Text mining in Biomedical informatics

Content:

The class in this week is very interesting. With the introduction by Dr.Gonzalez, I first time get the chance to touch what is text mining, which I felt mysterious and attractive for a long time. The most often application of the text mining technology in our daily life I think should be google, which provide a powerful text searching and analytical service in tons of web, articles and even pictures to find what we are looking for. Although I still do not know how the powerful google search engine realize the text mining technology and the detail about what kind of algorithms are involved, these two lectures absolutely stimulate my curiousness in text mining field. Other than web search engine, the text mining technology also has broad application in biomedical field. In biomedical research field, text mining technology is usually combined with natural language processing and computational linguistics to be applied in bioinformatics and medical informatics. One big application is what we have already heard thousand times, the NCBI PubMed, which use text mining technology to extract biomedical and molecular biology literature from increasing number of electronically available publications stored in database. The other main development of text mining in biomedical field is in the identification of biological entities, so called entity recognition, such as protein and gene names in free text, the association of gene clusters obtained by microarry experiments with the biological context provided by the corresponding literature, automatic extraction of protein interactions and associations of proteins to functional concepts. One sofware tool developed using text mining technology is the FABLE, which is a gene-centric text-mining search engine for MEDLINE. The interested one can go here to try it: http://fable.chop.edu/.

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Di Pan