ISMB 2003 Text Mining SIG Meeting Report

The third meeting of the Special Interest Group (SIG) for Text Mining was held in conjunction with ISMB in Australia this year, following the 2001 meeting in Copenhagen and the 2002 meeting in Edmonton. The Text Mining SIG has been organized by the BioLINK group (http://www.pdg.cnb.uam.es/BioLINK), with its main contributors Lynette Hirschman (MITRE, Bedford, MA, USA) and Alfonso Valencia (CNB, Madrid, Spain), together with this year’s local organizers Christian Blaschke (CNB), Marc Light (University of Iowa, USA) and Alexander Yeh (MITRE). The SIG’s main goal has been to foster communication in text mining and information extraction applied to biology and biomedicine. To this end, the BioLINK group holds regular open meetings to bring together researchers from the field to interchange ideas and share them with a wider community interested in the latest developments. In the past two meetings, the Text Mining SIG has included reports from related SIGs (e.g. BioOntologies and BioPathways). 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 and later Noam Chomsky. 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 (MUCs). There has also been a long history of research on applications in medicine. Applications to the medical field focus on two distinct sub-problems: (a) improved access to the medical literature; and (b) extraction of information from patient records. Despite the successes in other fields, Natural Language Processing (NLP) techniques were not introduced into biology until the late 1990s. The field has been dominated by two, not necessarily convergent, approaches: (a) application-orientated, where simple methods are used (possibly too simple) to address ‘real’ biological problems; and (b) tool-orientated, where complex, state-of-the-art NLP methods are used to address problems that are not always relevant to biologists. During the SIG meeting, it became apparent that three major bottlenecks hinder current development: