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From "Sean Finan (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-441) Labs Annotator
Date Mon, 01 May 2017 21:39:04 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-441?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15991600#comment-15991600
] 

Sean Finan commented on CTAKES-441:
-----------------------------------

Hi Kean,
Very nice, very simple and easy to understand.
Since it is one class (plus test!), and doesn't rely on any higher ctakes modules, do you
have anything against it being in ctakes-core?
Thanks,
Sean

It also points out that I should improve the OntologyConceptUtil to accept varargs in getAnnotationsByTui(..),
Cui(..)

> 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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