Indexing Initiative:TOOLS

TOOLS: MetaMap

Additional DataSets

MetaMap Optional Datasets

Table of Contents

Other Optional DataSets

2006 UMLS Base Datasets

2006 SPECIALIST Lexicon

Works with MetaMap 2013v2 through 2011
Tar/BZip2 Archive [md5sum] [sha1sum]
Additional configuration is needed to use the 2006 DB Lexicon, links to DB lexicon files must be added to any existing datasets: 
	$ cd public_mm/DB/DB.{umlssubset}.{year}{release}.{model}
	$ ln -s ../../lexicon/data/2012/* .
For Example: 
	$ cd public_mm/DB/DB.USAbase.2012AA.strict
	$ ln -s ../../lexicon/data/2012/* .
The lexicon files must be copied on Windows XP/7: 
	D:\workspace> cd public_mm\DB\DB.{umlssubset}.{year}{release}.{model}
	D:\workspace> copy ..\..\lexicon\data\2012\* .

2006 UMLS Datasets

Data common to both relaxed and strict models (not including the 2006 SPECIALIST lexicon)
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_2006aa_base.tar.bz2) (Bzip2 Tar - 442 MB). [sha1sum] [md5sum]
2006 Relaxed Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_2006aa_relaxed.tar.bz2) (Bzip2 Tar - 307 MB). [sha1sum] [md5sum]
Ancillary MetaMap 2011 Files for 2006 Relaxed Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_2006aa_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]
2006 Strict Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_2006aa_strict.tar.bz2) (Bzip2 Tar - 176 MB). [sha1sum] [md5sum]

1999 UMLS Datasets

1999 SPECIALIST Lexicon

Works with MetaMap 2013v2 through 2011
Tar/BZip2 Archive [md5sum] [sha1sum]

1999 UMLS Datasets

Data common to both relaxed and strict models
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_1999aa_base.tar.bz2) (Bzip2 Tar - 108 MB). [sha1sum] [md5sum]
1999 Relaxed Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_1999aa_relaxed.tar.bz2) (Bzip2 Tar - 138 MB). [sha1sum] [md5sum]
Ancillary MetaMap 2011 Files for 1999 Relaxed Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_1999aa_relaxed_sab.tar.bz2) (Bzip2 Tar - 1 MB). [sha1sum] [md5sum]
1999 Strict Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_1999aa_strict.tar.bz2) (Bzip2 Tar - 83 MB). [sha1sum] [md5sum]
Ancillary MetaMap 2011 Files for 1999 Strict Model Data
(https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_usabase_1999aa_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)
https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_efo_2014.tar.bz2 (Bzip2 Tar - 656 MB). [sha1sum] [md5sum]
The 2011 EFO data set has been recently updated (September 2, 2014) to support MetaMap 2013 and 2014 (MetaMap 2011 and 2012 should still work).
Relaxed, Strict, and Common Data (lexicon is not included)
https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/DataSets/public_mm_data_efo_2011_2014.tar.bz2 (Bzip2 Tar - 656 MB). [sha1sum] [md5sum]
How this dataset was created is described in document: Transforming the EFO Inferred Ontology for MetaMap. The both datasets expect the presence of the SPECIALIST Lexicon which is provided with the MetaMap Main Distribution