Discovery of Protein-Protein Interactions Using a Combination of Proximity and Linguistic Information

Many researchers have attempted to find relations in the Biomedical domain using strategies for recognizing protein and gene names, for example. By contrast, our strategy is to combine statistical and lexical techniques to find major noun and verb phrases of all types and compute relations by recurring proximity. We then can apply biomedical term recognition as a filter against the relations we discover. We report here on our work in discovering protein interactions using a standard collection of yeast protein abstracts. After adjusting our recognition algorithms to include complexes and resolve apparent false positives, we obtained a precision of 0.92 and a recall of 0.84. We also examined these relations using our graphical display of the computed relations. In this case it also helps us discover additional relations indirectly and indicates a fruitful avenue for further inquiry.

By: James W. Cooper

Published in: RC23060 in 2004


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