Using the iHOP Information Resource to Mine the Biomedical Literature on Genes, Proteins, and Chemical Compounds

Robert Hoffmann1

1 Massachusetts Institute of Technology, Cambridge, Massachusetts
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.16
DOI:  10.1002/0471250953.bi0116s20
Online Posting Date:  December, 2007
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Abstract

The iHOP (Information Hyperlinked over Proteins) resource employs sophisticated text‐mining methods to assist researchers in their quest for information on specific genes and proteins, their physical interactions and regulatory relationships, their relevance in pathologies, and their interactions with chemical compounds. iHOP parses thousands of PubMed documents every day and collects information specific to thousands of different biological molecules. Rather than providing long lists of entire abstracts upon keyword searches, iHOP selectively retrieves information that is specific to genes and proteins, and summarizes their interactions and functions. In iHOP, with genes and proteins acting as hyperlinks between sentences and abstracts, a large part of the PubMed knowledgebase becomes a giant navigable information network. Curr. Protoc. Bioinform. 20:1.16.1‐1.16.16. © 2007 by John Wiley & Sons, Inc.

Keywords: information resource; literature network; PubMed hyperlinked; gene‐guided exploration

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching for a Specific Gene in iHOP
  • Basic Protocol 2: Exploring Sentence Views in iHOP
  • Basic Protocol 3: Exploring the Gene Definition View in iHOP
  • Basic Protocol 4: Launching Enhanced PubMed or Google Queries from iHOP
  • Basic Protocol 5: Exploring Gene Overview Pages in iHOP
  • Basic Protocol 6: Changing Viewing Options and Large Scale Data Sources
  • Basic Protocol 7: Creating a Logbook or Gene Model in iHOP
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Hoffmann, R. and Valencia, A. 2004. A gene network for navigating the literature. Nat. Genet. 36:664.
   Hoffmann, R. and Valencia, A. 2005. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21:252‐258.
   Hoffmann, R., Krallinger, M., Andres, E., Tamames, J., Blaschke, C., and Valencia, A. 2005. Text mining for metabolic pathways, signaling cascades, and protein networks. Sci STKE 283:21.
Internet Resources
  http://www.ihop‐net.org
  The iHOP homepage. Online version by Hoffmann, R. (2004‐2007).
  http://www.ihop‐net.org/UniPub/iHOP/webservices/
  API that enables the integration of iHOP functionalities in bioinformatics workflows.
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