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i2b2 Sponsored Project - Mapping tools

A set of mapping tools have been created to assist with the assignment, verification, integration, export and import of mappings between two ontologies. In version 1.1 we add the ability to automate mappings to any UMLS ontology using the UMLS MetaMap.

The need for Mapping tools

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Workbenches are provided for both Windows and Mac.  These workbenches are pre-configured to point to a Demo MetaMap project instance on Amazon.   The new automate feature requires that you have or obtain a valid UMLS Terminology Services (UTS) account. (https://uts.nlm.nih.gov/home.html).

Download the workbench for Windows or Mac in the Mapping Software section, unzip.  Double click on the hive icon to get started.  i2b2 user name and password are demo/demouser.  To run the demo, select vocabulary = ICDCM, Knowledge source = 1415 and category = ICD9.

MetaMap Demo workbench for Windows

MetaMap Demo workbench for the Mac

 

 

Tutorials

Mapping Tools Overview  An overview of the tool's features.

Mapping Tools Users Guide  The users guide and definitive source for how to use the tools

Mapping Software

Below are packages for the Mapper Cell and workbenches preconfigured with the Mapping tools.  The workbenches supercede the demo packages listed above.  A set of mapping demo data is also provided that mimics the data on the Amazon demo instance. The workbench is also preconfigured to point to a Demo MetaMap instance on Amazon. i2b2 user name and password are demo/demouser. To run the demo, select vocabulary = ICDCM, Knowledge source = 1415 and category = ICD9.

Metamap Data Package  Collection of scripts to load sample data to map to ICD9

Ontology Mapping Data Installation Guide How to install the sample mapping data package.

Ontology_Mapper cell source code.package  Source code package for installing the Ontology Mapper cell.

Ontology_Mapping Cell Installation Guide  Installation guide for Ontology Mapper cell.  Works with 1.7 i2b2 hive.

MetaMap workbench for Windows version 1.1  Windows version of workbench including the new automated (MetaMap) mapping plugin.

MetaMap workbench for Mac version 1.1  Mac version of workbench including the new automated (MetaMap) mapping plugin.