#：#. Creating work Models using Text Mining and….ppt

22 April 2003 ? 2003, SNU BioIntelligence Lab, / 1 Outline ? Introduction to the Gene Expression To olkit ? work Models ? PathBinder ? Fuzzy Cognitive Map (FCM) Modeling To ol? Example ? Conclusions and Future Work 22 April 2003 ? 2003, SNU BioIntelligence Lab, / 2 Gene Expression Toolkit ? PathBinder: Automatic document proces sing system that automates the process of p ulling relationships from publications. ? ChipView: Explanatory models synthesize d by clustering techniques together with a ic algorithm-based data mining tool ? FCModeler: Predictive models summarize known regulatory relationships in fuzzy cognit ive maps (FCMs). 22 April 2003 ? 2003, SNU BioIntelligence Lab, / 3 Gene Expression ponents 22 April 2003 ? 2003, SNU BioIntelligence Lab, / 4 works ? works form the basis for accumulation of biomolecules anisms. ? works modulate the action of works, leading to physiological a nd morphological changes. ? Modeling tool represents the interactions with in and between works – Nodes represent specific biochemicals such as proteins, RNA, and small molecules, or sti muli, such as light, heat, or nutrients. – Links - interactions between nodes 22 April 2003 ? 2003, SNU BioIntelligence Lab, / 5 Link Types ? Conversion link (black arrow), a node is converted into a nother node, and used up in the process. ? Regulatory link (green and red arrows), node activates o r deactivates another node, not used up. ? Catalytic link (blue arrows) an enzyme that enables a ch emical conversion and not used up in the process. 22 April 2003 ? 2003, SNU BioIntelligence Lab, / 6 What is PathBinder? ? PathBinder extracts node-node interacti ons from MEDLINE ? The processing unit is single sentences: abstracts are parsed into individual sent ences, which in turn are searched for th e presence of a pair of node names and an interaction-related Verb. 22 A