MetaMap Optional Datasets

Optional Datasets

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.

• 2011 Specialist Lexicon

  Only required for MetaMap 2010, included in MetaMap 2011 Main Distribution

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011_lexicon.tar.bz2 (Bzip2 Tar - 40 MB). [sha1sum] [md5sum]

• 2011AB UMLS Base Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_2011base_strict.tar.bz2 (Bzip2 Tar - 1212 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_base_2011ab_relaxed.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_base_2011ab_base.tar.bz2 (Bzip2 Tar - 656 MB). [sha1sum] [md5sum]

  2011AB Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_base_2011ab_relaxed.tar.bz2 (Bzip2 Tar - 1078 MB). [sha1sum] [md5sum]

  2011AB Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_base_2011ab_strict.tar.bz2 (Bzip2 Tar - 557 MB). [sha1sum] [md5sum]

• 2011AB UMLS USAbase Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_2011usabase_strict.tar.bz2 (Bzip2 Tar - 1339 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_2011usabase_relaxed.tar.bz2 (Bzip2 Tar - 1415 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_usabase_2011ab_base.tar.bz2 (Bzip2 Tar - 707 MB). [sha1sum] [md5sum]

  2011AB Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_usabase_2011ab_relaxed.tar.bz2 (Bzip2 Tar - 1322 MB). [sha1sum] [md5sum]

  2011AB Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_usabase_2011ab_strict.tar.bz2 (Bzip2 Tar - 633 MB). [sha1sum] [md5sum]

• 2011AB UMLS NLM Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_2011nlm_strict.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_win32_nlm_2011ab_relaxed.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_nlm_2011ab_base.tar.bz2 (Bzip2 Tar - 746 MB). [sha1sum] [md5sum]

  2011AB Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_nlm_2011ab_relaxed.tar.bz2 (Bzip2 Tar - 1633 MB). [sha1sum] [md5sum]

  2011AB Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_nlm_2011ab_strict.tar.bz2 (Bzip2 Tar - 735 MB). [sha1sum] [md5sum]

• 2011AA UMLS Base Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011base_strict.tar.bz2 (Bzip2 Tar - 1212 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011base_relaxed.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011base_base.tar.bz2 (Bzip2 Tar - 656 MB). [sha1sum] [md5sum]

  2011AA Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011base_relaxed.tar.bz2 (Bzip2 Tar - 1078 MB). [sha1sum] [md5sum]

  2011AA Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011base_strict.tar.bz2 (Bzip2 Tar - 557 MB). [sha1sum] [md5sum]

• 2011AA UMLS USAbase Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011usabase_strict.tar.bz2 (Bzip2 Tar - 1339 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011usabase_relaxed.tar.bz2 (Bzip2 Tar - 1415 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011usabase_base.tar.bz2 (Bzip2 Tar - 707 MB). [sha1sum] [md5sum]

  2011AA Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011usabase_relaxed.tar.bz2 (Bzip2 Tar - 1322 MB). [sha1sum] [md5sum]

  2011AA Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011usabase_strict.tar.bz2 (Bzip2 Tar - 633 MB). [sha1sum] [md5sum]

• 2011AA UMLS NLM Datasets

  Windows XP/7 Strict Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011nlm_strict.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Windows XP/7 Relaxed Model Data

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_win32_data_2011nlm_relaxed.tar.bz2 (Bzip2 Tar - 1145 MB). [sha1sum] [md5sum]

  Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011nlm_base.tar.bz2 (Bzip2 Tar - 746 MB). [sha1sum] [md5sum]

  2011AA Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011nlm_relaxed.tar.bz2 (Bzip2 Tar - 1633 MB). [sha1sum] [md5sum]

  2011AA Strict Model Data

  (You must download the Common Data as well to use this distribution)
  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2011nlm_strict.tar.bz2 (Bzip2 Tar - 735 MB). [sha1sum] [md5sum]

MetaMap 2010 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.

• 2010AA UMLS Datasets

  Common Data and the 2010 SPECIALIST lexicon

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2010_common.tar.bz2) (Bzip2 Tar - 701 MB). [sha1sum] [md5sum]

  2010AA Relaxed Model Data

  (You must download the Common Data as well to use this distribution)
  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2010_relaxed.tar.bz2) (Bzip2 Tar - 1504 MB). [sha1sum] [md5sum]

  Ancillary 2010AA Relaxed Model Data Files for MetaMap 2011

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2010_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  2010AA Strict Model Data

  (You must download the Common Data as well to use this distribution)
  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2010_strict.tar.bz2) (Bzip2 Tar - 667 MB). [sha1sum] [md5sum]

  Ancillary 2010AA Strict Model Data Files for MetaMap 2011

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2010_strict_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

• 2010AB UMLS Datasets

  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 ...

  The available 2010AB distributions include:

  2010AB Common Data (Note: the lexicon is not included)

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1011_base.tar.bz2)
  (Bzip2 Tar - 709 MB). [sha1sum] [md5sum]

  2010AB Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1011_relaxed.tar.bz2)
  (Bzip2 Tar - 1593 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2010AB Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1011_relaxed_sab.tar.bz2)
  (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  2010AB Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1011_strict.tar.bz2)
  (Bzip2 Tar - 717 MB). (sha1sum: 383d4963164bc68153d10cd61c2df80677c3fe62) [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2010AB Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1011_strict_sab.tar.bz2)
  (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

• 2009AA UMLS Datasets

  Common Data and the 2009 SPECIALIST lexicon

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2009_common.tar.bz2) (Bzip2 Tar - 676 MB). [sha1sum] [md5sum]

  2009 Relaxed Model Data

  (http:///download/DataSets/public_mm_data_2009_relaxed.tar.bz2) (Bzip2 Tar - 523 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2009 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2009_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  2009 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2009_strict.tar.bz2) (Bzip2 Tar - 292 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2009 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2009_strict_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

• 2009AB (0910) UMLS Datasets

  Common Data and the 2009 SPECIALIST lexicon

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_0910_common.tar.bz2) (Bzip2 Tar - 676 MB). [sha1sum] [md5sum]

  0910 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_0910_relaxed.tar.bz2) (Bzip2 Tar - 535 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 0910 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_0910_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  0910 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_0910_strict.tar.bz2) (Bzip2 Tar - 292 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 0910 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_0910_strict_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

• 2006 UMLS Datasets

  Common Data (not including the 2006 SPECIALIST lexicon)

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2006_base.tar.bz2) (Bzip2 Tar - 442 MB). [sha1sum] [md5sum]

  2006 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2006_relaxed.tar.bz2) (Bzip2 Tar - 307 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2006 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2006_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  2006 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2006_strict.tar.bz2) (Bzip2 Tar - 176 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 2006 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_2006_strict_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

• 1999 UMLS Datasets

  Common Data and the 1999 SPECIALIST lexicon

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1999_common.tar.bz2) (Bzip2 Tar - 108 MB). [sha1sum] [md5sum]

  1999 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1999_relaxed.tar.bz2) (Bzip2 Tar - 138 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 1999 Relaxed Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1999_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

  1999 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1999_strict.tar.bz2) (Bzip2 Tar - 83 MB). [sha1sum] [md5sum]

  Ancillary MetaMap 2011 Files for 1999 Strict Model Data

  (http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_1999_strict_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]

Non UMLS Datasets

• EFO Inferred Ontology

  This dataset is derived from EFO Inferred Ontology.

  Relaxed, Strict, and Common Data (lexicon is not included)

  http://metamap.nlm.nih.gov/download/DataSets/public_mm_data_efo_2011.tar.bz2 (Bzip2 Tar - 656 MB). [sha1sum] [md5sum]

  How this dataset was created is described in document: Transforming the EFO Inferred Ontology for MetaMap.