OMOP_5.4_ER_ALL

OMOP_5.4_ER : Model

Entity - note_nlp link

Properties
Name Value
Description

 

NOTE_NLP

Table Description

The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note.

CDM Field User Guide ETL Conventions Datatype Required Primary Key Foreign Key FK Table FK Domain
note_nlp_id A unique identifier for the NLP record. integer Yes Yes No
note_id This is the NOTE_ID for the NOTE record the NLP record is associated to. integer Yes No No
section_concept_id The SECTION_CONCEPT_ID should be used to represent the note section contained in the NOTE_NLP record. These concepts can be found as parts of document panels and are based on the type of note written, i.e. a discharge summary. These panels can be found as concepts with the relationship ‘Subsumes’ to CONCEPT_ID 45875957. integer No No Yes CONCEPT
snippet A small window of text surrounding the term varchar(250) No No No
“offset” Character offset of the extracted term in the input note varchar(50) No No No
lexical_variant Raw text extracted from the NLP tool. varchar(250) Yes No No
note_nlp_concept_id integer No No Yes CONCEPT
note_nlp_source_concept_id integer No No Yes CONCEPT
nlp_system Name and version of the NLP system that extracted the term. Useful for data provenance. varchar(250) No No No
nlp_date The date of the note processing. date Yes No No
nlp_datetime The date and time of the note processing. datetime No No No
term_exists Term_exists is defined as a flag that indicates if the patient actually has or had the condition. Any of the following modifiers would make Term_exists false: Negation = true Subject = [anything other than the patient] Conditional = true/li> Rule_out = true Uncertain = very low certainty or any lower certainties A complete lack of modifiers would make Term_exists true. varchar(1) No No No
term_temporal Term_temporal is to indicate if a condition is present or just in the past. The following would be past:

- History = true - Concept_date = anything before the time of the report
varchar(50) No No No
term_modifiers For the modifiers that are there, they would have to have these values:

- Negation = false - Subject = patient - Conditional = false - Rule_out = false - Uncertain = true or high or moderate or even low (could argue about low). Term_modifiers will concatenate all modifiers for different types of entities (conditions, drugs, labs etc) into one string. Lab values will be saved as one of the modifiers.
varchar(2000) No No No

Data Model Physical
Primary Key Constraint Name xpk_note_nlp
Primary Key Clustered Unspecified
Unlogged false

Columns Summary
Column Name Data Type PK / FK Nullable Description
note_nlp_id int4 PK No
note_id int4 No
section_concept_id int4 PK / FK No
snippet varchar(250) Yes
offset varchar(50) Yes
lexical_variant varchar(250) No
note_nlp_concept_id int4 PK / FK No
note_nlp_source_concept_id int4 PK / FK No
nlp_system varchar(250) Yes
nlp_date date No
nlp_datetime timestamp(0) Yes
term_exists varchar(1) Yes
term_temporal varchar(50) Yes
term_modifiers varchar(2000) Yes

Relationships Summary
Name Begin End
 fpk_note_nlp_section_concept_id : Relationship
 concept : Entity
 note_nlp : Entity
 fpk_note_nlp_note_nlp_concept_id : Relationship
 concept : Entity
 note_nlp : Entity
 fpk_note_nlp_note_nlp_source_concept_id : Relationship
 concept : Entity
 note_nlp : Entity

Columns Detail
Name Value
Name note_nlp_id
Type int4
Nullable false
Unique false
Primary Key true
Index false
Length 0
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name note_id
Type int4
Nullable false
Unique false
Primary Key false
Index false
Length 0
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name section_concept_id
Type int4
Nullable false
Unique false
Primary Key true
Index false
Length 0
Scale 0
Id Generator native
Foreign Key true
Generated Unspecified
Sync To Attribute Yes

Name Value
Name snippet
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 250
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name offset
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 50
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name lexical_variant
Type varchar
Nullable false
Unique false
Primary Key false
Index false
Type Name varchar
Length 250
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name note_nlp_concept_id
Type int4
Nullable false
Unique false
Primary Key true
Index false
Length 0
Scale 0
Id Generator native
Foreign Key true
Generated Unspecified
Sync To Attribute Yes

Name Value
Name note_nlp_source_concept_id
Type int4
Nullable false
Unique false
Primary Key true
Index false
Length 0
Scale 0
Id Generator native
Foreign Key true
Generated Unspecified
Sync To Attribute Yes

Name Value
Name nlp_system
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 250
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name nlp_date
Type date
Nullable false
Unique false
Primary Key false
Index false
Type Name date
Length 0
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name nlp_datetime
Type timestamp
Nullable true
Unique false
Primary Key false
Index false
Type Name timestamp
Length 0
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name term_exists
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 1
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name term_temporal
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 50
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Name Value
Name term_modifiers
Type varchar
Nullable true
Unique false
Primary Key false
Index false
Type Name varchar
Length 2000
Scale 0
Id Generator native
Foreign Key false
Generated Unspecified
Sync To Attribute Yes

Relationships Detail
Name Value
Name fpk_note_nlp_section_concept_id
Foreign Key
note_nlp
 section_concept_id : Column
Primary Key
concept
 concept_id : Column
To Multiplicity 0..*
From Multiplicity 1
Sync To Association Yes
Data Model Physical

Name Value
Name fpk_note_nlp_note_nlp_concept_id
Foreign Key
note_nlp
 note_nlp_concept_id : Column
Primary Key
concept
 concept_id : Column
To Multiplicity 0..*
From Multiplicity 1
Sync To Association Yes
Data Model Physical

Name Value
Name fpk_note_nlp_note_nlp_source_concept_id
Foreign Key
note_nlp
 note_nlp_source_concept_id : Column
Primary Key
concept
 concept_id : Column
To Multiplicity 0..*
From Multiplicity 1
Sync To Association Yes
Data Model Physical

Appears In
Diagram
 Standardized_Tables : Entity Relationship Diagram
 Vocabulary_With_Standard : Entity Relationship Diagram
OMOP_5.4_ER_ALL