ID

35337

Beschrijving

OMOP Common Data Model (CDM) Note NLP The NOTE_NLP table will encode all output of NLP on clinical notes. Each row represents a single extracted term from a note. OMOP Common Data Model Version 6.0 Specifications 11October2018. The Observational Medical Outcomes Partnership (OMOP) was a public-private partnership established to inform the appropriate use of observational healthcare databases for studying the effects of medical products. © 2014 Observational Health Data Sciences and Informatics. This work is based on work by the Observational Medical Outcomes Partnership (OMOP) and used under license from the FNIH at http://omop.fnih.org/publiclicense. Version updated on 28.02.2019, from https://github.com/OHDSI/CommonDataModel/wiki/NOTE_NLP 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. 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)

Link

http://omop.fnih.org/publiclicense

Trefwoorden

Versies (1)
  1. 28-02-19 28-02-19 -
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Observational Medical Outcomes Partnership (OMOP)

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28 februari 2019

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Creative Commons BY-NC 3.0
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OMOP Common Data Model (CDM)

Engels

Note NLP

1 Formulieren  
  1. StudyEvent: ODM
    1. Note NLP
Note NLP
Beschrijving

Note NLP

Alias
UMLS CUI-1
C1317574
UMLS CUI-2
C0027489
Note NLP ID
Beschrijving

A unique identifier for each term extracted from a note.

Datatype

integer

Alias
UMLS CUI [1,1]
C1317574
UMLS CUI [1,2]
C0027489
UMLS CUI [1,3]
C1300638
Note ID
Beschrijving

A foreign key to the Note table note the term was

Datatype

integer

Alias
UMLS CUI [1,1]
C1317574
UMLS CUI [1,2]
C1300638
Section concept ID
Beschrijving

A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.

Datatype

integer

Alias
UMLS CUI [1,1]
C1828479
UMLS CUI [1,2]
C0178566
UMLS CUI [1,3]
C1300638
Snippet
Beschrijving

A small window of text surrounding the term. (Type varchar(250))

Datatype

text

Alias
UMLS CUI [1,1]
C2826302
UMLS CUI [1,2]
C1546922
Offset
Beschrijving

Character offset of the extracted term in the input note. (Type varchar(50))

Datatype

text

Alias
UMLS CUI [1,1]
C1711330
UMLS CUI [1,2]
C2826302
UMLS CUI [1,3]
C1708517
UMLS CUI [1,4]
C1317574
Lexical variant
Beschrijving

Raw text extracted from the NLP tool. (Type varchar(250))

Datatype

text

Alias
UMLS CUI [1,1]
C1527021
UMLS CUI [1,2]
C0027489
Note NLP concept ID
Beschrijving

A foreign key to the predefined Concept in the Standardized Vocabularies reflecting the normalized concept for the extracted term. Domain of the term is represented as part of the Concept table.

Datatype

integer

Alias
UMLS CUI [1,1]
C1317574
UMLS CUI [1,2]
C0027489
UMLS CUI [1,3]
C0178566
UMLS CUI [1,4]
C1300638
Note NLP source concept ID
Beschrijving

A foreign key to a Concept that refers to the code in the source vocabulary used by the NLP system

Datatype

integer

Alias
UMLS CUI [1,1]
C1317574
UMLS CUI [1,2]
C0027489
UMLS CUI [1,3]
C0449416
UMLS CUI [1,4]
C0178566
UMLS CUI [1,5]
C1300638
NLP system
Beschrijving

Name and version of the NLP system that extracted the term.Useful for data provenance. (Type varchar(250))

Datatype

text

Alias
UMLS CUI [1,1]
C0027489
UMLS CUI [1,2]
C0333052
NLP date
Beschrijving

The date of the note processing.Useful for data provenance.

Datatype

date

Alias
UMLS CUI [1,1]
C0027489
UMLS CUI [1,2]
C0011008
NLP datetime
Beschrijving

The date and time of the note processing. Useful for data provenance.

Datatype

datetime

Alias
UMLS CUI [1,1]
C0027489
UMLS CUI [1,2]
C0011008
UMLS CUI [1,3]
C0040223
Term exists
Beschrijving

A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying. (Type varchar(1))

Datatype

text

Alias
UMLS CUI [1,1]
C2826302
UMLS CUI [1,2]
C0150312
UMLS CUI [2,1]
C2826302
UMLS CUI [2,2]
C0332197
Term temporal
Beschrijving

An optional time modifier associated with the extracted term. (for now “past” or “present” only). Standardize it later. 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 (Type varchar(50))

Datatype

text

Alias
UMLS CUI [1,1]
C2826302
UMLS CUI [1,2]
C1444637
UMLS CUI [2,1]
C2826302
UMLS CUI [2,2]
C0150312
Term modifiers
Beschrijving

A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. “son has rash” ? “negated=no,subject=family, certainty=undef,conditional=false,general=false”). 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. A list of allowable modifiers (e.g., signature for medications) and their possible values will be standardized later. (Type varchar(2000))

Datatype

text

Alias
UMLS CUI [1,1]
C2826302
UMLS CUI [1,2]
C3840684
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Similar models

Note NLP

1 Formulieren
  1. StudyEvent: ODM
    1. Note NLP
Name
Type
Description | Question | Decode (Coded Value)
Datatype
Alias
Item Group
Note NLP
C1317574 (UMLS CUI-1)
C0027489 (UMLS CUI-2)
Note NLP ID
Item
Note NLP ID
integer
C1317574 (UMLS CUI [1,1])
C0027489 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Note ID
Item
Note ID
integer
C1317574 (UMLS CUI [1,1])
C1300638 (UMLS CUI [1,2])
Section concept ID
Item
Section concept ID
integer
C1828479 (UMLS CUI [1,1])
C0178566 (UMLS CUI [1,2])
C1300638 (UMLS CUI [1,3])
Snippet
Item
Snippet
text
C2826302 (UMLS CUI [1,1])
C1546922 (UMLS CUI [1,2])
Offset
Item
Offset
text
C1711330 (UMLS CUI [1,1])
C2826302 (UMLS CUI [1,2])
C1708517 (UMLS CUI [1,3])
C1317574 (UMLS CUI [1,4])
Lexical variant
Item
Lexical variant
text
C1527021 (UMLS CUI [1,1])
C0027489 (UMLS CUI [1,2])
Note NLP concept ID
Item
Note NLP concept ID
integer
C1317574 (UMLS CUI [1,1])
C0027489 (UMLS CUI [1,2])
C0178566 (UMLS CUI [1,3])
C1300638 (UMLS CUI [1,4])
Note NLP source concept ID
Item
Note NLP source concept ID
integer
C1317574 (UMLS CUI [1,1])
C0027489 (UMLS CUI [1,2])
C0449416 (UMLS CUI [1,3])
C0178566 (UMLS CUI [1,4])
C1300638 (UMLS CUI [1,5])
NLP system
Item
NLP system
text
C0027489 (UMLS CUI [1,1])
C0333052 (UMLS CUI [1,2])
NLP date
Item
NLP date
date
C0027489 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
NLP datetime
Item
NLP datetime
datetime
C0027489 (UMLS CUI [1,1])
C0011008 (UMLS CUI [1,2])
C0040223 (UMLS CUI [1,3])
Term exists
Item
Term exists
text
C2826302 (UMLS CUI [1,1])
C0150312 (UMLS CUI [1,2])
C2826302 (UMLS CUI [2,1])
C0332197 (UMLS CUI [2,2])
Term temporal
Item
Term temporal
text
C2826302 (UMLS CUI [1,1])
C1444637 (UMLS CUI [1,2])
C2826302 (UMLS CUI [2,1])
C0150312 (UMLS CUI [2,2])
Term modifiers
Item
Term modifiers
text
C2826302 (UMLS CUI [1,1])
C3840684 (UMLS CUI [1,2])
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