Learn to use PubMatrix, an on-line tool for multiplex literature mining of the PubMed database. This freely accessible, web-based tool performs automatic multiplex Boolean queries to create a matrix of hyperlinked term combinations.

You will learn:

  • how to load data into the PubMatrix tool
  • how to create effective search parameters
  • where to find public searches for useful lists of keywords
  • how to view completed searches
  • how to create graphic displays of results


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

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

XplorMed: eXploring Medline abstracts

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.


Mining figure legends. Huh.: Every so often something comes up in your weekly literature search that makes you go: huh. That happened to me today with a paper on text mining. Now, I have used a variety of text-mining tools (Textpr...

Navigating the literature: We have a slide we like to present at some trainings showing the rise in the amount of raw sequence data and number of complete genomes over the last 18 years. There is another slide we show that indic...


Recent BioMed Central research articles citing this resource

Grigoryev N. Dmitry et al., Identification of new biomarkers for Acute Respiratory Distress Syndrome by expression-based genome-wide association study Respiratory critical care. BMC Pulmonary Medicine (2015) doi:10.1186/s12890-015-0088-x

Grigoryev N Dmitry et al., Combined meta-analysis of systemic effects of allogeneic stem cell transplantation and systemic sclerosis. BMC Hematology (2014) doi:10.1186/2052-1839-14-7

Grigoryev N Dmitry et al., Meta-analysis of molecular response of kidney to ischemia reperfusion injury for the identification of new candidate genes Genetics. BMC Nephrology (2013) doi:10.1186/1471-2369-14-231

Chen Long et al., Combination of SLC administration and Tregs depletion is an attractive strategy for targeting hepatocellular carcinoma. Molecular Cancer (2013) doi:10.1186/1476-4598-12-153

Xiang Zuoshuang et al., A genome-wide MeSH-based literature mining system predicts implicit gene-to-gene relationships and networks Twelfth International Conference on Bioinformatics (InCoB2013): Systems Biology Asia Pacific Bioinformatics Network (APBioNet) Twelfth International Conference on Bioinformatics (InCoB2013). BMC Systems Biology (2013) doi:10.1186/1752-0509-7-S3-S9