MetaMapLite

Overview:

The primary goal of MetaMapLite to provide a near real-time named-entity recognizer which is not a rigorous as MetaMap but is much faster while allowing users to customize and augment its behavior for specific purposes.

It uses some of the tables used by MetaMap but all lexical variants used in the table are pre-processed. Named Entities are found using longest match. Restriction by UMLS source and Semantic type is optional. Part-of-speech tagging which improves precision by a small amount (at the cost of speed) is also optional. Negation detection is available using either Wendy Chapman's context or a native negation detection algorithm based on Wendy Chapman's NegEx which is somewhat less effective, but faster.

Prerequisites:

MetaMapLite requires a minimum of 16GB of disk space when it has been uncompressed.
MetaMapLite requires a minimum of 2GB of memory to run. At least 4GB is recommended.
You will need a working version of bunzip2 or WinZip or 7-Zip to uncompress the MetaMapLite download file depending on which one you download. If you do not have a copy of bunzip2, it is available from http://www.bzip.org/. Similarly, WinZip is available from http://www.winzip.com/. And 7-Zip is available at http://www.7-zip.org.
To run MetaMapLite, you will need the Java Runtime Environment (JRE). We have tested MetaMapLite with JRE 1.8. The JRE is available from: http://www.java.com
To use MetaMapLite, you must comply with the MetaMap Terms and Conditions.
To download MetaMapLite, you must have accepted the terms of the UMLS Metathesaurus License Agreement, which requires you to respect the copyrights of the constituent vocabularies and to file a brief annual report on your use of the UMLS. You also must have activated a UMLS Terminology Services (UTS) account. For information on how we use UTS authentication please select the Info icon to the right:

For details of the licenses see the UMLS Metathesaurus License Agreement and How to License and Access the Unified Medical Language System® (UMLS®) Data.

Downloads

MetaMapLite 3.6.1p1

The 3.6.1p1 version of MetaMapLite is a bugfix release that fixes the following issue:

Fixes an error where docid is not propagated to Entity records in output result.

MetaMapLite 2017 3.6.1p1 with Category 0 (Base) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1p1 with Category 0+4+9 (USAbase) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1p1 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1p1 SNAPSHOT USABase (Category 0+4+9) data Version (WinZip - 1.2GB), [sha1sum], [md5sum]

MetaMapLite 3.6.1

The 3.6.1 version of MetaMapLite is a bugfix release that fixes the following issue:

Fixes an error in the method which removes entities which are subsumed by a larger entity in which some entities that were not subsumed were removed.

MetaMapLite 2017 3.6.1 with Category 0 (Base) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1 with Category 0+4+9 (USAbase) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
MetaMapLite 2017 3.6.1 SNAPSHOT USABase (Category 0+4+9) data Version (WinZip - 1.2GB), [sha1sum], [md5sum]

MetaMapLite 3.6

The 3.6 version of MetaMapLite is a bugfix release that fixes the following issues:

Fixes an error in the longest match algorithm in which entities which were subsumed by a longer enitity were not removed.
Includes an example of creating a result formatter.
Readme documentation has been updated.

MetaMapLite 2017 3.6 with Category 0 (Base) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6 with Category 0+4+9 (USAbase) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.6 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
MetaMapLite 2017 3.6 SNAPSHOT USABase (Category 0+4+9) data Version (WinZip - 1.2GB), [sha1sum], [md5sum]

MetaMapLite 3.5

The 3.5 version of MetaMapLite is a bugfix release that fixes the following issues:

The negation status of a concept was not refected in the MMI fielded output.
The location of chunker model file was not user modifiable.
The default properties file was missing a reference to the treecodes file used for MMI fielded output.
Readme documentation has been updated.

MetaMapLite 2017 3.5 with Category 0 (Base) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.5 with Category 0+4+9 (USAbase) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.5 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]

MetaMapLite 3.4

The 3.4 version of MetaMapLite now optionally adds scoring similar to the original MetaMap of concept mapping results for BRAT output and ranked indexing results for MMI Output using MetaMap's Ranked Indexing algorithm. MMI Results may be somewhat different from MetaMap's due to differences in MetaMapLite's mapping scores which are supplied as input to the MMI Ranked Indexing algorithm.

MetaMapLite 2017 3.4 with Category 0 (Base) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
MetaMapLite 2017 3.4 with Category 0+4+9 (USAbase) 2017AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]

MetaMapLite 2016 3.1 SNAPSHOT

MetaMapLite 2016 3.1 SNAPSHOT Version (WinZip - 601 MB), [sha1sum], [md5sum]
MetaMapLite 2016 3.1 SNAPSHOT Version (Bzip2 Tar - 544 MB), [sha1sum], [md5sum]

MetaMapLite 2016 3.0 SNAPSHOT

MetaMapLite 2016 3.0 SNAPSHOT Version (Bzip2 Tar - 544 MB), [sha1sum], [md5sum]

Example MetaMapLite Servlet

Example of using MetaMapLite in a Servlet instance. The archive provides a minimal example of ANT project demonstrating the use of MetaMapLite in a servlet instance.

Documentation

Sources

The Source code for MetaMapLite is supplied with the distribution in the directory public_mm_lite/src. The source code is also available at the MetaMapLite Github Page.