Sections

The section annotator is used to identify the section of a document where concepts are found. For example, a patient’s discharge summary may contain a Family History section identifying medical diagnoses of the patient’s parents. In some instances, this information may not be relevant for a particular use case. Using the section annotator, annotations identified as belonging to the Family History section may be filtered out.

The section annotator provides a set of predefined section titles based on the Logical Observation Identifiers Names and Codes (LOINC) vocabulary. In addition to the predefined section titles, section headings are also identified based on a few simple formatting rules:

If a heading is in all uppercase letters followed by a ”:”, such as “VACCINES:”, the heading will be treated as a section header.
If a section title is followed or preceded by all uppercase letters (with ”/” in between), both the section title and the uppercase portion is considered the section header. If uppercase letters follow the dictionary entry, the uppercase portion may include parentheses. Examples include “RELEVANT/FamilyHistory:” and “Family History/(RELEVANT):“.
By default, a section will only be identified if the section title starts at the beginning of a line. To identify sections when the title appears later in the text, use the sections_can_start_anywhere configuration parameter.

A section includes all the text between two section headings. Annotations that exist within the section will be annotated with the section information in the sectionNormalizedName and sectionSurfaceForm< fields.

Configurations

Configuration	Values	Description
include_covered_text	true/false	When true, the coveredText feature for the section annotation is returned. When false (default), the coveredText feature is not returned.
turn_off_internal_triggers	true/false	When true, the predefined section titles are not used. When false (default), the predefined section titles are used to identify sections.
sections_can_start_anywhere	true/false	When true, section titles can be located in any portion of the text, not just at the beginning of a line. When false (default), section titles are only considered when beginning a line.

Annotation Types

Section

Section

Feature	Description
begin	The start position of the annotation as a character offset into the text. The smallest possible start position is 0.
end	The end position of the annotation as character offset into the text. The end position points at the first character after the annotation, such that end-begin equals the length of the coveredText.
coveredText	The text covered by an annotation as a string.
type	Annotation type for Section
trigger	Reason why the covered text was annotated.

Trigger

Feature	Description
begin	The start position of the annotation as a character offset into the text. The smallest possible start position is 0.
end	The end position of the annotation as character offset into the text. The end position points at the first character after the annotation, such that end-begin equals the length of the coveredText.
coveredText	The text that initiated the section annotation.
source	The dictionary source used to identify the section. For the predefined section titles, the value will be `internal`.

Sample Response

Sample response from the section annotator for the text: Family history:\nMaternal history of diabetes.

This example also show a concept that was annotated with the sectionSurfaceForm and sectionNormalizedName fields.

{
  "unstructured": [
    {
      "text": "Family history:\nMaternal history of diabetes.",
      "data": {
        "concepts": [
          {
            "cui": "C0011847",
            "preferredName": "Diabetes",

Annotators: Relation

Annotators: Smoking (Deprecated)