ctakes-notifications mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From "Kean Kaufmann (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (CTAKES-441) Labs Annotator
Date Tue, 02 May 2017 00:42:04 GMT

    [ https://issues.apache.org/jira/browse/CTAKES-441?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15991901#comment-15991901
] 

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

bq. Very nice, very simple and easy to understand.

Thanks, Sean -- high praise!

bq. do you have anything against it being in ctakes-core?

Nothing at all; I hoped it would find a home there.

bq. I should improve the OntologyConceptUtil to accept varargs in getAnnotationsByTui(..),
Cui(..)

I should be aware that the OntologyConceptUtil exists!  :p

> 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.



--
This message was sent by Atlassian JIRA
(v6.3.15#6346)

Mime
View raw message