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From "Kean Kaufmann (JIRA)" <j...@apache.org>
Subject [jira] [Created] (CTAKES-441) Labs Annotator
Date Sun, 30 Apr 2017 19:24:04 GMT
Kean Kaufmann created CTAKES-441:
------------------------------------

             Summary: Labs Annotator
                 Key: CTAKES-441
                 URL: https://issues.apache.org/jira/browse/CTAKES-441
             Project: cTAKES
          Issue Type: New Feature
            Reporter: Kean Kaufmann
            Priority: Minor
         Attachments: ctakes_contrib.zip

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,

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

yields

bq. "weight" -> "45.36 kg"

and

{noformat}
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
...
{noformat}

yields

{quote}
"Albumin" -> "2.2"
"Protein" -> "5.5"
"Alkaline Phosphatase" -> "844"
{quote}

(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.



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