LitMiner and WikiGene: Identifying problem-related key players of gene regulation using publication abstracts

Holger Maier, Stefanie Döhr, Korbinian Grote, Sean O'Keeffe, Thomas Werner, Martin Hrabé de Angelis, Ralf Schneider

Research output: Contribution to journalArticlepeer-review

40 Scopus citations

Abstract

The LitMiner software is a literature data-mining tool that facilitates the identification of major gene regulation key players related to a user-defined field of interest in PubMed abstracts. The prediction of gene-regulatory relationships is based on co-occurrence analysis of key terms within the abstracts. LitMiner predicts relationships between key terms from the biomedical domain in four categories (genes, chemical compounds, diseases and tissues). Owing to the limitations (no direction, unverified automatic prediction) of the co-occurrence approach, the primary data in the LitMiner database represent postulated basic gene - gene relationships. The usefulness of the LitMiner system has been demonstrated recently in a study that reconstructed disease-related regulatory networks by promoter modelling that was initiated by a LitMiner generated primary gene list. To overcome the limitations and to verify and improve the data, we developed WikiGene, a Wiki-based curation tool that allows revision of the data by expert users over the Internet. LitMiner (http://andromeda.gsf.de/litminer) and WikiGene (http://andromeda.gsf.de/wiki) can be used unrestricted with any Internet browser.

Original languageEnglish
Pages (from-to)W779-W782
JournalNucleic Acids Research
Volume33
Issue numberSUPPL. 2
DOIs
StatePublished - Jul 2005
Externally publishedYes

Fingerprint

Dive into the research topics of 'LitMiner and WikiGene: Identifying problem-related key players of gene regulation using publication abstracts'. Together they form a unique fingerprint.

Cite this