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:
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
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