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. >> * >>
