MetaMap 2007 Readme for Linux

MetaMap 2007 Readme for Linux

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Running MetaMap
Examples
- MetaMap with no options on a simple term from standard input
- MetaMap on a small MEDLINE Abstract to a named output file.

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/metamap07

Whichever option you decide on, the command line statement to run MetaMap is:

% metamap07 [Options] [InputFile] [OutputFile]

For more information on MetaMap usage, please refer to MetaMap 2007 Usage (HTML), or use the MetaMap help command:

% metamap07 --help

Examples:

Note: More examples, are available in MetaMap Options and Examples (PDF - 50 kb)

MetaMap with no options on a simple term from standard input


% metamap07

MetaMap (2007)


Control options:
  tag_text
  no_acros_abbrs
  an_derivational_variants
  stop_large_n
  plain_syntax
  candidates
  semantic_types
  mappings
  best_mappings_only
Initializing db_access (07)...
Berkeley DB databases (normal strict model) are open.
Static variants will come from table varsan.
Accessing lexicon /metamap/public_mm/lexicon/data/lexiconStatic2007.
Variant generation mode: static.
Initializing tagger on localhost...
|: Obstructive Sleep Apnea
|:


Processing 00000000.tx.1: Obstructive Sleep Apnea

Phrase: "Obstructive Sleep Apnea"
Meta Candidates (8):
  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]
   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.


% metamap07 cit00000 cit00000.output 
MetaMap (2007)


Control options:
  tag_text
  no_acros_abbrs
  an_derivational_variants
  stop_large_n
  plain_syntax
  candidates
  semantic_types
  mappings
  best_mappings_only
Initializing db_access (07)...
Berkeley DB databases (normal strict model) are open.
Static variants will come from table varsan.
Accessing lexicon /metamap/public_mm/lexicon/data/lexiconStatic2007.
Variant generation mode: static.
Initializing tagger on localhost...


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

Processing 9337195.ti.1: Obstructive Sleep Apnea

Batch processing is finished.

The MetaMap program will populate the output file, cit00000.output, with the processed contents of cit00000

Last Modified: June 08, 2009

ii-public

Links to Our Sites

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.

Lister Hill Center Homepage Link - Image of Lister Hill Center

Lister Hill National Center for Biomedical Communications

U.S. National Library of Medicine

National Institutes of Health

Department of Health and Human Services