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4.3 Bioinformatics Bio-entity recognition aims to identify and classify technical terms in the domain
of molecular biology that correspond to instances of concepts that are of interest
to biologists. Examples of such entities include the names of proteins, genes and
their locations of activity such as cells or organism names. Entity recognition is
becoming increasingly important with the massive increase in reported results
due to high throughput experimental methods. It can be used in several higher
level information access tasks such as relation extraction, summarization and
Recently the GENIA corpus was provided as a benchmark data set to compare
different entity extraction approaches (Kim et al. 2004). It contains 2,000
abstracts from the MEDLINE database which were hand annotated with 36 54 LDV-FORUM A Brief Survey of Text Mining
types of biological entities. The following sentence is an example: “We have
shown that <protein> interleukin-1 </protein> (<protein> IL-1 </protein>) and
<protein> IL-2 &l...
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