PIE the search: searching PubMed literature for protein interaction information

Bioinformatics. 2012 Feb 15;28(4):597-8. doi: 10.1093/bioinformatics/btr702. Epub 2011 Dec 22.


Motivation: Finding protein-protein interaction (PPI) information from literature is challenging but an important issue. However, keyword search in PubMed(®) is often time consuming because it requires a series of actions that refine keywords and browse search results until it reaches a goal. Due to the rapid growth of biomedical literature, it has become more difficult for biologists and curators to locate PPI information quickly. Therefore, a tool for prioritizing PPI informative articles can be a useful assistant for finding this PPI-relevant information.

Results: PIE (Protein Interaction information Extraction) the search is a web service implementing a competition-winning approach utilizing word and syntactic analyses by machine learning techniques. For easy user access, PIE the search provides a PubMed-like search environment, but the output is the list of articles prioritized by PPI confidence scores. By obtaining PPI-related articles at high rank, researchers can more easily find the up-to-date PPI information, which cannot be found in manually curated PPI databases.

Availability: http://www.ncbi.nlm.nih.gov/IRET/PIE/.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artificial Intelligence*
  • Protein Interaction Mapping
  • Proteins / metabolism*
  • PubMed


  • Proteins