MetaMap: TOOLS

MetaMap

Prerequisites:

  • MetaMap requires a minimum of 16GB of disk space when it has been uncompressed.
  • MetaMap requires a minimum of 2GB of memory to run. At least 4GB 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 Java Runtime Environment (JRE). We have tested MetaMap with JRE 1.7. The JRE is required to run the SKR/MedPost Part-of-Speech (POS) Tagger Server which is required for MetaMap to run properly. JRE 1.7 or greater is required for the Word Sense Disambiguation (WSD) Server which must be running if you intend on using the WSD option (-y) when running MetaMap. Also, if you using a 64-bit JRE, at least 6 gigabytes of memory is required for the WSD server, 3 gigabytes of memory is required for 32-bit JREs. The JRE is available from: http://www.java.com NOTE: if you plan on creating your own datasets using the MetaMap Datafile Builder suite, JRE 1.7 or greater is required.
  • To use MetaMap, you must comply with the MetaMap Terms and Conditions.
  • To download MetaMap, 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.

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 Indexing Initiative Research Information Site. We also recommend using 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 (see section below) and install our MetaMap program. 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.