Introduction
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.
Description
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
- If you would like to try out the Custom Taxonomy Builder; a service using the level0 version of UMLS is available at: at https://ii.nlm.nih.gov/ctb.
- A downloadable version of CTB including the 2016AB level0 UMLS is available at https://data.lhncbc.nlm.nih.gov/umls-restricted/ii/tools/MetaMap/download/new/ctb-level0-2016AB.zip.