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.MetaMapLite uses some of the tables originally developed for MetaMap. Currenty, MetaMapLite does not support dynamic variant generation. 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.
Use can use MetaMap on the web at the Interactive MetaMapLite Page.
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 3.6.2rc3
The 3.6.2rc2 version of MetaMapLite is a release candidate for version 3.6.2
- Fixed error in tokenization when calling OpenNLP's Part-of-Speech tagger
- Merged UTF-8 handling code from UTF branch into master
- MetaMapLite 2018 3.6.2rc3 with Category 0 (Base) 2018AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 with Category 0+4+9 (USAbase) 2018AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc3 USABase (Category 0+4+9) data Version (WinZip - 1.2GB), [sha1sum], [md5sum]
MetaMapLite 3.6.2rc2
The 3.6.2rc2 version of MetaMapLite is a release candidate for version 3.6.2 that fixes the following issues:
- When using EntityLookup4 (i.e., setting metamaplite.enable.scoring = false), disabling postagging (i.e., setting metamaplite.enable.postagging = false) significantly reduces the number of entities found. On the same collection, I go from a median of 50 entities per document (with postagging = true) to a median of 0 entities per document (with postagging = false).
- When using MetaMapLite, EntityLookup4 is initialized every time processDocumentList list is called and again each time processDocument is called, while EntityLookUp5 is only re-initialized when needed.
- When using a non-standard data directory, the property: opennlp.en-pos.bin.path: $DATA_DIR/ models/en-pos-maxent.bin must be set. This property is not supplied in the template config file and MML falls back to using the hardcoded default value which results in a crash. It may be helpful to add this property to the generated config file so if a user is customizing their data directory they will know to adjust the properties accordingly.
- When using a non-standard data directory, the following properties
must be set for MMI file output or null pointer exceptions are thrown:
- metamaplite.index.directory: $DATA_DIR/ivf/2017AA/Base/strict/indices/
- metamaplite.ivf.meshtcrelaxedindex: $DATA_DIR/ivf/2017AA/Base/strict/indices/meshtcrelaxed
- MetaMapLite 2018 3.6.2rc2 with Category 0 (Base) 2018AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 with Category 0+4+9 (USAbase) 2018AA UMLS dataset (WinZip - 1g), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 binaryonly Version Contains MetaMapLite sources, jar files, and configuration, but no UMLS dataset. (WinZip - 250m), [sha1sum], [md5sum]
- MetaMapLite 2018 3.6.2rc2 USABase (Category 0+4+9) data Version (WinZip - 1.2GB), [sha1sum], [md5sum]
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 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 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 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
MetaMapLite README Documentation
- MetaMapLite 3.6.1 README Documentation
- MetaMapLite 3.6 README Documentation
- MetaMapLite 3.1 README Documentation
- MetaMapLite 3.0 README Documentation (Last Updated: September 26, 2016)
MetaMapLite Java API Documentation
- MetaMapLite 3.6.2rc2 JavaDoc Documentation
- MetaMapLite 3.6.1 JavaDoc Documentation
- MetaMapLite 3.6 JavaDoc Documentation
- MetaMapLite 3.5 JavaDoc Documentation
- MetaMapLite 3.4 JavaDoc Documentation
MetaMapLite Source Code
Publications
MetaMap Lite: an evaluation of a new Java implementation of MetaMap. Demner-Fushman D., Rogers WJ, Aronson AR. JAMIA. Volume 24, Issue 4, July 2017. DOI: 10.1093/jamia/ocw177. URL: https://academic.oup.com/jamia/issue/24/4. ALT URL: https://www.ncbi.nlm.nih.gov/pubmed/28130331.Sources
The Source code for MetaMapLite is supplied with the distribution in the directorypublic_mm_lite/src
. The source code is
also available at
the MetaMapLite
Github Page.