title: Integrating PPI datasets with the PPI data from biomedical literature for protein complex detection.
abstract: BACKGROUND
  Protein complexes are important for understanding principles of cellular organization and function. High-throughput experimental techniques have produced a large amount of protein-protein interactions (PPIs), making it possible to predict protein complexes from protein-protein interaction networks. On the other hand, the rapidly growing biomedical literature provides a significantly large and readily available source of interaction data, which can be integrated into the protein network for better complex detection performance.
  
  
  METHODS
  We present an approach of integrating PPI datasets with the PPI data from biomedical literature for protein complex detection. The approach applies a sophisticated natural language processing system, PPIExtractor, to extract PPI data from biomedical literature. These data are then integrated into the PPI datasets for complex detection.
  
  
  RESULTS
  The experimental results of the state-of-the-art complex detection method, ClusterONE, on five yeast PPI datasets verify our method's effectiveness: compared with the original PPI datasets, the average improvements of 3.976 and 5.416 percentage units in the maximum matching ratio (MMR) are achieved on the new networks using the MIPS and SGD gold standards, respectively. In addition, our approach also proves to be effective for three other complex detection algorithms proposed in recent years, i.e. CMC, COACH and RRW.
  
  
  CONCLUSIONS
  The rapidly growing biomedical literature provides a significantly large, readily available and relatively accurate source of interaction data, which can be integrated into the protein network for better protein complex detection performance.
authors.forename: Zhi
authors.initials: Z
authors.lastname: Yang
authors.forename: Feng
authors.initials: F
authors.lastname: Yu
authors.forename: Hong
authors.initials: H
authors.lastname: Lin
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D005656:Fungal Proteins / Q000378:metabolism; D009323:Natural Language Processing; D025941:Protein Interaction Mapping; D011642:Publications
chemical_list: D005656:Fungal Proteins