OK, got it fixed and finding entities (I forgot to add the conceptFactoryName field to the dictionaryConceptPair), including both terms from the standard SNOMED+RxNORM dictionary and my customized dictionary. One problem I still have is that the custom entities (which have dummy CUIs and TUIs) are called EntityMention, when they probably should be EventMentions. I'll poke around a little bit to see if there is some way to control that, either in the code or with a better dictionary. Tim
On Tue, 2020-12-01 at 21:32 +0000, Miller, Timothy wrote: > * External Email - Caution * > > > FYI I was able to get the dictionary to load by putting in a dummy > TUI > in the vocab file and adding a ConceptFactory block to the > descriptor. > It's still not finding the terms in my custom dictionary but I'll > keep > debugging. > Tim > > On Tue, 2020-12-01 at 15:50 +0000, Miller, Timothy wrote: > > * External Email - Caution * > > > > > > I'm trying to use a custom BSV dictionary as in the examples. I got > > the > > piper file to point to the lookup descriptor, which is based off of > > ctakes-dictionary-lookup-fast- > > res/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/exa > > mp > > le > > /bsv/CustomCuiBsv.xml > > > > but when I run it I get an error (NPE) that sounds like it was > > looking > > for a ConceptFactory: > > > > Caused by: java.lang.NullPointerException > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescripto > > rP > > ar > > ser.parseConceptFactories(DictionaryDescriptorParser.java:218) > > at > > org.apache.ctakes.dictionary.lookup2.dictionary.DictionaryDescripto > > rP > > ar > > ser.parseDescriptor(DictionaryDescriptorParser.java:129) > > at > > org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator.i > > ni > > ti > > alize(AbstractJCasTermAnnotator.java:138) > > at > > org.apache.uima.analysis_engine.impl.PrimitiveAnalysisEngine_impl.i > > ni > > ti > > alizeAnalysisComponent(PrimitiveAnalysisEngine_impl.java:267) > > ... 26 more > > > > > > which that example descriptor doesn't contain. Do I need a concept > > factory line in my descriptor? What would that look like for a BSV > > file > > that is just: > > ID|Preferred term|Synonyms > > > > > > Tim > > > >
