The side effects annotator is really old (circa 2010). It was initially developed for psychiatric drugs and their side effects. Description is in this publication: http://jamia.oxfordjournals.org/content/18/Supplement_1/i144.abstract I am not quite sure how well the annotator works now... We are working on other methods for side effect extraction and are likely to publish them in spring of 2016.
I hope this helps. --Guergana Guergana Savova, PhD, FACMI Associate Professor PI Natural Language Processing Lab Boston Children's Hospital and Harvard Medical School 300 Longwood Avenue Mailstop: BCH3092 Enders 144.1 Boston, MA 02115 Tel: (617) 919-2972 Fax: (617) 730-0817 Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv -----Original Message----- From: Graham Pitson [mailto:[email protected]] Sent: Wednesday, December 16, 2015 2:58 PM To: [email protected] Subject: SideEffectAnnotator issues Hi, I'm hoping for some more insights into using the side effect annotator. As per Pie Chen's suggestion I've added the side effect annotator to the default AggregatePlaintextFastUMLSProcessor. The xml changes are shown below. Initially I was getting 'URI is not hierarchical' errors. After some searching I thought this might be due to a missing dictionary file and added sideEffect_dictionary.txt at 'apache-ctakes-3.2.2\resources\org\apache\ctakes\sideeffect\lookup'. This stopped the URI errors. I put some dummy content in the dictionary (shown below; using the full content from here didn't help either - https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dside-2Deffect-2Dres_src_main_resources_org_apache_ctakes_sideeffect_lookup_sideEffect-5Fdictionary.txt&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=SeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=cq3dLDFzFSH1DRnh30N1vwFozDMinGQA_mbzqpzsuXA&s=wosr80zHuzsbhDmk3ABFQB5BJckImO8OO9S1nrLQWMU&e= ). Now as per the log files, I'm getting null pointer exceptions within sideEffectAnnotator.java - at 2 different locations as shown below. Getting an exception is dependent on the text analysed: 'Seen today. On tamoxifen 20 mg daily which caused headaches.' causes an exception. 'Seen today. On tamoxifen 20 mg daily which caused something.' does not (of course there is no clinical finding in the second text). Given that others are using the side effect annotator, I'm guessing this is some kind of issue with my configuration/dictionary and would appreciate any advice. I'm running the latest version of cTakes 'as is'. Thanks in advance. Graham Pitson -----------------------------AggregatePlaintextFastUMLSProcessor.xml--------------------------------------------- <delegateAnalysisEngine key="SideEffectAnnotator"> <import location="SideEffectAnnotator.xml"/> </delegateAnalysisEngine> <node>ConstituencyParser</node> <node>SideEffectAnnotator</node> <!-- <node>AssertionAnnotator</node> --> <!-- <node>StatusAnnotator</node> --> <!-- <node>NegationAnnotator</node> --> <node>GenericCleartkAnalysisEngine</node> -------------------------test text------------------------------- 'Seen today. On tamoxifen 20 mg daily which caused headaches.' -------------------------------------------error logs (2 different exception locations)----------------------------------------------------------- 17/12/15 6:21:24 AM - 14: org.apache.uima.tools.cvd.MainFrame.handleException(526): SEVERE: Annotator processing failed. org.apache.uima.analysis_engine.AnalysisEngineProcessException: Annotator processing failed. at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:391) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.processAndOutputNewCASes(PrimitiveAnalysisEngine_impl.java:296) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.processUntilNextOutputCas(ASB_impl.java:567) at org.apache.uima.analysis_engine.asb.impl.ASB_impl$AggregateCasIterator.<init>(ASB_impl.java:409) at org.apache.uima.analysis_engine.asb.impl.ASB_impl.process(ASB_impl.java:342) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.processAndOutputNewCASes(AggregateAnalysisEngine_impl.java:267) at org.apache.uima.analysis_engine.impl.AnalysisEngineImplBase.process(AnalysisEngineImplBase.java:267) at org.apache.uima.tools.cvd.MainFrame.internalRunAE(MainFrame.java:1526) at org.apache.uima.tools.cvd.MainFrame.runAE(MainFrame.java:429) at org.apache.uima.tools.cvd.control.AnnotatorRerunEventHandler.actionPerformed(AnnotatorRerunEventHandler.java:40) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.AbstractButton.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$200(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.NullPointerException at org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.isInAllergySection(SideEffectAnnotator.java:759) at org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.getSideEffectsWithPrioritizedRule(SideEffectAnnotator.java:342) at org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.process(SideEffectAnnotator.java:180) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) ... 47 more at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) Caused by: java.lang.NullPointerException at org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.getPotentialSideEffects(SideEffectAnnotator.java:296) at org.apache.ctakes.sideeffect.ae.SideEffectAnnotator.process(SideEffectAnnotator.java:177) at org.apache.uima.analysis_component.JCasAnnotator_ImplBase.process(JCasAnnotator_ImplBase.java:48) at org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.callAnalysisComponentProcess(PrimitiveAnalysisEngine_impl.java:375) ... 47 more --------------------------------------------dummy dictionary---------------------------------------------------- //FORMAT: generic drug|brand drug|side effect1, side effect2,... Tamoxifen|Nolvadex,Tam|Hot flushes, nausea, endometrial cancer
