Table of Contents
Running MetaMap:
To run the MetaMap program from the command line, you have two options:- 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 - You can simply run the MetaMap command by specifying the full
path to the command.
<parent dir>/public_mm/bin/metamap09Whichever option you decide on, the command line statement to run MetaMap is:% metamap09 [Options] [InputFile] [OutputFile]For more information on MetaMap usage, please refer to MetaMap 2009 Usage (HTML), or use the MetaMap help command:% metamap09 --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 |
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% ./bin/metamap09 /test/linux/public_mm/bin/SKRrun -L 2009 -M /DATA/XDR -B /BDB4 \ -w /test/linux/public_mm/lexicon /test/linux/public_mm/bin/metamap09.BINARY -Z 09 MetaMap (2009) Control options: mm_data_year=09 Berkeley DB databases (normal strict 09 model) are open. Static variants will come from table varsan in /test/linux/public_mm/DB/BDB4/DB.normal.09.strict. Derivational Variants: Adj/noun ONLY. Accessing lexicon /test/linux/public_mm/lexicon/data/BDB4/lexiconStatic2009. Variant generation mode: static. |: Obstructive Sleep Apnea |: Established connection to Tagger Server on localhost. Processing 00000000.tx.1: Obstructive Sleep Apnea Phrase: "Obstructive Sleep Apnea" Meta Candidates (11): 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 Obstruction [Individual Behavior,Pathologic Function] 755 Sleepy [Finding] 755 Sleeplessness [Sign or Symptom] 755 Obstruction (Obstruction within Medical Device) [Phenomenon or Process] Meta Mapping (1000): 1000 Obstructive sleep apnoea (Sleep Apnea, Obstructive) [Disease or Syndrome] |: |
MetaMap on a small MEDLINE Abstract to a named output file. |
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% metamap09 cit00000 cit00000.output /test/linux/public_mm/bin/SKRrun -L 2009 -M /DATA/XDR -B /BDB4 \ -w /test/linux/public_mm/lexicon /test/linux/public_mm/bin/metamap09.BINARY -Z 09 MetaMap (2009) /nfsvol/nls/bin/SKRrun -L 2009 /nfsvol/nls/bin/metamap09.BINARY -Z 09 Control options: mm_data_year=09 Berkeley DB databases (normal strict 09 model) are open. Static variants will come from table varsan in /test/linux/public_mm/DB/BDB4/DB.normal.09.strict. Derivational Variants: Adj/noun ONLY. Accessing lexicon /test/linux/public_mm/lexicon/data/BDB4/lexiconStatic2009. Variant generation mode: static. Beginning to process cit00000 sending output to cit00000.output. Tagging will be done dynamically. Processing 9337195.ti.1: Obstructive Sleep Apnea Established connection to Tagger Server on localhost. Batch processing is finished. % |
MetaMap will populate the output file cit00000.output with the processed contents of cit00000.