title: Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications.
abstract: Providing prior knowledge about biological properties of chemicals, such as kinetic values, protein targets, or toxic effects, can facilitate many aspects of drug development. Chemical information is rapidly accumulating in all sorts of free text documents like patents, industry reports, or scientific articles, which has motivated the development of specifically tailored text mining applications. Despite the potential gains, chemical text mining still faces significant challenges. One of the most salient is the recognition of chemical entities mentioned in text. To help practitioners contribute to this area, a good portion of this review is devoted to this issue, and presents the basic concepts and principles underlying the main strategies. The technical details are introduced and accompanied by relevant bibliographic references. Other tasks discussed are retrieving relevant articles, identifying relationships between chemicals and other entities, or determining the chemical structures of chemicals mentioned in text. This review also introduces a number of published applications that can be used to build pipelines in topics like drug side effects, toxicity, and protein-disease-compound network analysis. We conclude the review with an outlook on how we expect the field to evolve, discussing its possibilities and its current limitations.
authors.affiliation: Centro Nacional de Investigaciones Oncológicas, Biología Computacional y Estructural, Madrid, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Vazquez
authors.affiliation: Centro Nacional de Investigaciones Oncológicas, Biología Computacional y Estructural, Madrid, Spain.
authors.forename: Martin
authors.initials: M
authors.lastname: Krallinger
authors.affiliation: Centro Nacional de Investigaciones Oncológicas, Biología Computacional y Estructural, Madrid, Spain.
authors.forename: Florian
authors.initials: F
authors.lastname: Leitner
authors.affiliation: Centro Nacional de Investigaciones Oncológicas, Biología Computacional y Estructural, Madrid, Spain. valencia@cnio.es.
authors.forename: Alfonso
authors.initials: A
authors.lastname: Valencia
keywords: Chemical compounds; Drugs; Information extraction; Named entity recognition; Text mining