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Text Mining in Biomedical Research

Text Mining in Biomedical Research. QI LI 03/28/14. references. http:// en.wikipedia.org/wiki/Text_mining D. Rebholz-Schuhmann et al., Text-mining solutions for biomedical research: enabling integrative biology , Nature Reviews Genetics 13, 829-839 (December 2012 )

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Text Mining in Biomedical Research

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  1. Text Mining in Biomedical Research QI LI 03/28/14

  2. references • http://en.wikipedia.org/wiki/Text_mining • D. Rebholz-Schuhmann et al., Text-mining solutions for biomedical research: enabling integrative biology, Nature Reviews Genetics 13, 829-839 (December 2012) • R. King et al., The Automation of Science, Science 324, 85 (2009) • http://www.aber.ac.uk/~dcswww/Research/bio/robotsci/

  3. The usual way biomedical research is done • Read a lot of papers on a topic • Propose one or more hypotheses • Design a series of experiments • Perform the experiments • Prove or disprove the hypotheses • Publish the results on a journal Pic: http://www1.plymouth.ac.uk/courses/undergraduate/0732/pages/coursedetail.aspx

  4. Why do we need text mining • Scientists publish papers, not relations or data instances • We need to reconstruct the knowledge out of the publications • Then, computers will be able to help us analyze the knowledge base, probably bringing us new ideas

  5. Overview of the process Figure: Text-mining solutions for biomedical research: enabling integrative biology [2]

  6. Some of the Techniques Figure: Text-mining solutions for biomedical research: enabling integrative biology [2]

  7. One prototype application: robot scientist “adam” Pics: http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/pictures/

  8. Not just experiments: hypotheses generation, too • Gather information from a knowledge base • Propose hypotheses • Design a series of experiments • Run the experiments physically • Interpret the results • Publish the results on a journal (NOT YET)

  9. See it in action! • http://www.aber.ac.uk/en/cs/research/cb/projects/robotscientist/video/

  10. Thank you!

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