Xanthusbase: adapting wikipedia principles to a model organism database

被引:10
作者
Arshinoff, Bradley I.
Suen, Garret
Just, Eric M.
Merchant, Sohel M.
Kibbe, Warren A.
Chisholm, Rex L.
Welch, Roy D. [1 ]
机构
[1] Syracuse Univ, Dept Biol, Syracuse, NY 13244 USA
[2] Northwestern Univ, Ctr Med Genet, Feinberg Sch Med, Chicago, IL 60611 USA
关键词
D O I
10.1093/nar/gkl881
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.
引用
收藏
页码:D422 / D426
页数:5
相关论文
共 24 条
[1]   Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].
Altschul, SF ;
Madden, TL ;
Schaffer, AA ;
Zhang, JH ;
Zhang, Z ;
Miller, W ;
Lipman, DJ .
NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402
[2]   Beyond the data deluge: Data integration and bio-ontologies [J].
Blake, Judith A. ;
Bult, Carol J. .
JOURNAL OF BIOMEDICAL INFORMATICS, 2006, 39 (03) :314-320
[3]   dictyBase, the model organism database for Dictyostelium discoideum [J].
Chisholm, Rex L. ;
Gaudet, Pascale ;
Just, Eric M. ;
Pilcher, Karen E. ;
Fey, Petra ;
Merchant, Sohel N. ;
Kibbe, Warren A. .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D423-D427
[4]   The Distributed Annotation System [J].
Dowell, Robin D. ;
Jokerst, Rodney M. ;
Day, Allen ;
Eddy, Sean R. ;
Stein, Lincoln .
BMC BIOINFORMATICS, 2001, 2 (1)
[5]  
DWORKIN M, 1993, MYXOBACTERIA, V2
[6]   Pfam:: clans, web tools and services [J].
Finn, Robert D. ;
Mistry, Jaina ;
Schuster-Bockler, Benjamin ;
Griffiths-Jones, Sam ;
Hollich, Volker ;
Lassmann, Timo ;
Moxon, Simon ;
Marshall, Mhairi ;
Khanna, Ajay ;
Durbin, Richard ;
Eddy, Sean R. ;
Sonnhammer, Erik L. L. ;
Bateman, Alex .
NUCLEIC ACIDS RESEARCH, 2006, 34 :D247-D251
[7]  
FORTE A, 2005, GROUP 2005 C SAN ISL
[8]   Fermentation, purification, formulation, and pharmacological evaluation of a prolyl endopeptidase from Myxococcus xanthus:: Implications for Celiac sprue therapy [J].
Gass, J ;
Ehren, J ;
Strohmeier, G ;
Isaacs, I ;
Khosla, C .
BIOTECHNOLOGY AND BIOENGINEERING, 2005, 92 (06) :674-684
[9]   Internet encyclopaedias go head to head [J].
Giles, J .
NATURE, 2005, 438 (7070) :900-901
[10]   Evolution of sensory complexity recorded in a myxobacterial genome [J].
Goldman, B. S. ;
Nierman, W. C. ;
Kaiser, D. ;
Slater, S. C. ;
Durkin, A. S. ;
Eisen, J. ;
Ronning, C. M. ;
Barbazuk, W. B. ;
Blanchard, M. ;
Field, C. ;
Halling, C. ;
Hinkle, G. ;
Iartchuk, O. ;
Kim, H. S. ;
Mackenzie, C. ;
Madupu, R. ;
Miller, N. ;
Shvartsbeyn, A. ;
Sullivan, S. A. ;
Vaudin, M. ;
Wiegand, R. ;
Kaplan, H. B. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (41) :15200-15205