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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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Varietas: a functional variation database portal

Jussi Paananen, Robert Ciszek, Garry Wong

Database, Volume 2010, 2010, baq016, https://doi.org/10.1093/database/baq016

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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

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Review

Human variation databases

Jan Küntzer, Daniela Eggle, Stefan Klostermann, Helmut Burtscher

Database, Volume 2010, 2010, baq015, https://doi.org/10.1093/database/baq015

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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

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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

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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