Sorry if I wasted anyone's time but this was caused by a dumb mistake. I'd commented out the line of code that added the SNOMED hits while trying to switch to ICD9 and didn't fully roll-back my changes.
From: Vogel, James Sent: Monday, September 30, 2013 10:14 PM To: 'dev@ctakes.apache.org' Subject: Text not matched No concept or annotation is created for "Birbeck granule deficiency" when I run the clinical pipeline in the CVD. I see it in the UMLS Metathesaurus Browser at https://uts.nlm.nih.gov//metathesaurus.html#C3150657;0;1;CUI;2012AB;EXACT_MATCH;*<https://uts.nlm.nih.gov/metathesaurus.html#C3150657;0;1;CUI;2012AB;EXACT_MATCH;*>; I see that its semantic type of T047 is in LookupDesc_DB.xml for the clinical pipeline. Is there additional configuration needed to match this term? "deficiency" is annotated. ________________________________ IMPORTANT WARNING: Information contained in this email is intended for the use of the individual to whom it is addressed, and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If you are not the intended recipient, or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution, or copying of this communication is STRICTLY FORBIDDEN. If you have received this communication in error, please notify us immediately by return email and delete this document. Thank you.
