Biomedical Text Mining and Its Applications

Mining Host-Pathogen Interactions

“…Rapid growth of published biomedical research has resulted in the development of a number of methods for biomedical literature mining over the last decade (Krallinger and Valencia 2005;Rodriguez-Esteban 2009). The methods dealing with the biomolecular information can be generally divided into three categories based on the domain of biomedical knowledge they target: (i) automated protein or gene name identification in a text Seki and Mostafa 2005;Tanabe, Xie et al 2005), (ii) literature-based functional annotation of genes and proteins (Chiang and Yu 2003;Jaeger, Gaudan et al 2008), and (iii) extracting the information on the relationships between biological molecules, such as proteins and RNAs, or genes (Hu, Narayanaswamy et al 2005;Shatkay, Hˆglund et al 2007;Lee, Yi et al 2008).…”

Biomedical Web, Collections and Meta-Analysis Literature Applications

“…It is used to generate new knowledge interesting, plausible, and intelligible (Ananiadou et al, 2006). Linking two or more literature concepts that have so far not been linked (i.e., disjoint) through the use of software and algorithms designed for this purpose (Rodriguez-Esteban, 2009). …”

Towards Confidence Estimation for Typed Protein-Protein Relation Extraction

“…The ever increasing body of biomedical literature has motivated a growing interest over the past 20 years in natural language processing (NLP) and information extraction (IE) techniques to retrieve, organize and index the knowledge it contains (Rodriguez-Esteban, 2009;Subramaniam et al, 2003). It has also spurred a number of (shared) tasks and system competitions of which the best known are the BioNLP Shared Task 1 and the BioCreative challenge 2 .…”