced_id
1experienced_id

Value: Column(...)

ExperiencerRelation.experiencer
1experiencer

Value: relationship(...)

ExperiencerRelation.experienced
1experienced

Value: relationship(...)

ExperiencerRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.MeasurementRelation

1class emtellipro.db.schemas.legacy.models.MeasurementRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing measurement relations.

MeasurementRelation.id
1id

Value: Column(...)

MeasurementRelation.subject_id
1subject_id

Value: Column(...)

MeasurementRelation.value_id
1value_id

Value: Column(...)

MeasurementRelation.subject
1subject

Value: relationship(...)

MeasurementRelation.value
1value

Value: relationship(...)

MeasurementRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.QualifierRelation

1class emtellipro.db.schemas.legacy.models.QualifierRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing qualifier relations.

QualifierRelation.id
1id

Value: Column(...)

QualifierRelation.qualifier_type
1qualifier_type

Value: Column(...)

QualifierRelation.qualifier_id
1qualifier_id

Value: Column(...)

QualifierRelation.qualifies_id
1qualifies_id

Value: Column(...)

QualifierRelation.qualifier
1qualifier

Value: relationship(...)

QualifierRelation.qualifies
1qualifies

Value: relationship(...)

QualifierRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelation

1class emtellipro.db.schemas.legacy.models.MedicationRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing medication relations.

MedicationRelation.id
1id

Value: Column(...)

MedicationRelation.drug_entity_id
1drug_entity_id

Value: Column(...)

MedicationRelation.drug
1drug

Value: relationship(...)

MedicationRelation.dosages
1dosages

Value: relationship(...)

MedicationRelation.frequencies
1frequencies

Value: relationship(...)

MedicationRelation.modes
1modes

Value: relationship(...)

MedicationRelation.quantities
1quantities

Value: relationship(...)

MedicationRelation.routes
1routes

Value: relationship(...)

MedicationRelation.necessities
1necessities

Value: relationship(...)

MedicationRelation.modifiers
1modifiers

Value: relationship(...)

MedicationRelation.durations
1durations

Value: relationship(...)

MedicationRelation.indications
1indications

Value: relationship(...)

MedicationRelation.date_times
1date_times

Value: relationship(...)

MedicationRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.TemporalityRelation

1class emtellipro.db.schemas.legacy.models.TemporalityRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing temporality relations.

TemporalityRelation.id
1id

Value: Column(...)

TemporalityRelation.polarity
1polarity

Value: Column(...)

TemporalityRelation.category
1category

Value: Column(...)

TemporalityRelation.temporal_entity_id
1temporal_entity_id

Value: Column(...)

TemporalityRelation.subject_id
1subject_id

Value: Column(...)

TemporalityRelation.temporal_entity
1temporal_entity

Value: relationship(...)

TemporalityRelation.subject
1subject

Value: relationship(...)

TemporalityRelation.modifiers
1modifiers

Value: relationship(...)

TemporalityRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelation

1class emtellipro.db.schemas.legacy.models.ReportedEventRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing reported event relations.

ReportedEventRelation.id
1id

Value: Column(...)

ReportedEventRelation.polarity
1polarity

Value: Column(...)

ReportedEventRelation.category
1category

Value: Column(...)

ReportedEventRelation.subject_id
1subject_id

Value: Column(...)

ReportedEventRelation.subject
1subject

Value: relationship(...)

ReportedEventRelation.to_entities
1to_entities

Value: relationship(...)

ReportedEventRelation.from_entities
1from_entities

Value: relationship(...)

ReportedEventRelation.methods
1methods

Value: relationship(...)

ReportedEventRelation.time_expressions
1time_expressions

Value: relationship(...)

ReportedEventRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.AnatomicSiteRelation

1class emtellipro.db.schemas.legacy.models.AnatomicSiteRelation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing anatomic site relations.

AnatomicSiteRelation.id
1id

Value: Column(...)

AnatomicSiteRelation.site_id
1site_id

Value: Column(...)

AnatomicSiteRelation.situated_entity_id
1situated_entity_id

Value: Column(...)

AnatomicSiteRelation.site
1site

Value: relationship(...)

AnatomicSiteRelation.situated_entity
1situated_entity

Value: relationship(...)

AnatomicSiteRelation.confidence
1confidence

Value: Column(...)

emtellipro.db.schemas.legacy.models.SectionLocation

1class emtellipro.db.schemas.legacy.models.SectionLocation

Bases: emtellipro.db.schemas.legacy.models.Base

Table containg section locations.

SectionLocation.id
1id

Value: Column(...)

SectionLocation.name
1name

Value: Column(...)

SectionLocation.level
1level

Value: Column(...)

SectionLocation.parent_id
1parent_id

Value: Column(...)

SectionLocation.text
1text

Value: Column(...)

SectionLocation.children
1children

Value: relationship(...)

SectionLocation.spans
1spans

Value: relationship(...)

SectionLocation.pages
1pages

Value: relationship(...)

SectionLocation.sentences
1sentences

Value: relationship(...)

emtellipro.db.schemas.legacy.models.SentenceSection

1class emtellipro.db.schemas.legacy.models.SentenceSection

Bases: emtellipro.db.schemas.legacy.models.Base

Table containing links between sentences and section, with a composite primary key of sentence_id and section_id.

SentenceSection.sentence_id
1sentence_id

Value: Column(...)

SentenceSection.section_id
1section_id

Value: Column(...)

SentenceSection.sentence
1sentence

Value: relationship(...)

SentenceSection.section
1section

Value: relationship(...)

emtellipro.db.schemas.legacy.models.DocumentConcept

1class emtellipro.db.schemas.legacy.models.DocumentConcept

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking documents to concepts.

DocumentConcept.document_id
1document_id

Value: Column(...)

DocumentConcept.concept_id
1concept_id

Value: Column(...)

DocumentConcept.concept_ontology
1concept_ontology

Value: Column(...)

DocumentConcept.__table_args__
1__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.FoundEntityConcept

1class emtellipro.db.schemas.legacy.models.FoundEntityConcept

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking found entities to concepts.

FoundEntityConcept.found_entity_id
1found_entity_id

Value: Column(...)

FoundEntityConcept.concept_id
1concept_id

Value: Column(...)

FoundEntityConcept.concept_ontology
1concept_ontology

Value: Column(...)

FoundEntityConcept.confidence
1confidence

Value: Column(...)

FoundEntityConcept.__table_args__
1__table_args__

Value: ()

emtellipro.db.schemas.legacy.models.FoundEntityLocation

1class emtellipro.db.schemas.legacy.models.FoundEntityLocation

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking found entities to locations.

FoundEntityLocation.found_entity_id
1found_entity_id

Value: Column(...)

FoundEntityLocation.location_id
1location_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelationImageFinding

1class emtellipro.db.schemas.legacy.models.ImageLinkRelationImageFinding

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking image link relations to entities specified as image findings.

1imagelink_id

Value: Column(...)

ImageLinkRelationImageFinding.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ImageLinkRelationReference

1class emtellipro.db.schemas.legacy.models.ImageLinkRelationReference

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking image link relations to entities specified as references.

1imagelink_id

Value: Column(...)

ImageLinkRelationReference.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelationProcedure

1class emtellipro.db.schemas.legacy.models.FollowupRelationProcedure

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking followup relations to entities specified as procedures.

FollowupRelationProcedure.followup_id
1followup_id

Value: Column(...)

FollowupRelationProcedure.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.FollowupRelationReason

1class emtellipro.db.schemas.legacy.models.FollowupRelationReason

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking followup relations to entities specified as reasons.

FollowupRelationReason.followup_id
1followup_id

Value: Column(...)

FollowupRelationReason.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDosage

1class emtellipro.db.schemas.legacy.models.MedicationRelationDosage

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as dosage

MedicationRelationDosage.id
1id

Value: Column(...)

MedicationRelationDosage.medication_id
1medication_id

Value: Column(...)

MedicationRelationDosage.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationFrequency

1class emtellipro.db.schemas.legacy.models.MedicationRelationFrequency

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as frequency

MedicationRelationFrequency.id
1id

Value: Column(...)

MedicationRelationFrequency.medication_id
1medication_id

Value: Column(...)

MedicationRelationFrequency.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationMode

1class emtellipro.db.schemas.legacy.models.MedicationRelationMode

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as mode

MedicationRelationMode.id
1id

Value: Column(...)

MedicationRelationMode.medication_id
1medication_id

Value: Column(...)

MedicationRelationMode.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationQuantity

1class emtellipro.db.schemas.legacy.models.MedicationRelationQuantity

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as quantity

MedicationRelationQuantity.id
1id

Value: Column(...)

MedicationRelationQuantity.medication_id
1medication_id

Value: Column(...)

MedicationRelationQuantity.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationRoute

1class emtellipro.db.schemas.legacy.models.MedicationRelationRoute

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationRoute.id
1id

Value: Column(...)

MedicationRelationRoute.medication_id
1medication_id

Value: Column(...)

MedicationRelationRoute.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationNecessity

1class emtellipro.db.schemas.legacy.models.MedicationRelationNecessity

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationNecessity.id
1id

Value: Column(...)

MedicationRelationNecessity.medication_id
1medication_id

Value: Column(...)

MedicationRelationNecessity.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationModifier

1class emtellipro.db.schemas.legacy.models.MedicationRelationModifier

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as route

MedicationRelationModifier.id
1id

Value: Column(...)

MedicationRelationModifier.medication_id
1medication_id

Value: Column(...)

MedicationRelationModifier.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDuration

1class emtellipro.db.schemas.legacy.models.MedicationRelationDuration

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as duration

MedicationRelationDuration.id
1id

Value: Column(...)

MedicationRelationDuration.medication_id
1medication_id

Value: Column(...)

MedicationRelationDuration.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationIndication

1class emtellipro.db.schemas.legacy.models.MedicationRelationIndication

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as indication

MedicationRelationIndication.id
1id

Value: Column(...)

MedicationRelationIndication.medication_id
1medication_id

Value: Column(...)

MedicationRelationIndication.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.MedicationRelationDatetime

1class emtellipro.db.schemas.legacy.models.MedicationRelationDatetime

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking medication relations to entities specified as datetimes.

MedicationRelationDatetime.id
1id

Value: Column(...)

MedicationRelationDatetime.medication_id
1medication_id

Value: Column(...)

MedicationRelationDatetime.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.TemporalityRelationModifier

1class emtellipro.db.schemas.legacy.models.TemporalityRelationModifier

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking temporality relations to entities specified as modifiers

TemporalityRelationModifier.id
1id

Value: Column(...)

TemporalityRelationModifier.temporality_id
1temporality_id

Value: Column(...)

TemporalityRelationModifier.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationToEntity

1class emtellipro.db.schemas.legacy.models.ReportedEventRelationToEntity

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were recipients of the communication.

ReportedEventRelationToEntity.reported_event_id
1reported_event_id

Value: Column(...)

ReportedEventRelationToEntity.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationFromEntity

1class emtellipro.db.schemas.legacy.models.ReportedEventRelationFromEntity

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were sources of the communication.

ReportedEventRelationFromEntity.reported_event_id
1reported_event_id

Value: Column(...)

ReportedEventRelationFromEntity.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationMethod

1class emtellipro.db.schemas.legacy.models.ReportedEventRelationMethod

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were the methods of communication

ReportedEventRelationMethod.reported_event_id
1reported_event_id

Value: Column(...)

ReportedEventRelationMethod.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.ReportedEventRelationTimeExpression

1class emtellipro.db.schemas.legacy.models.ReportedEventRelationTimeExpression

Bases: emtellipro.db.schemas.legacy.models.Base

Association table linking reported-event relations to entities which were the time expressions that indicate when the communication took place

ReportedEventRelationTimeExpression.reported_event_id
1reported_event_id

Value: Column(...)

ReportedEventRelationTimeExpression.entity_id
1entity_id

Value: Column(...)

emtellipro.db.schemas.legacy.models.recreate_indexes

1emtellipro.db.schemas.legacy.models.recreate_indexes(connection)

Re-create all the full text search indexes.

This is normally executed by the migrate and create-db commands

Parameters:

connection

this is an SQLAlchemy connection object

Returns:

number of indexes created