Learn to use Textpresso an open source web-based tool that allows you to text-mine the biological literature. Textpresso acts as both an information retrieval and information extraction tool allowing you to quickly and concisely find the right documents from the scientific literature and extract the pertinent facts. Textpresso is unique in that it searches the full-text of papers (not just abstracts) and employs a text-processing system that allows sentences to be extracted and presented to the user. Perfect for students and scientists writing papers, grants, or reviews. Learn to use Textpresso and you will find the right documents for your writing and research needs with increased efficiency and effectiveness.

You will learn:

  • how Textpresso works
  • the layout for all Textpresso sites
  • how to perform both basic and advanced searches
  • how to use Textpresso as an information retrieval and extraction tool
  • take a tour of different Textpresso installations


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

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.


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Recent BioMed Central research articles citing this resource

Liu Bingqiang et al., An integrative and applicable phylogenetic footprinting framework for cis -regulatory motifs identification in prokaryotic genomes Prokaryote microbial genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2982-x

Srinivasan Padmini et al., Ferret: a sentence-based literature scanning system Knowledge-based analysis. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0630-0

Khosravi Pegah et al., Inferring interaction type in gene regulatory networks using co-expression data. Algorithms for Molecular Biology (2015) doi:10.1186/s13015-015-0054-4

Horinouchi Takaaki et al., Phenotypic convergence in bacterial adaptive evolution to ethanol stress. BMC Evolutionary Biology (2015) doi:10.1186/s12862-015-0454-6

Ernst Patrick et al., KnowLife: a versatile approach for constructing a large knowledge graph for biomedical sciences Knowledge-based analysis. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0549-5