Thematic Session: Text Mining in Biomedicine

Abstract

This thematic session follows a series of workshops and conferences recently dedicated to bio text mining in Biology. This interest is due to the overwhelming amount of biomedical literature, Medline alone contains over 14M abstracts, and the urgent need to discover and organise knowledge extracted from texts. Text mining techniques such as information extraction, named entity recognition etc. have been successfully applied to biomedical texts with varying results. A variety of approaches such as machine learning, SVMs, shallow, deep linguistic analyses have been applied to biomedical texts to extract, manage and organize information. There are over 300 databases containing crucial information on biological data. One of the main challenges is the integration of such heterogeneous information from factual databases to texts. One of the major knowledge bottlenecks in biomedicine is terminology. In such a dynamic domain, new terms are constantly created. In addition there is not always a mapping among terms found in databases, controlled vocabularies, ontologies and “actual” terms which are found in texts. Term variation and term ambiguity have been addressed in the past but more solutions are needed. The confusion of what is a descriptor, a term, an index term accentuates the problem. Solving the terminological problem is paramount to biotext mining, as relationships linking new genes, drugs, proteins (i.e. terms) are important for effective information extraction. Mining for relationships between terms and their automatic extraction is important for the semi-automatic updating and populating of ontologies and other resources needed in biomedicine. Text mining applications such as question-answering, automatic summarization, intelligent information retrieval are based on the existence of shared resources, such as annotated corpora (GENIA) and terminological resources. The field needs more concentrated and integrated efforts to build these shared resources. In addition, evaluation efforts such as BioCreaTive, Genomic Trec are important for biotext mining techniques and applications.

The aim of text mining in biology is to provide solutions to biologists, to aid curators in their task. We hope this thematic session addressed techniques and applications which aid the biologists in their research.