Hi Tanmay, Good question. The short answer to >Does this AE contain annotator to annotate Lab data? Is "no".
> can someone suggest any different annotator that could identify lab values. Kean Kaufmann was kind enough to contribute an annotator that creates labmentions. A great description plus a .zip with the code can be found at https://issues.apache.org/jira/browse/CTAKES-441 I need to check it in to trunk for the next release ... I just assigned it to myself so that I don't forget. :^( Somebody out there may have another engine or post-processor that does. It should also be pretty easy to make your own "post-processor" annotator if Kean's doesn't fit your purposes. All of the concepts are stored with a semantic type that can be used to determine whether or not a medication, finding, etc. is what you a consider a LabMention. Use OntologyConceptUtil .getTuis(..) or .getAnnotationsByTui(..) to help you with this. http://ctakes.apache.org/apidocs/4.0.0/ A semantic type to tui map is here: https://mmtx.nlm.nih.gov/MMTx/semanticTypes.shtml Sean -----Original Message----- From: Das, Tanmay [mailto:tanmay....@optum.com] Sent: Tuesday, June 27, 2017 3:39 AM To: dev@ctakes.apache.org Subject: Annotating Lab data [EXTERNAL] Hi, When using the CVD bundled with cTAKES along with AggrigatePlainTextFastUMLSProcessor I found that no laboratory data was annotated, even after providing it. For an input like: LABORATORY DATA: Hemoglobin 10.6, hematocrit 31.7, white cell count 5.8, platelet 377. Magnesium 2.6, glucose 98, BUN 13, creatinine 0.5, sodium 138, potassium 3.9, chloride 103. INR is 1.5. The IdentifiedAnnotations classified them as Medication, Procedures etc but not as LabMention. Does this AE contain annotator to annotate Lab data? If not, can someone suggest any different annotator that could identify lab values. This e-mail, including attachments, may include confidential and/or proprietary information, and may be used only by the person or entity to which it is addressed. If the reader of this e-mail is not the intended recipient or his or her authorized agent, the reader is hereby notified that any dissemination, distribution or copying of this e-mail is prohibited. If you have received this e-mail in error, please notify the sender by replying to this message and delete this e-mail immediately.
