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1. Download the dictionary resources. | No example | ||||||||||
2. Put the resources in the proper place. | Windows:
Linux:
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3. UMLS user ID and password.
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In order to integrate the dictionaries you will need to do two things:
(1) Change the UMLSUser and UMLSPW <nameValuePair> strings in these descriptor files with your UMLS username and password.
- Dictionary Lookup: <cTAKES_HOME>/desc/ctakes-dictionary-lookup/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
- (optional) Drug NER: <cTAKES_HOME>/desc/ctakes-drug-ner/desc/analysis_engine/DictionaryLookupAnnotatorUMLS.xml
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seems like drugner The following shows where in the files you would make the changes. (Do not change the <configurationParameters> by the same name.)
(2) Include the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within your aggregate Analysis Engine or switch to the ones provided by cTAKES. cTAKES has provided duplicates of shipped Analysis Engine descriptors, put UMLS in the name, and placed DictionaryLookupAnnotatorUMLS.xml within them for these components:
So you simply need to switch to using those descriptors. For example, if you were using AggregateCdaProcessor.xml in the Clinical Documents pipeline you would switch to using AggregateCdaUMLSProcessor.xml instead and you will now hook into the complete dictionaries. You can, of course, modify your own aggregate Analysis Engine files and place the DictionaryLookupAnnotatorUMLS.xml Analysis Engine within them. If you would like to go back to using the small sample dictionaries that do not require a UMLS username, use the DictionaryLookupAnnotator.xml (UMLS is not in the file name) Analyis Engine descriptor in your aggregate. Just removing your password from the DictionaryLookupAnnotatorUMLS.xml files will not switch you back to the small sample dictionaries. LVGWe have successfully tested the 2008 release of the full LVG data. In order to use this release of the full LVG data you should:
Building Your Own DictionariesIt is not likely that the UMLS dictionaries will match to your underlying data completely. Other local terms may be required, etc. To install customized dictionaries for RxNorm, SNOMED-CT, or other vocabularies that are available through the UMLS, see the following posts on the cTAKES forums: |
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cTAKES developers need to see if these posts still apply to cTAKES 3.0
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Models
Some models included in cTAKES may not represent your data distribution well. If you want to build or train your own models, please read the cTAKES 3.0 Component Use Guide, particularly:
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