OMOP/Documentation/CommonDataModel_Wiki_Files/StandardizedClinicalDataTables/NOTE_NLP.md

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

Field | Required | Type | Description
:------------------------------- | :-------- | :------------ | :---------------------------------------------------
note_nlp_id 				| Yes | integer | A unique identifier for each term extracted from a note.
note_id 					| Yes | integer | A foreign key to the Note table note the term was extracted from.
section_concept_id 			| No | integer | A foreign key to the predefined Concept in the Standardized Vocabularies representing the section of the extracted term.
snippet 					| No | varchar(250) | A small window of text surrounding the term.
offset 						| No | varchar(50) | Character offset of the extracted term in the input note.
lexical_variant 			| Yes | varchar(250) | Raw text extracted from the NLP tool.
note_nlp_concept_id 		| No | integer | 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.
note_nlp_source_concept_id  | No | integer | A foreign key to a Concept that refers to the code in the source vocabulary used by the NLP system
nlp_system 					| No | varchar(250) | Name and version of the NLP system that extracted the term.Useful for data provenance.
nlp_date 					| Yes | date | The date of the note processing.Useful for data provenance.
nlp_date_time 				| No | datetime | The date and time of the note processing. Useful for data provenance.
term_exists 				| No | varchar(1) | A summary modifier that signifies presence or absence of the term for a given patient. Useful for quick querying. *
term_temporal 				| No | varchar(50) | An optional time modifier associated with the extracted term. (for now <20>past<73> or <20>present<6E> only). Standardize it later.
term_modifiers 				| No | varchar(2000) | A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. <20>son has rash<73> ? <20>negated=no,subject=family, certainty=undef,conditional=false,general=false<73>).

### Conventions

**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
* 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)

**Term_temporal**
Term_temporal is to indicate if a condition is <20>present<6E> or just in the <20>past<73>.

The following would be past:
 
* History = true
* Concept_date = anything before the time of the report

**Term_modifiers**
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.