The explosion of free text in healthcare (such as electronic health records, and research papers) creates important opportunities that can benefit from Natural Language Processing (NLP) technologies for mining information and knowledge from the text. Examples include extracting patients’ background (occupation, HIV stats, prescription) from their records, or labelling protein, DNA/RNA and cell types from biomedical literature.

GATE is a free and open source NLP toolkit that provides support for a wide variety of biomedical NLP tasks. Examples of GATE biomedical applications include:

  1. UMLS named entity linking tool
  2. NER from prescriptions, extracting drug names and dosages
  3. Expansion, annotation and coreference of biomedical abbreviations and acronyms
  4. Extraction of organism mentions from the biomedical literature
  5. Provision of GATE wrappers for various Biomedical applications
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