MetaMap 2008 ReadMe for Linux
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Running MetaMap:

To run the MetaMap program from the Linux command line, you have two options:

1. Put the directory containing the MetaMap program in the PATH environment variable and then you can run MetaMap from any directory.
# in C Shell (csh or tcsh)
setenv PATH <parent dir>/public_mm/bin:$PATH

# in Bourne Again Shell (bash)
export PATH=<parent dir>/public_mm/bin:$PATH

# Bourne Shell (sh)
PATH=<parent dir>/public_mm/bin:$PATH
export PATH
2. You can simply run the MetaMap command by specifying the full path to the command.
<parent dir>/public_mm/bin/metamap08
Whichever option you decide on, the command line statement to run MetaMap is:
% metamap08 [Options] [InputFile] [OutputFile]
For more information on MetaMap usage, please refer to MetaMap 2008 Usage (HTML), or use the MetaMap help command:
% metamap08 --help
Examples:

Note: The pathnames in the examples below are those from the NLM site; your pathnames will differ.
More examples are available in MetaMap Options and Examples (PDF - 50 kb)

MetaMap with no options on a simple term from standard input 

% metamap08
/nfsvol/nls/bin/SKRrun -L 2008 /nfsvol/nls/bin/metamap08.BINARY -Z 08

/nfsvol/nls/bin/metamap08 (2008)


Control options:
  mm_data_year=08
Berkeley DB databases (normal strict 08 model) are open.
Static variants will come from table varsan.
Accessing lexicon /nfsvol/nls/specialist/SKR/src/lexicon/data/lexiconStatic2008.
Variant generation mode: static.
Initializing tagger on skr1...

|: Obstructive Sleep Apnea
|: 


Processing 00000000.tx.1: Obstructive Sleep Apnea

Phrase: "Obstructive Sleep Apnea"
Meta Candidates (9):
  1000 Obstructive sleep apnoea (Sleep Apnea, Obstructive) [Disease or Syndrome]
   901 Apnea, Sleep (Sleep Apnea Syndromes) [Disease or Syndrome]
   827 APNOEA (Apnea) [Pathologic Function]
   827 Sleep [Organism Function]
   827 Obstructive (Obstructed) [Functional Concept]
   827 Apnea (Apnea Adverse Event) [Finding]
   793 Sleeping (Asleep) [Finding]
   755 Sleepy [Finding]
   727 Sleeplessness [Sign or Symptom]
Meta Mapping (1000):
  1000 Obstructive sleep apnoea (Sleep Apnea, Obstructive) [Disease or Syndrome]
|:


MetaMap on a small MEDLINE Abstract to a named output file. 

% metamap08 cit00000 cit00000.output 
MetaMap (2008)

/nfsvol/nls/bin/SKRrun -L 2008 /nfsvol/nls/bin/metamap08.BINARY -Z 08

/nfsvol/nls/bin/metamap08 (2008)


Control options:
  mm_data_year=08
Berkeley DB databases (normal strict 08 model) are open.
Static variants will come from table varsan.
Accessing lexicon /nfsvol/nls/specialist/SKR/src/lexicon/data/lexiconStatic2008.
Variant generation mode: static.
Initializing tagger on skr1...

Beginning to process cit00000 sending output to output.
Tagging will be done dynamically.

Processing 9337195.ti.1: Obstructive Sleep Apnea

Batch processing is finished.
%
MetaMap will populate the output file cit00000.output with the processed contents of cit00000.



Last Modified: December 16, 2010 ii-public2
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MetaMap Public Release
NEW: Distributable version of the actual MetaMap program.
Indexing Initiative (II)
Investigating computer-assisted and fully automatic methodologies for indexing biomedical text. Includes the NLM Medical Text Indexer (MTI).
Semantic Knowledge Representation (SKR)
Develop programs to provide usable semantic representation of biomedical text. Includes the MetaMap and SemRep programs.
MetaMap Transfer (MMTx)
Java-Based distributable version of the MetaMap program.
Word Sense Disambiguation (WSD)
Test collection of manually curated MetaMap ambiguity resolution in support of word sense disambiguation research.
MEDLINE Baseline Repository (MBR)
Static MEDLINE® Baselines for use in research involving biomedical citations. Allows for query searches and test collection creation.
Structured Abstracts (SA)
Information about NLM's research on Structured Abstracts in the MEDLINE® Baselines.
 
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