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:
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
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
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