Literature DB >> 15016385

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data.

Andrey Rzhetsky1, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboué, Wubin Weng, W John Wilbur, Vasileios Hatzivassiloglou, Carol Friedman.   

Abstract

The immense growth in the volume of research literature and experimental data in the field of molecular biology calls for efficient automatic methods to capture and store information. In recent years, several groups have worked on specific problems in this area, such as automated selection of articles pertinent to molecular biology, or automated extraction of information using natural-language processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays is an integrated system that combines several such subtasks. It analyzes interactions between molecular substances, drawing on multiple sources of information to infer a consensus view of molecular networks. GeneWays is designed as an open platform, allowing researchers to query, review, and critique stored information.

Mesh:

Year:  2004        PMID: 15016385     DOI: 10.1016/j.jbi.2003.10.001

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  87 in total

1.  Using systems and structure biology tools to dissect cellular phenotypes.

Authors:  Aris Floratos; Barry Honig; Dana Pe'er; Andrea Califano
Journal:  J Am Med Inform Assoc       Date:  2011-11-10       Impact factor: 4.497

Review 2.  Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana.

Authors:  Elena A Vidal; Karem P Tamayo; Rodrigo A Gutierrez
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2010 Nov-Dec

3.  Visualizing information across multidimensional post-genomic structured and textual databases.

Authors:  Ying Tao; Carol Friedman; Yves A Lussier
Journal:  Bioinformatics       Date:  2004-12-14       Impact factor: 6.937

4.  MachineProse: an ontological framework for scientific assertions.

Authors:  Deendayal Dinakarpandian; Yugyung Lee; Kartik Vishwanath; Rohini Lingambhotla
Journal:  J Am Med Inform Assoc       Date:  2005-12-15       Impact factor: 4.497

5.  Quantitative assessment of dictionary-based protein named entity tagging.

Authors:  Hongfang Liu; Zhang-Zhi Hu; Manabu Torii; Cathy Wu; Carol Friedman
Journal:  J Am Med Inform Assoc       Date:  2006-06-23       Impact factor: 4.497

6.  The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks.

Authors:  Carolyn J Mattingly; Michael C Rosenstein; Allan Peter Davis; Glenn T Colby; John N Forrest; James L Boyer
Journal:  Toxicol Sci       Date:  2006-05-04       Impact factor: 4.849

7.  Bio-Ontology and text: bridging the modeling gap.

Authors:  Carol Friedman; Tara Borlawsky; Lyudmila Shagina; H Rosie Xing; Yves A Lussier
Journal:  Bioinformatics       Date:  2006-07-26       Impact factor: 6.937

8.  Global mapping of gene/protein interactions in PubMed abstracts: a framework and an experiment with P53 interactions.

Authors:  Xin Li; Hsinchun Chen; Zan Huang; Hua Su; Jesse D Martinez
Journal:  J Biomed Inform       Date:  2007-01-17       Impact factor: 6.317

9.  VirtualPlant: a software platform to support systems biology research.

Authors:  Manpreet S Katari; Steve D Nowicki; Felipe F Aceituno; Damion Nero; Jonathan Kelfer; Lee Parnell Thompson; Juan M Cabello; Rebecca S Davidson; Arthur P Goldberg; Dennis E Shasha; Gloria M Coruzzi; Rodrigo A Gutiérrez
Journal:  Plant Physiol       Date:  2009-12-09       Impact factor: 8.340

10.  Advances in translational bioinformatics: computational approaches for the hunting of disease genes.

Authors:  Maricel G Kann
Journal:  Brief Bioinform       Date:  2009-12-10       Impact factor: 11.622

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