Hello Ctakes Dev
This is a general set of question which may reflect a bad install on my part or
something going on in the 3.2 version that is more than just a set of boundary
case bugs. I am a newcomer to CTakes, but have spent a lot of time with
StanfordCoreNLP, writing annotators, and with SemRep etc.... so not completely
naive.
I have a UMLS license which is recognized by Ctakes as well as the resource
dictionary set and I get no errors there, but I am not getting a number of
annotations for even simple cases, and exceptions when enabling others. If any
of these point to ignorance or a bad installation, on my part, can you please
point me to any other documentation besides what's exposed on your site that
could help? Each of these issues is something that was demonstrated as working
in one or other of the videos on your site, but does not work on mine. Here
are some examples
1. When encountering a Medication. It finds the ontology codes, but does
not tease out the start, end, dose, route etc except in a very few cases
2. When encountering a Sign or Symptom it finds no relevant details besides
the codes
3. Negation never works ( I have tried enabling it in my copy of the
pipeline but that doesn't help )
4. I cannot figure out how to wire in the TemporalAnnotation engine. When
I try to do that I get an initialization exception for the
"temporal.ae.BackwardsTimeAnnotator" (there's no exception information
written to the logfile"
Here's an example of points 2 and 3.
Pipeline - a copy of FastUMLSPlainText with Negation enabled in the workflow
and declarations
...
<delegateAnalysisEngine key="NegationAnnotator">
<import
location="../../../ctakes-ne-contexts/desc/NegationAnnotator.xml"/>
</delegateAnalysisEngine>
...
<node>DependencyParser</node>
<node>SemanticRoleLabeler</node>
<node>ConstituencyParser</node>
<!-- <node>AssertionAnnotator</node> -->
<node>StatusAnnotator</node>
<node>NegationAnnotator</node>
<node>GenericCleartkAnalysisEngine</node>
<node>HistoryCleartkAnalysisEngine</node>
....
Input text
the patient denies having any left-side numbness or chest pain in the last 48
hours
The SignSymptomMention for numbness
[cid:03CAA036-F27E-44B3-B05A-2245794F177E]
