[jira] [Commented] (CTAKES-441) Labs Annotator

["Kean Kaufmann (JIRA)" <ji...@apache.org>]

    [ https://issues.apache.org/jira/browse/CTAKES-441?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15990352#comment-15990352 ] 

Kean Kaufmann commented on CTAKES-441:
--------------------------------------

[~Pei.Chen@childrens.harvard.edu], [~Sean.Finan@childrens.harvard.edu] - Here's the Labs Annotator we discussed last month. Feedback welcome.


> 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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