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Posted to user@ctakes.apache.org by Robert Hatch <ro...@ndcn.ox.ac.uk> on 2020/08/13 22:59:16 UTC
Beginners Advice
Hi sorry to clutter up your inboxes, I am struggling to add date / time data to the coding objects outputted by cTakes. I am modifying the Default Clinical Pipeline which is otherwsie working well however, any modification i make doesn't result in the metadata making it into the output.
Could anyone point me in the right direction?
Many thanks
Rob
Re: Beginners Advice [EXTERNAL]
Posted by Robert Hatch <ro...@ndcn.ox.ac.uk>.
Thanks so much for getting back to me and sorry for the delay in responding. I have taken this (the default clinical pipeline):
// Load a simple token processing pipeline from another pipeline file
load DefaultTokenizerPipeline.piper
// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger
// Add Chunkers
load ChunkerSubPipe.piper
// Default fast dictionary lookup
add DefaultJCasTermAnnotator
// Add Cleartk Entity Attribute annotators
load AttributeCleartkSubPipe.piper
and then added a custom dictionary (which works well), I copied in the contents of some of the includes so that I could try to work out where I was going wrong and attempted to add the data annotator:
// Load a simple token processing pipeline from another pipeline file
add SimpleSegmentAnnotator
add SentenceDetector
add TokenizerAnnotatorPTB
// Add non-core annotators
add ContextDependentTokenizerAnnotator
addDescription POSTagger
// Add Chunkers
add Chunker
addDescription adjuster.ChunkAdjuster NP,NP 1
addDescription adjuster.ChunkAdjuster NP,PP,NP 2
// Dictionary Lookup (Default)
// Annotates clinically-relevant terms. Terms must match dictionary entries exactly.
# DictionaryDescriptor Path to Dictionary spec xml
add org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator DictionaryDescriptor=org\apache\ctakes\dictionary\lookup\fast\icd10.xml
// Add Cleartk Entity Attribute annotators
// Add the Dependency parser for use by cleartk
addDescription ClearNLPDependencyParserAE
// Add the Semantic Role Labeler parser for use by cleartk
addLogged ClearNLPSemanticRoleLabelerAE
// Add the cleartk package for cleartk class lookups
package org.apache.ctakes.assertion.medfacts.cleartk
// Add the cleartk attribute engines
addDescription PolarityCleartkAnalysisEngine
addDescription UncertaintyCleartkAnalysisEngine
addDescription HistoryCleartkAnalysisEngine
addDescription ConditionalCleartkAnalysisEngine
addDescription GenericCleartkAnalysisEngine
addDescription SubjectCleartkAnalysisEngine
// Date Annotator
// Annotates Dates based upon whether or not text can be normalized to a date.
add org.apache.ctakes.ytex.uima.annotators.DateAnnotator
I am sure I am doing something very fundamentally wrong! Any help would be very much appreciated.
Many thanks
Rob
________________________________
From: Miller, Timothy <Ti...@childrens.harvard.edu>
Sent: 14 August 2020 11:34
To: user@ctakes.apache.org <us...@ctakes.apache.org>
Subject: Re: Beginners Advice [EXTERNAL]
Can you show us a snippet of your code that attempts to make
modifications?
Tim
On Thu, 2020-08-13 at 22:59 +0000, Robert Hatch wrote:
> * External Email - Caution *
>
> Hi sorry to clutter up your inboxes, I am struggling to add date /
> time data to the coding objects outputted by cTakes. I am modifying
> the Default Clinical Pipeline which is otherwsie working well
> however, any modification i make doesn't result in the metadata
> making it into the output.
>
> Could anyone point me in the right direction?
>
> Many thanks
>
> Rob
Re: Beginners Advice [EXTERNAL]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Can you show us a snippet of your code that attempts to make
modifications?
Tim
On Thu, 2020-08-13 at 22:59 +0000, Robert Hatch wrote:
> * External Email - Caution *
>
> Hi sorry to clutter up your inboxes, I am struggling to add date /
> time data to the coding objects outputted by cTakes. I am modifying
> the Default Clinical Pipeline which is otherwsie working well
> however, any modification i make doesn't result in the metadata
> making it into the output.
>
> Could anyone point me in the right direction?
>
> Many thanks
>
> Rob