MiningtoConsolidatetheSetofKnownHumanProtein.pptVIP

Using Biomedical Literature Mining to Consolidate the Set of Known Human Protein-Protein Interactions Outline Introduction Motivation. Two benchmark tests of accuracy. Framework for the extraction of interactions. Future Work. Conclusions. Introduction Large scale protein networks facilitate a better understanding of the interactions between proteins. Most complete for yeast. Minimal progress for human. Most known interactions between human proteins are reported in Medline. Reactome, BIND, HPRD: databases with protein interactions manually curated from Medline. Motivation Many interactions from Medline are not covered by current databases. Databases are generally biased for different classes of interactions. Manually extracting interactions is a very laborious process. Outline Introduction Motivation. Two benchmark tests of accuracy. Functional Annotation. Physical Interaction. Framework for the extraction of interactions. Future Work. Conclusions. Accuracy Benchmarks – Shared Functional Annotations Accuracy of interaction datasets correlates well with % of interaction partners sharing functional annotations. Functional annotation ? a pathway between the two proteins in a particular ontology: KEGG: 55 pathways at lowest level. GO: 1356 pathways at level 8 of biological process annotation. Accuracy Benchmarks – Shared Known Physical Interactions Assumption: Accurate datasets are more enriched in pairs of proteins known to participate in a physical interaction. Reactome and BIND are more accurate than others ? use them as source of known physical interactions. Total: 11,425 interactions between 1,710 proteins. Accuracy Benchmarks – LLR Scoring Scheme Use the log-likelihood ratio (LLR) of protein pairs with respect to: Sharing functional annotations. Physically interacting. Outline Introduction Motivation. Two benchmark tests of accuracy. Framework for the extraction of interactions. Future Work. Conclusions. Framework for Interaction Extraction F