Hi Eugenia,

>1.
-  A few years ago Kean Kaufmann wrote a nice annotator that can discover lab 
values.  https://issues.apache.org/jira/browse/CTAKES-441  
It is in ctakes as org.apache.ctakes.core.ae.LabValueFinder
It may not be exactly what you are looking for, but you can see from the 
comments in jira that TUIs may be used to fetch lab annotations.

>2.
I am definitely not the expert on the temporal module, so somebody else may 
write me wrong ...
> I was looking into the "event-time" features
I think that is a good route to take.

I would take a look at the CalendarUtil class in org.apache.ctakes.core.util
You may be able to use the method Calendar getCalendar( Annotation )    or   
Calendar getCalendar( String )
Use the TemporalTextRelations, looking for those relating an Event with a 
Timex.  Then call the getCalendar method with the Timex.
Note that the relation will have a category indicating relativity such as the 
event being before, after, or overlapping the time.


Though I have never used it, there is some time normalization in a 
ctakes-temporal ae named WithinSentenceBeforeRelationAnnotator.  
I think that Steven Bethard contributed the code there and in the 
ctakes-temporal Utils class to integrate with his timenorm project   
https://github.com/clulab/timenorm


You can also take a look at lines #145 - #155 in the class 
org.apache.ctakes.temporal.utils.CalendarUtil        Calendar getCalendar( 
String )
You will see that the method uses a 3rd party library named jChronic   
https://github.com/samtingleff/jchronic
Chronic.parse( String )  returns a Span object that contains a normalized start 
and end date.  This can be useful for spans of time in addition to points in 
time.

Sean

________________________________________
From: Monogyiou, Eugenia <eugenia.monogy...@nttdata.com>
Sent: Wednesday, December 2, 2020 8:32 AM
To: dev@ctakes.apache.org
Subject: Lab entity and Temporal attributes related enquiries [EXTERNAL]

* External Email - Caution *


Hello and happy Wednesday,

Two independent functionality topics this time :)

1. Labs : As I understand "Labs" in the refSem namespace is a separate core 
clinical element from "Procedure" but I haven't managed to get any Lab 
annotations regardless of which pipeline I am using and I have tried a few. Is 
there a specific NER component or configuration that produces such annotations?

2. Temporal attributes : I have included the TemporalSubPipe from the trunk  in 
my custom pipeline and I do get the "DocTimeRel" features but the "startTime" 
and "endTime" event attributes are never populated. I am interested in 
retrieving the actual date associated with a prescription or diagnosis in a 
clinical letter hence I was looking into the "event-time" features rather than 
"event-event" features but I am not sure whether I am looking in the right 
place or have I even identified the right attributes, properties etc. Also, I 
am not sure whether this retrieval would require re-training of a model or with 
code.

Any ideas/ guidance would be greatly appreciated!

Many thanks in advance

Kind Regards,

Eugenia

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