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.

You will 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


This tutorial is a part of the tutorial group Text-related tools. You might find the other tutorials in the group interesting:

PubMatrix: PubMatrix, an on-line tool for multiplex literature mining of the PubMed database.

iHOP: Information Hyperlinked Over Proteins text mining resource

STRING: known and predicted protein-protein interactions

Textpresso: Text-mining the biological literature

Gene Ontology: Gene Ontology controlled vocabularies in biology

GoMiner: Ascribe biological significance to large lists of genes by annotating them with their corresponding GO categories

Controlled Vocabularies: Standardized term lists that can enhance interactions with biological databases

DAVID: A tool that analyzes large lists of genes to provide biological meaning

Entrez Overview: Overview of NCBI's Entrez Search Resource

PubMed: PubMed access to biomedical research literature


Literature and Text Mining : Tools which are related to scientific literature. Repositories, query tools, and mining resources are included.


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Recent BioMed Central research articles citing this resource

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

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

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

Smalheiser R Neil et al., Anne O"Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results. Journal of Biomedical Discovery and Collaboration (2008) doi:10.1186/1747-5333-3-2