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.

Field	Required	Type	FK Table	Description
note_nlp_id	Yes	bigint		A unique identifier for each term extracted from a note.
note_id	Yes	bigint		A foreign key to the Note table note the term was extracted from.
section_concept_id	No	bigint	CONCEPT	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(250)		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	bigint	CONCEPT	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	bigint	CONCEPT	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 UTC date of the note processing. Useful for data provenance.
nlp_datetime	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 “past” or “present” only).
term_modifiers	No	varchar(2000)		A compact description of all the modifiers of the specific term extracted by the NLP system. (e.g. for “son has rash?”: “negated=no,subject=family,certainty=undef,conditional=false,general=false”).

Conventions

Field term_exists

The field 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)

Field term_temporal

The field 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

Field term_modifiers

The field 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.