Tutorial and training materials
Learn to use the XplorMed software, a web-based tool which allows researchers to access a text-mining algorithm. Researchers can improve upon standard PubMed searches by mining abstracts for word frequencies and combinations. Learn to use the XplorMed tool as a means of discovery of new relationships, or as a method to more quickly find the most relevant articles by understanding the context of words of interest.
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
Textpresso: Text-mining the biological literature
Gene Ontology: Gene Ontology controlled vocabularies in biology
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.
Video Tip of the Week: eGIFT, extracting gene information from text: eGIFT, as the tag line says, is a tool to extract gene information from text. It's a tool that allows you to search for and explore terms and documents related to a gene or set of genes. There are ma...
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...
New and Updated Online Tutorials for GoMiner and XplorMed: Comprehensive tutorials on the publicly available GoMiner and XplorMed databases enable researchers to quickly and effectively use these invaluable resources Seattle, WA (PRWEB) February 16, 2010 -- Op...
Peer Bork wins 2009 award: Royal Society and Académie des sciences Microsoft Award was won by Peer Bork this year. The award is funded by Microsoft (250,000 euro) and is given to recognise and reward scientists working in Europ...
Recent BioMed Central research articles citing this resource
Barbosa-Silva Adriano et al., PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics (2011) doi:10.1186/1471-2105-12-435
Sy Mohameth-François et al., User centered and ontology based information retrieval system for life sciences Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010 Semantic Web Applications and Tools for Life Sciences (SWAT4LS) 2010. BMC Bioinformatics (2011) doi:10.1186/1471-2105-13-S1-S4
Tudor O Catalina et al., eGIFT: Mining Gene Information from the Literature. BMC Bioinformatics (2010) doi:10.1186/1471-2105-11-418
Dietze Heiko et al., GoWeb: a semantic search engine for the life science web Semantic Web Applications and Tools for Life Sciences, 2008 Semantic Web Applications and Tools for Life Sciences, 2008. BMC Bioinformatics (2009) doi:10.1186/1471-2105-10-S10-S7
Smalheiser R Neil et al., Anne O"Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results. Journal of Biomedical Discovery and Collaboration (2008) doi:10.1186/1747-5333-3-2