The BioLink SIG Workshop at ISMB2004

The Special Interest Group (SIG) on Text Mining (or BioLINK — Biological Literature, Information and Knowledge; http://www.pdg.cnb.uam.es/BioLINK/) was created to address the need for communication and interchange of ideas in the field of text mining and information extraction applied to biology and biomedicine. Information extraction (IE) is an outgrowth of work in automated natural language processing, which began in the 1950s with work on transformational grammar by Zellig Harris [5,6] and later Noam Chomsky [3,4]. Information extraction technology made rapid progress starting in the late 1980s, thanks to a series of conferences focused on evaluation of IE: the Message Understanding Conferences [1]. There is also a long history of research on applications in medicine. Applications to the medical field focus on two distinct sub-problems: improved access to the medical literature and extraction of information from patient records. Despite these successes in other fields, natural language processing (NLP) techniques were not introduced in biology until the late 1990s. Even today, there are two distinct groups: on the one hand, researchers with a background in computer science, and on the other hand, their colleagues with a background in the life sciences, with only limited interaction between the two groups. To improve this situation, the BioLINK group holds regular open meetings to bring together researchers developing text data mining tools and related language processing methods to manage the information explosion in the biomedical field. They include invited and contributed papers, with a focus on developing shared infrastructure (tools, corpora, ontologies) and challenge evaluations, in the style of the KDD Challenge Cups [2]. This year, the BioLINK SIG meeting focused on resources and tools for text mining, with special emphasis on the evaluation of these tools. Speakers from the following areas were invited: