The Bio Term Hub provides access to biomedical terminology resources in a unified format. We envision its main use as a basis for text mining systems.
Select any of the external resources on the left to obtain a custom terminology list. The list is a tab-separated table with the following six fields:
CUI, source, native ID, term, preferred name, entity type
Each term (name/synonym) is on a separate row. As a recent addition (January 2019), the corresponding UMLS identifier (CUI) is given in the first column, if defined. The contents of the fields source and entity type can be modified using replacement patterns (uncover the Renaming section below using the triangle button). Submit your request with the Create resource button at the bottom of the page. Afterwards you will be offered the opportunity to annotate a text with the selected resources.
Aggregating, filtering, reformatting, and optionally renaming all this information takes time. Creation time mainly depends on the size of each resource. Compiling a list of all terminologies except for EntrezGene takes approximately 90 seconds; however, EntrezGene is very large, and processing it requires 3 to 4 minutes.
The requested terminology list is compiled on the fly, based on local copies of the external terminology resources. Whenever one of the local copies becomes out-of-date with respect to its remote source, an
Update button is shown next to the corresponding resource name. This button triggers downloading the latest version to our server. Please note that, due to data volume and bandwidth restrictions, updating may take several minutes for some of the resources.