GATE in Biomedical
Text Processing
Biomedical entity linking
Entity linking is the task of recognising and disambiguating entities from free text. Entity linking can be used in information retrieval systems to improve search performance and enable semantic search.
Bio-Yodie is a biomedical entity linking tool derived from GATE Yodie. It links mentions in biomedical text to their referents in the UMLS, a large and popular compendium of medical vocabularies. Bio-Yodie has been used in several biomedical information retrieval systems such as Kconnect, Khresmoi and CogStack.
Why we need Bio-Yodie in information retrieval systems
The explosion of biomedical paper and electronic health records requires more robust and faster search to find useful information. Documents annotated with Bio-Yodie are able to provide search engines with such abilities. For example, with the Khresmoi Search we can quickly find the patient records that mention drugs used to treat disorders commonly associated with depression.