PPLook: an automated data mining tool for protein-protein interaction

Abstract

Background: Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.

Results: We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI) from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface.

Conclusions: PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at http://meta.usc.edu/softs/PPLook.

Figure 1

Architecture of PPLook. PPLook contains four modules: (i) submission authentication module aims to identify whether the query word is a protein name or not; (ii) article parser module acts as a collector to pick up sentences containing the query protein name; (iii) full-sentence parser module determines the PPI and (iv) PPI visualization module displays the PPI in the form of a 3-D graph.

Figure 2

An example of PPLook search results for the protein IL-2. (A) is the protein semantic class selection window, (B) is the IL-2 protein input window, (C) is the text results output window, and (D) is the 3-D display output window.

Figure 3

Heterogeneous Search results: Structure information and MEDLINE results for the protein IL-2. The top left window is the protein IL-2 structure information coming from PDB database. The bottom right window is the Google search results.