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eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature

  • Cecilia N. ArighiEmail author
  • Amy Y. Siu
  • Catalina O. Tudor
  • Jules A. Nchoutmboube
  • Cathy H. Wu
  • Vijay K. Shanker
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 694)

Abstract

Technologies and experimental strategies have improved dramatically in the field of genomics and proteomics facilitating analysis of cellular and biochemical processes, as well as of proteins networks. Based on numerous such analyses, there has been a significant increase of publications in life sciences and biomedicine. In this respect, knowledge bases are struggling to cope with the literature volume and they may not be able to capture in detail certain aspects of proteins and genes. One important aspect of proteins is their phosphorylated states and their implication in protein function and protein interacting networks. For this reason, we developed eFIP, a web-based tool, which aids scientists to find quickly abstracts mentioning phosphorylation of a given protein (including site and kinase), coupled with mentions of interactions and functional aspects of the protein. eFIP combines information provided by applications such as eGRAB, RLIMS-P, eGIFT and AIIAGMT, to rank abstracts mentioning phosphorylation, and to display the results in a highlighted and tabular format for a quick inspection. In this chapter, we present a case study of results returned by eFIP for the protein BAD, which is a key regulator of apoptosis that is posttranslationally modified by phosphorylation.

Key words

Text mining BioNLP Information extraction Phosphorylation Protein–protein interaction PPI Knowledge discovery 

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Cecilia N. Arighi
    • 1
    Email author
  • Amy Y. Siu
    • 1
  • Catalina O. Tudor
    • 1
  • Jules A. Nchoutmboube
    • 1
  • Cathy H. Wu
    • 1
  • Vijay K. Shanker
    • 1
  1. 1.Department of Computer and Information SciencesUniversity of DelawareNewarkUSA

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