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
TUTORIAL RELATED CONTENT

TUTORIALS

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

CATEGORIES

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

BLOG POSTS

Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...

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...

Textpresso for Mouse now available: Just a quick announcement I got from the Textpresso mailing list today: Hello! We have set up a full text search engine for mouse literature. It can be accessed at http://www.textpresso.org/mouse Any f...

New and Updated Online Tutorials for Textpresso and Gene Ontology: Comprehensive tutorials on the Gene Ontology and Textpresso databases enable researchers to quickly and effectively use these invaluable resources. Seattle, WA (PRWEB) December 8, 2008 -- OpenHelix tod...

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...

BIOMED CENTRAL

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

AlQuraishi Mohammed et al., An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system Structural analysis. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0819-2

Žitnik Slavko et al., Sieve-based relation extraction of gene regulatory networks from biological literature BioNLP Shared Task 2013: Part 2 BioNLP Shared Task 2013. BMC Bioinformatics (2015) doi:10.1186/1471-2105-16-S16-S1

Irla Marta et al., Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape. BMC Genomics (2015) doi:10.1186/s12864-015-1239-4

Mao Xizeng et al., Revisiting operons: an analysis of the landscape of transcriptional units in E. coli Results and data. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0805-8