With the 2010 Release of MetaMap, we are retiring three previous versions of MetaMap,
namely MetaMap07, MetaMap08, and MetaMap08V2.
Only the MetaMap binary executables are being retired;
the MetaMap UMLS datasets corresponding to these releases
(i.e., 2007AA, 2008AA, and 2008AB) will remain available.
MetaMap2010 will be released for Linux and Mac OS/X;
we are currently working on deploying subsequent versions of MetaMap on Windows as well.
Please contact us if you need a Solaris version of MetaMap.
MetaMap 2010 includes less new functionality than previous releases
because the bulk of our development efforts since MetaMap09V2
have focused on converting MetaMap from
Quintus Prolog
to
SICStus Prolog,
which will henceforth be the principal implementation vehicle of MetaMap.
We migrated from Quintus to SICStus for several reasons:
We also converted MetaMap 2010 to version 4.8.24 of Berkeley DB,
which was recommended by SICS.
New functionality and enhancements delivered in MetaMap 2010 include the following:
Phrase: "tx" Meta Candidates (7): 1000 TX (Texas) [Geographic Area] 1000 TX (Turkmenistan) [Geographic Area] 1000 TX (Therapeutic procedure) [Therapeutic or Preventive Procedure] 1000 TX (Tumor stage TX) [Finding] 1000 TX (CASP4 gene) [Gene or Genome] 1000 TX (CASP4 protein, human) [Amino Acid, Peptide, or Protein,Enzyme] 1000 TX (CASP4 wt Allele) [Gene or Genome] Meta Mapping (1000): 1000 TX (CASP4 gene) [Gene or Genome] Meta Mapping (1000): 1000 TX (CASP4 protein, human) [Amino Acid, Peptide, or Protein,Enzyme] Meta Mapping (1000): 1000 TX (CASP4 wt Allele) [Gene or Genome] Meta Mapping (1000): 1000 TX (Texas) [Geographic Area] Meta Mapping (1000): 1000 TX (Therapeutic procedure) [Therapeutic or Preventive Procedure] Meta Mapping (1000): 1000 TX (Tumor stage TX) [Finding] Meta Mapping (1000): 1000 TX (Turkmenistan) [Geographic Area]
Some or all of these concepts may be considered undesirable by certain users
because of their ambiguity.
Of course they could all be excluded by using the
-k (exclude_semtypes) option to MetaMap,
but we now provide a simpler and more straightforward way to achieve that goal:
To exclude all concepts of length < 3, for example,
we can now call MetaMap with the command-line options --min_length 3,
and none of the two-character concepts above will be retrieved;
consequently no mappings will be constructed in the above example,
because all candidate concepts are of length < 3.
For another example, running MetaMap 2010 (strict model) on
the input text heart attack will generate the output
Phrase: "heart attack" Meta Candidates (8): 1000 Heart attack (Myocardial Infarction) [Disease or Syndrome] 861 Heart [Body Part, Organ, or Organ Component] 861 Attack, NOS (Onset of illness) [Finding] 861 Attack (Attack device) [Medical Device] 861 attack (Attack behavior) [Social Behavior] 861 Heart (Entire heart) [Body Part, Organ, or Organ Component] 861 Attack (Observation of attack) [Finding] 827 Attacked (Assault) [Injury or Poisoning] Meta Mapping (1000): 1000 Heart attack (Myocardial Infarction) [Disease or Syndrome]
If, however, we specify --min_length 6, the output will be instead
Phrase: "heart attack" Meta Candidates (6): 1000 Heart attack (Myocardial Infarction) [Disease or Syndrome] 861 Attack, NOS (Onset of illness) [Finding] 861 Attack (Attack device) [Medical Device] 861 attack (Attack behavior) [Social Behavior] 861 Attack (Observation of attack) [Finding] 827 Attacked (Assault) [Injury or Poisoning] Meta Mapping (1000): 1000 Heart attack (Myocardial Infarction) [Disease or Syndrome]
The final mapping does not change in this case,
but the two candidate concepts
861 Heart [Body Part, Organ, or Organ Component]
and
861 Heart (Entire heart) [Body Part, Organ, or Organ Component]
are not generated with --min_length 6
because heart contains only five characters.
<flang@indlx6> 491 : metamap10 INPUT /nfsvol/nls/bin/SKRrun.10 -L 2010 /nfsvol/nls/bin/metamap10.BINARY.Linux -Z 10 INPUT Berkeley DB databases (normal 10 strict model) are open. Static variants will come from table varsan in /nfsvol/nls3aux18/DB/DB.normal.10.strict. Derivational Variants: Adj/noun ONLY. Accessing lexicon /nfsvol/nls/specialist/SKR/src/lexicon//data/lexiconStatic2010. Variant generation mode: static. Beginning to process INPUT sending output to INPUT.out. Tagging will be done dynamically. metamap10.BINARY.SICStus.Linux (2010) Control options: mm_data_year=10 Processing 00000000.tx.1: heart attack. Established connection to Tagger Server on 130.14.111.123. Batch processing is finished. <flang@indlx6> 492 :
If, however, the --silent option is provided on the command line, the interaction will be far less verbose:
<flang@indlx6> 491 : metamap10 --silent INPUT /nfsvol/nls/bin/SKRrun.10 -L 2010 /nfsvol/nls/bin/metamap10.BINARY.Linux -Z 10 INPUT <flang@indlx6> 492 :