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Database - The Journal of Biological Databases and Curation, Volume 2010

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Volume 2010, 2010

Original article

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  - journals/biodb/DallOlioBL10
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Giovanni Marco Dall'Olio, Jaume Bertranpetit, Hafid Laayouni:
The annotation and the usage of scientific databases could be improved with public issue tracker software.
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  - journals/biodb/TurinskyRTDW10
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Andrei L. Turinsky, Sabry Razick, Brian Turner, Ian M. Donaldson, Shoshana J. Wodak:
Literature curation of protein interactions: measuring agreement across major public databases.
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  - journals/biodb/BouffardPBMTR10
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Marc Bouffard, Michael S. Phillips, Andrew M. K. Brown, Sharon Marsh, Jean-Claude Tardif, Tibor van Rooij:
Damming the genomic data flood using a comprehensive analysis and storage data structure.
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  - journals/biodb/AndersonKE10
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Cynthia M. Anderson, Patrick D. Kidd, Sepehr Eskandari:
GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database.
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  - journals/biodb/BaxterMNWP10
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Laura Baxter, R. Travis Moreland, Anh-Dao Nguyen, Tyra G. Wolfsberg, William J. Pavan:
A curated online resource for SOX10 and pigment cell molecular genetic pathways.
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  - journals/biodb/LiechtiCBSSBSFLSKTNEMBMLHJX10
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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, C. Victor Jongeneel, Ioannis Xenarios:
EuroDia: a beta-cell gene expression resource.
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  - journals/biodb/TurnerRTVCCMDW10
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Brian Turner, Sabry Razick, Andrei L. Turinsky, James Vlasblom, Edgard K. Crowdy, Emerson Cho, Kyle Morrison, Ian M. Donaldson, Shoshana J. Wodak:
iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence.
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  - journals/biodb/SatagopamTSPPB0H10
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Venkata P. Satagopam, Margarita C. Theodoropoulou, Christos K. Stampolakis, Georgios A. Pavlopoulos, Nikolaos Papandreou, Pantelis G. Bagos, Reinhard Schneider, Stavros J. Hamodrakas:
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques.
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  - journals/biodb/ChenYIBLD10
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Tsute Chen, Wen-Han Yu, Jacques Izard, Oxana V. Baranova, Abirami Lakshmanan, Floyd E. Dewhirst:
The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information.
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  - journals/biodb/SmedleySCAABBBBBBCCEFGGGHLMMRRRSSTZH10
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Damian Smedley, Paul N. Schofield, Chao-Kung Chen, Vassilis Aidinis, Crysanthi Ainali, Jonathan B. L. Bard, Rudi Balling, Ewan Birney, Andrew Blake, Erik Bongcam-Rudloff, Anthony J. Brookes, Gianni Cesareni, Christina Chandras, Janan T. Eppig, Paul Flicek, Georgios V. Gkoutos, Simon Greenaway, Michael Gruenberger, Jean-Karim Hériché, Andrew Lyall, Ann-Marie Mallon, Dawn Muddyman, Florian Reisinger, Martin Ringwald, Nadia A. Rosenthal, Klaus Schughart, Morris A. Swertz, Gudmundur A. Thorisson, Michael Zouberakis, John M. Hancock:
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences.
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  - journals/biodb/KarpinetsRSKSLSPSU10
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Tatiana V. Karpinets, Margaret F. Romine, Denise Schmoyer, Guruprasad Kora, Mustafa H. Syed, Michael R. Leuze, Margrethe H. Serres, Byung-Hoon Park, Nagiza F. Samatova, Edward C. Uberbacher:
Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions.
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  - journals/biodb/TripletSGSPR10
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Thomas Triplet, Matthew D. Shortridge, Mark A. Griep, Jaime L. Stark, Robert Powers, Peter Z. Revesz:
PROFESS: a PROtein Function, Evolution, Structure and Sequence database.
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  - journals/biodb/ZouberakisCSSGBSRHSKA10
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Michael Zouberakis, Christina Chandras, Morris A. Swertz, Damian Smedley, Michael Gruenberger, Jonathan B. L. Bard, Klaus Schughart, Nadia A. Rosenthal, John M. Hancock, Paul N. Schofield, George Kollias, Vassilis Aidinis:
Mouse Resource Browser - a database of mouse databases.
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  - journals/biodb/StehrDLBB10
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Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, Dan M. Bolser:
PDBWiki: added value through community annotation of the Protein Data Bank.
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  - journals/biodb/SenHSASCL10
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Taner Z. Sen, Lisa C. Harper, Mary L. Schaeffer, Carson M. Andorf, Trent E. Seigfried, Darwin A. Campbell, Carolyn J. Lawrence:
Choosing a genome browser for a Model Organism Database: surveying the Maize community.
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  - journals/biodb/HutchinsDSSYVCG10
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Lucie N. Hutchins, Yueming Ding, Jin P. Szatkiewicz, Randy von Smith, Hyuna Yang, Fernando Pardo-Manuel de Villena, Gary A. Churchill, Joel H. Graber:
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs.
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Mario Latendresse, Peter D. Karp:
An advanced web query interface for biological databases.
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  - journals/biodb/Knowles-BarleyLA10
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Seymour Knowles-Barley, Mark Longair, J. Douglas Armstrong:
BrainTrap: a database of 3D protein expression patterns in the Drosophila brain.
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Dina Sokol, Firat Atagun:
TRedD - A database for tandem repeats over the edit distance.
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Robin Liechti, Anne Gleizes, Dmitry Kuznetsov, Lydie Bougueleret, Philippe Le Mercier, Amos Bairoch, Ioannis Xenarios:
OpenFluDB, a database for human and animal influenza virus.
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  - journals/biodb/MadupuBHWBLH10
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Ramana Madupu, Lauren M. Brinkac, Jennifer L. Harrow, Laurens G. Wilming, Ulrike Böhme, Philippe Lamesch, Linda I. Hannick:
Meeting report: a workshop on Best Practices in Genome Annotation.
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  - journals/biodb/HoCL10
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Meng-Ru Ho, Chun-Houh Chen, Wen-Chang Lin:
Gene-oriented ortholog database: a functional comparison platform for orthologous loci.
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  - journals/biodb/StarkSBLDBTS10
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Chris Stark, Ting-Cheng Su, Ashton Breitkreutz, Pedro Lourenco, Matthew Dahabieh, Bobby-Joe Breitkreutz, Mike Tyers, Ivan Sadowski:
PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae.
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Vanessa Neveu, Jara Perez-Jimenez, Femke Vos, Vanessa Crespy, Lerman du Chaffaut, Louise Mennen, Craig Knox, Roman Eisner, Joseph A. Cruz, David S. Wishart, Augustin Scalbert:
Phenol-Explorer: an online comprehensive database on polyphenol contents in foods.

Database tool

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  - journals/biodb/VohraHHKB10
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Shabana Vohra, Benjamin A. Hall, Daniel A. Holdbrook, Syma Khalid, Philip C. Biggin:
Bookshelf: a simple curation system for the storage of biomolecular simulation data.
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  - journals/biodb/NarangRCMMD10
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Ankita Narang, Rishi Das Roy, Amit Chaurasia, Arijit Mukhopadhyay, Mitali Mukerji, Debasis Dash:
IGVBrowser-a genomic variation resource from diverse Indian populations.
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  - journals/biodb/JassalJCBSHD10
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Bijay Jassal, Steven Jupe, Michael Caudy, Ewan Birney, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The systematic annotation of the three main GPCR families in Reactome.
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Jussi Paananen, Robert Ciszek, Garry Wong:
Varietas: a functional variation database portal.
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  - journals/biodb/SasakiS10
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Naobumi V. Sasaki, Naoki Sato:
CyanoClust: comparative genome resources of cyanobacteria and plastids.

Review

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Jan Küntzer, Daniela Eggle, Stefan Klostermann, Helmut Burtscher:
Human variation databases.

Database update

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Lorenz Bülow, Yuri Brill, Reinhard Hehl:
AthaMap-assisted transcription factor target gene identification in Arabidopsis thaliana.
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  - journals/biodb/LardenoisGCCP10
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Aurélie Lardenois, Alexandre Gattiker, Olivier Collin, Frédéric Chalmel, Michael Primig:
GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle.
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  - journals/biodb/SafranDARSSNBDKSOGSHL10
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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:
GeneCards Version 3: the human gene integrator.
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  - journals/biodb/TourasseOK10
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Nicolas J. Tourasse, Ole Andreas Økstad, Anne-Brit Kolstø:
HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population.

Tutorial

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  - journals/biodb/KinjoYN10
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Akira R. Kinjo, Reiko Yamashita, Haruki Nakamura:
PDBj Mine: design and implementation of relational database interface for Protein Data Bank Japan.

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