3.2 KiB
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 “past” or “present” 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. “son has rash” ? “negated=no,subject=family, certainty=undef,conditional=false,general=false”). |
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 “present” or just in the “past”.
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.