Sean & Pei -- Glad it can be useful! Haven't done this before, so please bear with me.
Pei: I've signed up at issues.apache.org; I'll open an issue and attach some code sometime in the next week or so. Is Java 8 ok? Sean: Our type-system tweaks are oversimplifications; I didn't wrap my head around the relation-extraction KR. May I sanity-check with you? So, let's see... there's org.apache.ctakes.typesystem.type.textsem.LabMention, whose labValue is a ResultOfTextRelation... which I don't see actually used in the codebase... but whose arg1 seems as if it should be (a RelationArgument wrapping) the lab concept annotation (e.g. "weight" or "Albumin"), arg2 the value annotation (e.g. "46 kg" or "2.2"). Does that seem right? If my understanding is incomplete/incorrect, please let me know. Thanks, -Kean On Wed, Mar 29, 2017 at 9:32 AM, Pei Chen <chen...@apache.org> wrote: > Kean, > This would be really useful. If you would like make a contribution, > could you please open a Jira and attach the patch or code? When you > submit a patch via jira/attachment, it has legal verberage about > donating the code, etc. > > --Pei > > > On Wed, Mar 29, 2017 at 9:30 AM, Finan, Sean > <sean.fi...@childrens.harvard.edu> wrote: > > Fantastic! > > > > I would really like to work with you to get this into ctakes 4.1. Let > me know how you would like to proceed. Would you like to send me or > another committer the code or have somebody review it remotely? The > "tweaks" may be something useful to ctakes, but if not I'm sure that we can > create a decent interfacing. > > > > Cheers, > > Sean > > > > -----Original Message----- > > From: Kean Kaufmann [mailto:k...@recordsone.com] > > Sent: Wednesday, March 29, 2017 7:59 AM > > To: dev@ctakes.apache.org > > Subject: Re: Labs annotator? > > > >> > >> 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. > >> * > >> >
