These optional datasets are configured for the 2010 and later versions of MetaMap, so they will not work with previous releases of MetaMap unless otherwise specified. See the documentation on "Using Additional Datasets with Public MetaMap" for information on installing optional datasets.
Important Note: When using MetaMap 2011 with the following data sets, users may experience problems when applying the --restrict_to_sources and --exclude_sources options. The additional files necessary for the proper operation of MetaMap 2011 are provided by the Ancillary Data Files for MetaMap 2011. These files are available for the data sets below. See the documentation on using "Using Additional Datasets with Public MetaMap" for information on installing Ancillary Data Files. If you already have downloaded one of the pre-2011 data sets, it is only necessary to download the Ancillary Files for that dataset to allow the dataset to work properly with MetaMap 2011. Otherwise, you need to download the common (or base), model, and ancillary data files for the data set you wish to use.
NOTE: The current metamap10 script erroneously expects the 2011 lexicon to be present with 2010AA UMLS. To fix this, the temporary stopgap measure is to create symbolic links making the 2010 lexicon appear as if it were the 2011 lexicon:
$ cd public_mm/lexicon/data $ ln -s lexiconStatic2010 lexiconStatic2011 $ ln -s lexiconStatic2010IndByEui.dbx lexiconStatic2011IndByEui.dbx $ ln -s lexiconStatic2010IndByInfl.dbx lexiconStatic2011IndByInfl.dbx
Alternatively, you can use the script metamap.TEMPLATE directly to specify use of the 2010 Lexicon:
bin/metamap.TEMPLATE 10 -Z 1011 -L 10 args ...
This dataset is derived from EFO Inferred Ontology.