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eXploring Medline abstracts

Tutorial and training materials by OpenHelix

Learn to use the XplorMed software, a web-based tool which allows researchers to access a text-mining algorithm. Researchers can improve upon standard PubMed searches by mining abstracts for word frequencies and combinations. Learn to use the XplorMed tool as a means of discovery of new relationships, or as a method to more quickly find the most relevant articles by understanding the context of words of interest.
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You'll learn:

  • how to extract fascinating relationships among PubMed abstracts
  • to use stored sets of abstracts to discover new information
  • to start with identifiers of interest and collect relevant abstracts for further examination


Related tutorials

This tutorial is a part of the tutorial group Bork Group Resources. You might find the other tutorials in the group interesting:

  • STRING: known and predicted protein-protein interactions
  • SMART: Protein domain annotation and analysis of domain architectures

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Recent BioMed Central research articles citing this resource

Barbosa-Silva Adriano et al., PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics (2011) doi:10.1186/1471-2105-12-435

Sy Mohameth-François et al., User centered and ontology based information retrieval system for life sciences Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010 Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010. BMC Bioinformatics (2011) doi:10.1186/1471-2105-13-S1-S4

Tudor O Catalina et al., eGIFT: Mining Gene Information from the Literature. BMC Bioinformatics (2010) doi:10.1186/1471-2105-11-418

Dietze Heiko et al., GoWeb: a semantic search engine for the life science web Semantic Web Applications and Tools for Life Sciences, 2008 Semantic Web Applications and Tools for Life Sciences, 2008. BMC Bioinformatics (2009) doi:10.1186/1471-2105-10-S10-S7

Alexopoulou Dimitra et al., Terminologies for text-mining; an experiment in the lipoprotein metabolism domain A Semantic Web for Bioinformatics: Goals, Tools, Systems, Applications Seventh International Workshop on Network Tools and Applications in Biology (NETTAB 2007). BMC Bioinformatics (2008) doi:10.1186/1471-2105-9-S4-S2

More about the resource:

XplorMed came originally from the Bork Group at EMBL. The original site for XplorMed, hosted at EMBL, has been discontinued, but you may still find the URL for it in some references and web pages. A new site from the Ottawa Health Research Institute (OHRI) Bioinformatics Group maintains and hosts XplorMed at this time.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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