Release Announcement for MetaMap and MetaMap Tools

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Wednesday, September 24, 2008 Announcing release of the MetaMap and MetaMap Tools In 1999, the MMTx (MetaMap Transfer) project was started with the goal of developing a publicly distributable version of MetaMap to provide users outside of the U.S. National Library of Medicine (NLM) with access to the processing capabilities of the MetaMap program and to allow users to process on their own machines using their own databases if they wished. MMTx was created at the time because there were no technical means of distributing MetaMap itself. We launched the first version of MMTx in mid 2001, and have subsequently provided nine additional versions including the current 2.4.C version of MMTx. In late 2007, the MetaMap/MMTx group started discussing the possibility of releasing the actual MetaMap program to the public. The technology was finally in place to allow for the possibility of a release, and MMTx users had been complaining about the speed and consistency of MMTx for some time. On February 6, 2008, we launched a survey of users who had downloaded MMTx to introduce the idea of a MetaMap public release and to gauge how our users might feel about a change of this magnitude. The survey responses provided us with a good idea of the different platforms being used, and how much users were modifying the MMTx program and databases. We've reviewed all of the survey responses and incorporated as many suggestions as we could, and now feel that we are finally ready to begin releasing the actual MetaMap program. We are looking to phase the release of MetaMap with a version for Linux first and then follow with a version for Windows. MetaMap is now available from our new web site: http://metamap.nlm.nih.gov Important Notes There are no immediate plans to drop MMTx. We are looking at freezing the current version of MMTx, doing major bug fixes as time permits, and providing new datasets until support is stopped on MMTx. We are going to develop a Java-based API for MetaMap to allow existing programs to swap out MMTx and use MetaMap instead. The DataFileBuilder Java software will still be provided and supported to allow users to create their own databases to be used with both MMTx and MetaMap. Benefits of MetaMap versus MMTx The biggest benefit users will see is speed! MetaMap is two to five times faster then MMTx depending on the options you are using and the makeup of your data. Consistency with results from the SKR Interactive and Batch facilities is also a big benefit. All through the MMTx development cycle we’ve tried to get the results to match those of MetaMap and were only able to do so for about 92% of the cases. The public release of MetaMap provides users with the exact same version of MetaMap used in-house and the results should be identical. MetaMap is our development code base and thus has the latest modifications, while MMTx will be frozen at the current release and support will be limited to major bug fixes only with the public release of MetaMap. Downsides of MetaMap versus MMTx Currently there is no Java API for MetaMap. MMTx is easily integrated into Java programs and we will build a Java API for MetaMap before MMTx is retired. Quintus Prolog (http://www.sics.se/quintus/) from the Swedish Institute of Computer Science (SICS) will be required if you want to modify any of the MetaMap source code. Quintus requires a fee for the use of their Prolog. MMTx on the other hand only required Java which is freely available. MetaMap is currently only available for Linux and we are working on Windows. MMTx is supported on Solaris, Linux, Windows, and MacOS. MetaMap will not be supported under Solaris -- we are being moved over to Linux and Solaris will not be supported in the future. MetaMap will not run under MacOS due to limitations of the Prolog we are using. We are looking to migrate to a different version of Prolog that has better Windows and MacOS support.

Last Modified: September 24, 2008							ii-public
Links to Our Sites MetaMap Public Release NEW: Distributable version of the actual MetaMap program. Indexing Initiative (II) Investigating computer-assisted and fully automatic methodologies for indexing biomedical text. Includes the NLM Medical Text Indexer (MTI). Semantic Knowledge Representation (SKR) Develop programs to provide usable semantic representation of biomedical text. Includes the MetaMap and SemRep programs. MetaMap Transfer (MMTx) Java-Based distributable version of the MetaMap program. Word Sense Disambiguation (WSD) Test collection of manually curated MetaMap ambiguity resolution in support of word sense disambiguation research. Medline Baseline Repository (MBR) Static MEDLINE Baselines for use in research involving biomedical citations. Allows for query searches and test collection creation.
	Lister Hill National Center for Biomedical Communications			U.S. National Library of Medicine			National Institutes of Health
							Department of Health and Human Services
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