Hi Bharat, I’m not sure whether it’s the ideal way to connect to local MySQL DB for running cTAKES CVD. But this is what I did to make it work:
I updated ‘UmlsLookupAnnotator.xml’ in ‘apache-ctakes-4.0.0\desc\ctakes-dictionary-lookup-fast\desc\analysis_engine’ folder to point to ‘customDictionary.xml’ instead of ‘sno_rx_16ab.xml’ ‘customDictionary.xml’ is the file which I generated by using cTAKES dictionary creator GUI. This XML file contains the details of MySQL DB. You can have a look at the XML under https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-web-rest/src/main/resources/org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml Then you can load ‘AggregatePlaintextFastUMLSProcessor.xml’ under ‘apache-ctakes-4.0.0\desc\ctakes-clinical-pipeline\desc\analysis_engine’ folder for analysis. I also found ‘DictionaryLookupAnnotatorDB.xml’ under ‘apache-ctakes-4.0.0\desc\ctakes-dictionary-lookup\desc\analysis_engine’ folder which can be used to load dictionary from local DB but I could not able to make it work as I don’t have much expertise in defining custom metadata in ‘LookupDesc_Db.xml’ Regards, Gandhi From: Bharat Shetty <[email protected]> Sent: Sunday, November 11, 2018 8:01 PM To: [email protected] Subject: Connecting the local UMLS DB to run clinical pipelines Can anyone please help me on proper file/location to enter the MySQL credentials for connecting the local UMLS DB (MySQL) to run advanced ctakes NLP pipelines that make use of UML data. In nutshell, any documentation or guidance on connecting to the local MySQL server that houses the UML data, so that the ctakes clinical pipelines which are run using runctakesCVD.sh will be able to connect to the local mysql DB will be most useful. Regards, - Bharat This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to whom they are addressed. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender or system manager by email immediately if you have received this e-mail by mistake and delete this e-mail from your system. If you are not the intended recipient you are notified that disclosing, copying, distributing or taking any action in reliance on the contents of this information is strictly prohibited and against the law.
