Biomedical Named Entity Recognition: A Survey of Machine-Learning Tools

It is well known that the rapid growth and dissemination of the Internet has resulted in huge amounts of information generated and shared, available in the form of textual data, images, videos or sounds. This overwhelming surge of data is also true for specific areas such as biomedicine, where the number of published documents, such as articles, books and technical reports, is increasing exponentially. For instance, the MEDLINE literature database contains over 20 million references to journal papers, covering a wide range of biomedical fields. In order to organize and manage these data, several manual curation efforts have been set up to identify, in texts, information regarding entities (e.g. genes and proteins) and their relations (e.g. protein-protein interactions). The extracted information is stored in structured knowledge resources, such as Swiss-Prot [1] and GenBank [2]. However, the ef‐ fort required to continually update these databases makes this a very demanding and ex‐ pensive task, naturally leading to increasing interest in the application of Text Mining (TM) systems to help perform those tasks.