MetaMap 2009
(30 Jul 2009)

• Release Notes (HTML)
• Readme (HTML)
• Usage (HTML)

MetaMap 2008 v2
(25 Mar 2009)

• Release Notes (HTML)

MetaMap 2008
(24 Sep 2008)

• Release Notes (HTML)
• Readme (HTML)
• Usage (HTML)

MetaMap 2007
(24 Sep 2008)

• Readme (HTML)
• Usage (HTML)

• Usage Statistics

About MetaMap

MetaMap is a highly configurable program developed by Dr. Alan (Lan) Aronson at the National Library of Medicine (NLM) to map biomedical text to the UMLS Metathesaurus or, equivalently, to discover Metathesaurus concepts referred to in text. MetaMap uses a knowledge intensive approach based on symbolic, natural language processing (NLP) and computational linguistic techniques. Besides being applied for both IR and data mining applications, MetaMap is one of the foundations of NLM's Medical Text Indexer (MTI) which is being applied to both semiautomatic and fully automatic indexing of biomedical literature at NLM. For more information on MetaMap and related research, see the the SKR Research Information Site. (http://skr.nlm.nih.gov/papers/index.shtml)

Avenues to MetaMap:

Web Access	Our Semantic Knowledge Representation (SKR) website provides both Interactive and Batch facilities that allow users to send text to our internal machines and run various programs including the MetaMap program. The Interactive facility is designed for testing options and running small amounts of text. The Batch facility runs large amounts of text through our Scheduler program which distributes the workload over a large pool of clients.	GO TO SKR
MetaMap	Distributable version of the original Prolog MetaMap program. Currently only includes binary distribution for Solaris and Linux platforms.	GO TO MetaMap
SKR API	Java-based API to the SKR Scheduler facility was created to provide users with the ability to programmatically submit jobs to the Scheduler Interactive and Batch facilities instead of using the web-based interfaces. We have tried to reproduce full functionality for all of the programs under the SKR Scheduler umbrella. The SKR API has been tested on the Solaris, Linux, and Windows XP platforms.	GO TO SKR API
NOTE: MMTx is no longer supported except for major bug fixes. We recommend all users switch to the downloadable MetaMap (described above) if possible.
MMTx	MetaMap Transfer (MMTx) is a java-based distributable version of the MetaMap program. Includes binary and source distributions and is supported on Solaris, Linux, Windows, and Mac platforms. MMTx was an early attempt at providing a distributable version of MetaMap and is currently being phased out in favor of the original Prolog version of MetaMap. There are two reasons for the phase out of MMTx: 1) The original Prolog version of MetaMap is much faster, especially now with the new speed enhancements (V2). 2) We were never able to make the results the same between MMTx and MetaMap - there was always about a 20% difference in the overall results MMTx would produce.	GO TO MMTx

New to MetaMap, or confused as to what you should use?

If you are new to MetaMap, or are unsure where to start, we would recommend starting with our research papers on MetaMap at the MetaMap section of the SKR Research Information Site (URL: http://skr.nlm.nih.gov/papers/index.shtml#MetaMap). We also recommend that people use our Interactive web interface first to get a feel for how MetaMap works and how the various options affect the results. Once you have a good feel for what you would like to do, the decision comes down to how much control you want of your data. If you need to run everything locally, you are going to need to download and install either our MetaMap program or our MMTx program depending on what is available for your platform of choice. If you do not need to maintain control of your data, we offer a Batch facility for processing large sets of data through our pool of clients. You can access our Batch facility through our SKR web site, or through our Java-based SKR API. In either case, your data is uploaded to our web site, processed by our Scheduler program, and then the results are provided to you. We maintain your data and results for a maximum of 15 days and then they are purged from our systems. Only you and our team have access to the data and results. We only review Batch jobs when there is a specific request, or we see a Batch job causing problems with the Scheduler.

Prerequisites:

• MetaMap requires a minimum of 7GB of disk space when it has been uncompressed.
• MetaMap requires a minimum of 1GB of memory to run. At least 2GB is recommended.
• You will need a working version of bunzip2 to uncompress the MetaMap download file. If you do not have a copy of bunzip2, it is available from http://www.bzip.org/.
• To run MetaMap, you will need the Sun Java Runtime Environment (JRE). We have tested MetaMap with Sun's JRE 1.4.2, 1.5, and 1.6.0_07-b06. The JRE is required to run the SKR/MedPost Part-of-Speech (POS) Tagger Server which is required for MetaMap to run properly. The JRE is also used for the Word Sense Disambiguation (WSD) Server which must be running if you intend on using the WSD option (-y) when running MetaMap. The Sun JRE is available from: http://java.sun.com
• To use MetaMap, you must comply with the MetaMap Terms and Conditions.
• To download MetaMap, you must have access to a UMLSKS account. For more information about how we use UMLSKS authentication data, or for information on how to acquire a UMLSKS account, please see the UMLSKS Account Information Page.

  UMLS agreement.

  The UMLS agreement requires those who use the UMLS to file a brief report once a year to summarize their use of the UMLS. It also requires the acknowledgment that the UMLS contains copyrighted material and that those copyright restrictions be respected. The UMLS agreement requires users to agree to obtain agreements for EACH copyrighted source prior to it's use within a commercial or production application - Use of all the sources is permitted if the application is used for research purposes only.

Downloads:

PLEASE NOTE: The downloads are restricted and require a valid UMLSKS username and password! Please see the above list of prerequisites before attempting to download MetaMap.

NOTE: If you have already installed the 2008 MetaMap, you will just need to use the Binary Update download and Binary Update Installation instructions. You do not need to do a complete re-install.

Currently, each of the full downloads contains a binary version of MetaMap compiled specifically for either Linux or Solaris, and we have included the Strict Data Model for each of the years respectively. We plan to also include the Relaxed Data Model for each year and we are working on updating the DataFileBuilder to work with MetaMap. These features will be phased in as they are completed and tested.

Installation:

Move the downloaded file into a directory where you want to install MetaMap. This directory will then be referred to as <parent_directory> throughout the rest of the installation instructions.

To extract the MetaMap distribution, use the following bunzip2 and tar commands substituting the appropriate name of the file you downloaded (e.g., public_mm_linux_2008.tar.bz2, public_mm_solaris_2008.tar.bz2, public_mm_linux_2007.tar.bz2, or public_mm_solaris_2007.tar.bz2):

To begin the initial install, go to the directory created when you extracted the distribution (public_mm).

To find out where your java installation is located, use the following command:

setenv JAVA_HOME /usr/local/jre1.4.2

export JAVA_HOME=/usr/local/jre1.4.2

JAVA_HOME=/usr/local/jre1.4.2
export JAVA_HOME

setenv PATH <parent dir>/public_mm/bin:$PATH

export PATH=<parent dir>/public_mm/bin:$PATH

PATH=<parent dir>/public_mm/bin:$PATH
export PATH

% cd <parent dir>/public_mm
% ./bin/install.sh
Enter basedir of installation [<parent dir>/public_mm] <user hits return to get the default>
Basedir is set to <parent dir>/public_mm.

The WSD Server requires Sun's Java Runtime Environment (JRE)
Sun's Java Developer Kit (JDK) will work as well. if the
command: "which" java returns /usr/local/jre1.4.2/bin/java, then the
JRE resides in /usr/local/jre1.4.2/.

Where does your distribution of Sun's JRE reside?
Enter home path of JRE (JDK) [/usr]: /nfsvol/nls/tools/Linux-i686/java1.4.2
Using /nfsvol/nls/tools/Linux-i686/java1.4.2 for JAVA_HOME.

<parent dir>/public_mm/WSD_Server/config/disambServer.cfg generated
<parent dir>/public_mm/WSD_Server/config/log4j.properties generated
<parent dir>/public_mm/bin/SKRrun generated.
<parent dir>/public_mm/bin/metamap07 generated.
<parent dir>/public_mm/bin/wsdserverctl generated.
<parent dir>/public_mm/bin/skrmedpostctl generated.
Install complete.

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MetaMap requires the starting of one or two servers depending on how you plan to use MetaMap. The SKR/MedPost Part-of-Speech Tagger Server is required regardless of how you use MetaMap. The Word Sense Disambiguation (WSD) Server is optional and only needs to be started if you want/plan to use the WSD option (-y) with MetaMap. They can be started and stopped as follows. Both servers will automatically run in the background when started.

Starting the SKR/Medpost Part-of-Speech Tagger Server:

MetaMap (2007)

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

Processing 00000000.tx.1: lung cancer

Phrase: "lung cancer"
Meta Candidates (8):
  1000 C0242379:Lung Cancer (Malignant neoplasm of lung) [Neoplastic Process]
  1000 C0684249:Lung Cancer (Carcinoma of lung) [Neoplastic Process]
  861 C0006826:Cancer (Malignant Neoplasms) [Neoplastic Process]
  861 C0024109:Lung [Body Part, Organ, or Organ Component]
  861 C0998265:Cancer (Cancer Genus) [Invertebrate]
  861 C1278908:Lung (Entire lung) [Body Part, Organ, or Organ Component]
  861 C1306459:Cancer (Primary malignant neoplasm) [Neoplastic Process]
  768 C0032285:Pneumonia [Disease or Syndrome]
Meta Mapping (1000):
  1000 C0684249:Lung Cancer (Carcinoma of lung) [Neoplastic Process]
Meta Mapping (1000):
  1000 C0242379:Lung Cancer (Malignant neoplasm of lung) [Neoplastic Process] 

Binary Update Installation:

Before you update MetaMap, if you run the following command, you should receive an error. Afterwards, the command should work fine.

#### ERROR: skr_phrase failed on 00000000.tx.1 lung cancer

Before you extract the binary distribution files, you should backup the affected files.

% cd public_mm/bin
% mkdir Backup
% cp metamap08.BINARY install.sh SKRrun.in Backup
% cd ../..

Un-Install:

% cd <parent directory of installation>
% ./public_mm/bin/uninstall.sh
Do you really want to uninstall MetaMap? [no/yes] yes
Removing Tagger Server
Removing WSD Server
Removing Lexicon
Removing MetaMap Databases
Removing Programs
Removing Base Directory
Removal of MetaMap installation successful.
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