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Database Cover Image for Volume 2010
Volume 2010
2010
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EISSN 1758-0463

Volume 2010, 2010

Original Articles

The annotation and the usage of scientific databases could be improved with public issue tracker software
Giovanni Marco Dall'Olio, Jaume Bertranpetit, Hafid Laayouni
Database, Volume 2010, 2010, baq035, https://doi.org/10.1093/database/baq035
Literature curation of protein interactions: measuring agreement across major public databases
Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson, Shoshana J. Wodak
Database, Volume 2010, 2010, baq026, https://doi.org/10.1093/database/baq026
Damming the genomic data flood using a comprehensive analysis and storage data structure
Marc Bouffard, Michael S. Phillips, Andrew M.K. Brown, Sharon Marsh, Jean-Claude Tardif, Tibor van Rooij
Database, Volume 2010, 2010, baq029, https://doi.org/10.1093/database/baq029
GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database
Cynthia M. Anderson, Patrick D. Kidd, Sepehr Eskandari
Database, Volume 2010, 2010, baq028, https://doi.org/10.1093/database/baq028
A curated online resource for SOX10 and pigment cell molecular genetic pathways
Laura L. Baxter, R. Travis Moreland, Anh-Dao Nguyen, Tyra G. Wolfsberg, William J. Pavan
Database, Volume 2010, 2010, baq025, https://doi.org/10.1093/database/baq025
EuroDia: a beta-cell gene expression resource
Robin Liechti, Gábor Csárdi, Sven Bergmann, Frédéric Schütz, Thierry Sengstag, Sylvia F. Boj, Joan-Marc Servitja, Jorge Ferrer, Leentje Van Lommel, Frans Schuit, Sonia Klinger, Bernard Thorens, Najib Naamane, Decio L. Eizirik, Lorella Marselli, Marco Bugliani, Piero Marchetti, Stephanie Lucas, Cecilia Holm … Ioannis Xenarios
Database, Volume 2010, 2010, baq024, https://doi.org/10.1093/database/baq024
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence
Brian Turner, Sabry Razick, Andrei L. Turinsky, James Vlasblom, Edgard K. Crowdy, Emerson Cho, Kyle Morrison, Ian M. Donaldson, Shoshana J. Wodak
Database, Volume 2010, 2010, baq023, https://doi.org/10.1093/database/baq023
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques
Venkata P. Satagopam, Margarita C. Theodoropoulou, Christos K. Stampolakis, Georgios A. Pavlopoulos, Nikolaos C. Papandreou, Pantelis G. Bagos, Reinhard Schneider, Stavros J. Hamodrakas
Database, Volume 2010, 2010, baq019, https://doi.org/10.1093/database/baq019
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
Tsute Chen, Wen-Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst
Database, Volume 2010, 2010, baq013, https://doi.org/10.1093/database/baq013
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences
Damian Smedley, Paul Schofield, Chao-Kung Chen, Vassilis Aidinis, Chrysanthi Ainali, Jonathan Bard, Rudi Balling, Ewan Birney, Andrew Blake, Erik Bongcam-Rudloff, Anthony J. Brookes, Gianni Cesareni, Christina Chandras, Janan Eppig, Paul Flicek, Georgios Gkoutos, Simon Greenaway, Michael Gruenberger, Jean-Karim Hériché … John M. Hancock
Database, Volume 2010, 2010, baq014, https://doi.org/10.1093/database/baq014
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions
Tatiana V. Karpinets, Margaret F. Romine, Denise D. Schmoyer, Guruprasad H. Kora, Mustafa H. Syed, Michael R. Leuze, Margrethe H. Serres, Byung H. Park, Nagiza F. Samatova, Edward C. Uberbacher
Database, Volume 2010, 2010, baq012, https://doi.org/10.1093/database/baq012
PROFESS: a PROtein Function, Evolution, Structure and Sequence database
Thomas Triplet, Matthew D. Shortridge, Mark A. Griep, Jaime L. Stark, Robert Powers, Peter Revesz
Database, Volume 2010, 2010, baq011, https://doi.org/10.1093/database/baq011
Mouse Resource Browser—a database of mouse databases
Michael Zouberakis, Christina Chandras, Morris Swertz, Damian Smedley, Michael Gruenberger, Jonathan Bard, Klaus Schughart, Nadia Rosenthal, John M. Hancock, Paul N. Schofield, George Kollias, Vassilis Aidinis
Database, Volume 2010, 2010, baq010, https://doi.org/10.1093/database/baq010
PDBWiki: added value through community annotation of the Protein Data Bank
Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser
Database, Volume 2010, 2010, baq009, https://doi.org/10.1093/database/baq009
Choosing a genome browser for a Model Organism Database: surveying the Maize community
Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence
Database, Volume 2010, 2010, baq007, https://doi.org/10.1093/database/baq007
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs
Lucie N. Hutchins, Yueming Ding, Jin P. Szatkiewicz, Randy Von Smith, Hyuna Yang, Fernando Pardo-Manuel de Villena, Gary A. Churchill, Joel H. Graber
Database, Volume 2010, 2010, baq008, https://doi.org/10.1093/database/baq008
An advanced web query interface for biological databases
Mario Latendresse, Peter D. Karp
Database, Volume 2010, 2010, baq006, https://doi.org/10.1093/database/baq006
BrainTrap: a database of 3D protein expression patterns in the Drosophila brain
Seymour Knowles-Barley, Mark Longair, J Douglas Armstrong
Database, Volume 2010, 2010, baq005, https://doi.org/10.1093/database/baq005
TRedD—A database for tandem repeats over the edit distance
Dina Sokol, Firat Atagun
Database, Volume 2010, 2010, baq003, https://doi.org/10.1093/database/baq003
OpenFluDB, a database for human and animal influenza virus
Robin Liechti, Anne Gleizes, Dmitry Kuznetsov, Lydie Bougueleret, Philippe Le Mercier, Amos Bairoch, Ioannis Xenarios
Database, Volume 2010, 2010, baq004, https://doi.org/10.1093/database/baq004
Meeting report: a workshop on Best Practices in Genome Annotation
Ramana Madupu, Lauren M. Brinkac, Jennifer Harrow, Laurens G. Wilming, Ulrike Böhme, Philippe Lamesch, Linda I. Hannick
Database, Volume 2010, 2010, baq001, https://doi.org/10.1093/database/baq001
Gene-oriented ortholog database: a functional comparison platform for orthologous loci
Meng-Ru Ho, Chun-houh Chen, Wen-chang Lin
Database, Volume 2010, 2010, baq002, https://doi.org/10.1093/database/baq002
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae
Chris Stark, Ting-Cheng Su, Ashton Breitkreutz, Pedro Lourenco, Matthew Dahabieh, Bobby-Joe Breitkreutz, Mike Tyers, Ivan Sadowski
Database, Volume 2010, 2010, bap026, https://doi.org/10.1093/database/bap026
Phenol-Explorer: an online comprehensive database on polyphenol contents in foods
V. Neveu, J. Perez-Jiménez, F. Vos, V. Crespy, L. du Chaffaut, L. Mennen, C. Knox, R. Eisner, J. Cruz, D. Wishart, A. Scalbert
Database, Volume 2010, 2010, bap024, https://doi.org/10.1093/database/bap024

Database Tool

Bookshelf: a simple curation system for the storage of biomolecular simulation data
Shabana Vohra, Benjamin A. Hall, Daniel A. Holdbrook, Syma Khalid, Philip C. Biggin
Database, Volume 2010, 2010, baq033, https://doi.org/10.1093/database/baq033
IGVBrowser–a genomic variation resource from diverse Indian populations
Ankita Narang, Rishi Das Roy, Amit Chaurasia, Arijit Mukhopadhyay, Mitali Mukerji, Indian Genome Variation Consortium, Debasis Dash
Database, Volume 2010, 2010, baq022, https://doi.org/10.1093/database/baq022
The systematic annotation of the three main GPCR families in Reactome
Bijay Jassal, Steven Jupe, Michael Caudy, Ewan Birney, Lincoln Stein, Henning Hermjakob, Peter D’Eustachio
Database, Volume 2010, 2010, baq018, https://doi.org/10.1093/database/baq018
Varietas: a functional variation database portal
Jussi Paananen, Robert Ciszek, Garry Wong
Database, Volume 2010, 2010, baq016, https://doi.org/10.1093/database/baq016
CyanoClust: comparative genome resources of cyanobacteria and plastids
Naobumi V. Sasaki, Naoki Sato
Database, Volume 2010, 2010, bap025, https://doi.org/10.1093/database/bap025

Review

Human variation databases
Jan Küntzer, Daniela Eggle, Stefan Klostermann, Helmut Burtscher
Database, Volume 2010, 2010, baq015, https://doi.org/10.1093/database/baq015

Database Update

AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana
Lorenz Bülow, Yuri Brill, Reinhard Hehl
Database, Volume 2010, 2010, baq034, https://doi.org/10.1093/database/baq034
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle
Aurélie Lardenois, Alexandre Gattiker, Olivier Collin, Frédéric Chalmel, Michael Primig
Database, Volume 2010, 2010, baq030, https://doi.org/10.1093/database/baq030
GeneCards Version 3: the human gene integrator
Marilyn Safran, Irina Dalah, Justin Alexander, Naomi Rosen, Tsippi Iny Stein, Michael Shmoish, Noam Nativ, Iris Bahir, Tirza Doniger, Hagit Krug, Alexandra Sirota-Madi, Tsviya Olender, Yaron Golan, Gil Stelzer, Arye Harel, Doron Lancet
Database, Volume 2010, 2010, baq020, https://doi.org/10.1093/database/baq020
HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population
Nicolas J. Tourasse, Ole Andreas Økstad, Anne-Brit Kolstø
Database, Volume 2010, 2010, baq017, https://doi.org/10.1093/database/baq017

Tutorial

PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan
Akira R. Kinjo, Reiko Yamashita, Haruki Nakamura
Database, Volume 2010, 2010, baq021, https://doi.org/10.1093/database/baq021

Front Matter/Back Matter

DATABASE Editorial Board 2010
Database, Volume 2010, 2010, baq032, https://doi.org/10.1093/database/baq032
All issues

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