Hi Bruce, I would venture to say that this is neither expected nor desired.
Before you fix it (or in addition to a fix), try to run with the new dictionary lookup. It will have a different behavior, and it will be the default dictionary lookup in future releases of cTakes – making fixes to the current module slightly less urgent. Sean From: Bruce Tietjen [mailto:bruce.tiet...@perfectsearchcorp.com] Sent: Wednesday, October 08, 2014 11:38 AM To: dev@ctakes.apache.org Subject: Differences in MedicationMention annotations on subsequent processing runs I have encountered a situation in which the cTakes clinical pipeline output differs between multiple runs on the same text with the same configuration. The following snippets from a single document are sufficient to demonstrate the issue: a gentle curve going into. irrigated with Bacitracin. The source of the difference is that the DictionaryLookupAnnotator uses a map to filter out duplicate annotations for a single document location: // used to prevent duplicate hits // key = hit begin,end key (java.lang.String) // val = Set of MetaDataHit objects private Map<String,Set<MetaDataHit>> iv_dupMap = new HashMap<>(); This map is shared between both the umls_ms_2011ab lookup and the umls_ms_2011an_rxnorm lookup, If both dictionaries contain the same term, the order of dictionary lookup execution determines the output.If the rxnorm lookup runs first, then a MedicationMention annotation for Bacitracin appears in the final output. If the standard umls lookup runs first, then there is no MedicationMention annotation for Bacitracin. I will attach the output from the subsequent runs. (Hopefully the attachment will make it through the system) Is this expected behavior? If not, what would be the expected behavior? [Image removed by sender. IMAT Solutions]<http://imatsolutions.com> Bruce Tietjen Senior Software Engineer [Image removed by sender. Mobile:]801.634.1547 bruce.tiet...@imatsolutions.com<mailto:bruce.tiet...@imatsolutions.com>
