TOOLS: MetaMap

CTB - Custom Taxonomy Builder


For users interested in creating their vocabulary in an online Graphical User Interface (GUI), we developed a Custom Taxonomy Builder (CTB) that allows submitting a set of seed terms for a given task or phenotype, edit the automatically-generated taxonomy, and download the custom-built files for use with MetaMap Lite or MetaMap.


Given a list of seed terms and a set of UMLS files, the Custom Taxonomy Builder (CTB) generates a set of new UMLS-like concept records along with a subset the of UMLS containing the supplied terms and their word-based variants. CTB attempts to use sub-synonymy to infer which concepts map to a term in the termlist. If a mapping can not be found a synthetic concept outside of the UMLS is used. The set of mappings generated by the tool is then displayed to the user in a tree editor were the can select which terms in each concept should be used in the custom dataset. The tool will generate UMLS-like MRCONSO and MRSTY files using the supplied terms and the selected set of term synonyms.

CTB Resources