> > I'm sure that people would love to see lab values in ctakes! Could you > please write a small summary of what it does? Maybe an example or two > could suffice.
Hi Sean, 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) I'd need to check in with you to make sure it plays nicely with the cTAKES type system; we've tweaked ours a bit. Best, -kk On Tue, Mar 28, 2017 at 11:45 AM, Finan, Sean < sean.fi...@childrens.harvard.edu> wrote: > Hi Kean, > > I'm sure that people would love to see lab values in ctakes! Could you > please write a small summary of what it does? Maybe an example or two > could suffice. > > We can definitely put it into ctakes in release 4.1 - maybe next quarter? > > Cheers, > Sean > > -----Original Message----- > From: Kean Kaufmann [mailto:k...@recordsone.com] > Sent: Tuesday, March 28, 2017 11:34 AM > To: dev@ctakes.apache.org > Subject: Labs annotator? > > On Tue, Mar 28, 2017 at 11:23 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > > > > > If anybody out there has something that they would like to contribute > > to ctakes, please do! > > > > I recently wrote an annotator for lab values. There was some discussion > of this on the dev list a couple of years ago; did anything come of it? > Happy to contribute if it's helpful. > > -- > _____________________________________________________ > *Kean Kaufmann* > NLP Developer > > RecordsOne > nSight Driven | *Priority. Clarity. Integrity. * > > *mobile* | > 240-401-6131 > > *Twitter: **@R1_RecordsOne* > *See us in Vegas @ ACDIS 2017 * > *See us in Los Angeles @ AHIMA 2017* > > ------------------------------------------------------------ > --------------------------------------- > *Confidentiality Notice: *This email, including any attachments is the > property of RecordsOne, LLC and is intended for the sole use of the > intended recipient(s). It may contain information that is privileged and > confidential. Any unauthorized review, use, disclosure, or distribution is > prohibited. If you are not the intended recipient, please reply to the > sender that you have received the message in error, then delete this > message. > ------------------------------------------------------------ > --------------------------------------- > *Mailing*: 10641 Airport Pulling Road, Suite 30 | Naples, FL 34109 > *Main*: 239.451.6112 > > *Please consider the environmental impact before printing this email. * >
