[CTAKES-441] Labs Annotator

• Type: New Feature
• Status: Closed
• Priority: Minor
• Resolution: Delivered
• Fix Version/s: 4.0.1
• Assignee: Sean Finan
• Reporter: Kean Kaufmann
• Created: 30/Apr/17 19:23
• Updated: 15/Nov/17 00:06
• Resolved: 15/Nov/17 00:06

Description

The labs annotator identifies likely lab phrases by TUI (T059 et al.),
and relates them to the nearest following number-ish value –
NumToken, FractionAnnotation, MeasurementAnnotation or (as a last resort) RangeAnnotation –
that isn't part of a Date or TimeAnnotation.
A whitelist of lab-value words can also be specified, e.g. "positive", "negative", "normal", "elevated", "decreased", ...

For example,

Weight / BMI:  Recent weight (as of 05/05/16) is 45.36 kg (100 lb) 

yields

"weight" -> "45.36 kg"

and

HEPATIC FUNCTION PANEL
    Result Value Ref Range
 Albumin 2.2 (*) 3.7 - 5.1 g/dL
 Total Protein 5.5 (*) 5.8 - 8.0 g/dL
 Alkaline Phosphatase 844 (*) 42 - 121 IU/L
...

yields

"Albumin" -> "2.2"
"Protein" -> "5.5"
"Alkaline Phosphatase" -> "844"

(without trying to fill in the units or referenceRangeNarrative values).

Configuration parameters:

• ids of segments to annotate
• TUIs indicating labs - I use T059, T060 and T121
• CUIs too general to be useful, e.g. C1443182, "Calculated (procedure)"
• Whitelist of words allowed as lab values
• Maximum number of newlines permitted between lab and value (0 = must be on same line)

The enclosed code is packaged as a Maven module, so you can run mvn test to see how it works.