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Database - The Journal of Biological Databases and Curation, Volume 2013

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Volume 2013, 2013

Original Articles

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  - journals/biodb/SilbermannWPF13
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Jascha Silbermann, Catrin Wernicke, Heike Pospisil, Marcus Frohme:
RefPrimeCouch - a reference gene primer CouchApp.
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  - journals/biodb/DavisWRKLLSJKGHMEM13
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Allan Peter Davis, Thomas C. Wiegers, Phoebe M. Roberts, Benjamin L. King, Jean M. Lay, Kelley Lennon-Hopkins, Daniela Sciaky, Robin J. Johnson, Heather Keating, Nigel Greene, Robert Hernandez, Kevin J. McConnell, Ahmed Enayetallah, Carolyn J. Mattingly:
A CTD-Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug-disease and drug-phenotype interactions.
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  - journals/biodb/YoungFDSWZSQPB13
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Jasmine Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John D. Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman:
Chemical annotation of small and peptide-like molecules at the Protein Data Bank.
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  - journals/biodb/EvansJLBCPM13
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Kate Evans, Sook Jung, Taein Lee, Lisa Brutcher, Ilhyung Cho, Cameron Peace, Dorrie Main:
Addition of a breeding database in the Genome Database for Rosaceae.
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Yi-Yu Hsu, Hung-Yu Kao:
CoIN: a network analysis for document triage.
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  - journals/biodb/KhuranaSJS13
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Pankaj Khurana, Ragumani Sugadev, Jaspreet Jain, Shashi Bala Singh:
HypoxiaDB: a database of hypoxia-regulated proteins.
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  - journals/biodb/SandersonFCJFBM13
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Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, F. Alex Feltus, Kirstin E. Bett, Dorrie Main:
Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases.
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  - journals/biodb/NagaiI13
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Yoko Nagai, Tadashi Imanishi:
RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations.
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  - journals/biodb/SaundersIRJH13
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Rebecca E. Saunders, Rachael Instrell, Rossella Rispoli, Ming Jiang, Michael Howell:
HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects.
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  - journals/biodb/PercudaniCP13
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Riccardo Percudani, Davide Carnevali, Vincenzo Puggioni:
Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa.
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  - journals/biodb/WanichthanarakCMP13
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Kwanjeera Wanichthanarak, Marija Cvijovic, Andrea Molt, Dina Petranovic:
yApoptosis: yeast apoptosis database.
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Kim Van Roey, Sandra E. Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson:
Capturing cooperative interactions with the PSI-MI format.
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  - journals/biodb/ComeauDCCKLLPRTVVWWW13
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Donald C. Comeau, Rezarta Islamaj Dogan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC: a minimalist approach to interoperability for biomedical text processing.
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  - journals/biodb/TraversPSHK13
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Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp:
Groups: knowledge spreadsheets for symbolic biocomputing.
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  - journals/biodb/KongCFZQ13
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Lei Kong, Lu Cheng, Liya Fan, Min Zhao, Hong Qu:
IQdb: an intelligence quotient score-associated gene resource for human intelligence.
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  - journals/biodb/TripathiCBHHTBKL13
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Sushil Tripathi, Karen R. Christie, Rama Balakrishnan, Rachael P. Huntley, David P. Hill, Liv Thommesen, Judith A. Blake, Martin Kuiper, Astrid Lægreid:
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort.
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  - journals/biodb/LyneSLAHKSM13
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Mike Lyne, Richard N. Smith, Rachel Lyne, Jelena Aleksic, Fengyuan Hu, Alex Kalderimis, Radek Stepan, Gos Micklem:
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.
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  - journals/biodb/LiLDXD13
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Qingyan Li, Shuabin Lian, Zhiming Dai, Qian Xiang, Xianhua Dai:
BGDB: a database of bivalent genes.
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  - journals/biodb/WileySB13
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Laura K. Wiley, R. Michael Sivley, William S. Bush:
Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.
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Hongen Xu, Hua-Hao Zhang, Tian Xia, Min-Jin Han, Yi-Hong Shen, Ze Zhang:
BmTEdb: a collective database of transposable elements in the silkworm genome.
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  - journals/biodb/VeraPPLKP13
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Roberto Vera, Yasset Pérez-Riverol, Sonia Pérez, Balázs Ligeti, Attila Kertész-Farkas, Sándor Pongor:
JBioWH: an open-source Java framework for bioinformatics data integration.
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  - journals/biodb/MahajanAIOBS13
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Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard O. Offmann, Alexandre G. de Brevern, Narayanaswamy Srinivasan:
DoSA: Database of Structural Alignments.
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  - journals/biodb/BhartiyaPGKJPJSSSRSS13
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Deeksha Bhartiya, Koustav Pal, Sourav Ghosh, Shruti Kapoor, Saakshi Jalali, Bharat Panwar, Sakshi Jain, Satish Sati, Shantanu Sengupta, Chetana Sachidanandan, Gajendra Pal Singh Raghava, Sridhar Sivasubbu, Vinod Scaria:
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs.
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  - journals/biodb/BalakrishnanHHAC13
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Rama Balakrishnan, Midori A. Harris, Rachael P. Huntley, Kimberly Van Auken, J. Michael Cherry:
A guide to best practices for Gene Ontology (GO) manual annotation.
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  - journals/biodb/BianchiCCAFH13
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Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich:
DBATE: database of alternative transcripts expression.
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  - journals/biodb/GobeillPVR13
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Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases.
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  - journals/biodb/WangLHSPLNDWMSJ13
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Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Jennifer R. Smith, Victoria Petri, Timothy Lowry, Rajni Nigam, Melinda R. Dwinell, Elizabeth A. Worthey, Diane H. Munzenmaier, Mary Shimoyama, Howard J. Jacob:
Analysis of disease-associated objects at the Rat Genome Database.
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  - journals/biodb/XuBDCTKKLM13
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Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor Lemischka, Avi Ma'ayan:
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
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  - journals/biodb/MathiasHYZBUO13
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Stephen L. Mathias, Jarrett Hines-Kay, Jeremy J. Yang, Gergely Zahoránszky-Köhalmi, Cristian Bologa, Oleg Ursu, Tudor I. Oprea:
The CARLSBAD Database: A Confederated Database of Chemical Bioactivities.
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  - journals/biodb/RossARHW13
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Karen Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu:
Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint.
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  - journals/biodb/GrandvalFGBBFWBO13
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Philippe Grandval, Aurélie J. Fabre, Pascaline Gaildrat, Stéphanie Baert-Desurmont, Marie-Pierre Buisine, Anthony Ferrari, Qing Wang, Christophe Béroud, Sylviane Olschwang:
UMD-MLH1/MSH2/MSH6 databases: description and analysis of genetic variations in French Lynch syndrome families.
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  - journals/biodb/StewardGTSKGWRH13
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Charles A. Steward, Jose M. Gonzalez, Stephen J. Trevanion, Daniel Sheppard, Giselle Kerry, James G. R. Gilbert, Linda S. Wicker, Jane Rogers, Jennifer L. Harrow:
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes.
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  - journals/biodb/DrocLGYTGDHADLBCPDRRB13
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Gaëtan Droc, Delphine Larivière, Valentin Guignon, Nabila Yahiaoui, Dominique This, Olivier Garsmeur, Alexis Dereeper, Chantal Hamelin, Xavier Argout, Jean-François Dufayard, Juliette Lengelle, Franc-Christophe Baurens, Alberto Cenci, Bertrand Pitollat, Angélique D'Hont, Manuel Ruiz, Mathieu Rouard, Stéphanie Bocs:
The Banana Genome Hub.
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  - journals/biodb/JamiesonRRSN13
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Daniel G. Jamieson, Phoebe M. Roberts, David L. Robertson, Ben Sidders, Goran Nenadic:
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions.
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  - journals/biodb/PujarMBESM13
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Anuradha Pujar, Naama Menda, Aureliano Bombarely, Jeremy D. Edwards, Susan Strickler, Lukas A. Mueller:
From manual curation to visualization of gene families and networks across Solanaceae plant species.
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  - journals/biodb/SadowskiBSSDRBODBT13
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Ivan Sadowski, Bobby-Joe Breitkreutz, Chris Stark, Ting-Cheng Su, Matthew Dahabieh, Sheetal Raithatha, Wendy Bernhard, Rose Oughtred, Kara Dolinski, Kris Barreto, Mike Tyers:
The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update.
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  - journals/biodb/PriyaJ13
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Pushp Priya, Mukesh Jain:
RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis.
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  - journals/biodb/SmedleyOKRWRLM13
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Damian Smedley, Anika Oellrich, Sebastian Köhler, Barbara J. Ruef, Monte Westerfield, Peter N. Robinson, Suzanna Lewis, Christopher J. Mungall:
PhenoDigm: analyzing curated annotations to associate animal models with human diseases.
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  - journals/biodb/LiJAKR13
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Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, Dietrich Rebholz-Schuhmann:
PCorral - interactive mining of protein interactions from MEDLINE.
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  - journals/biodb/SalekHCHWMMBRSS13
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Reza M. Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Susanna-Assunta Sansone, Christoph Steinbeck:
The MetaboLights repository: curation challenges in metabolomics.
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  - journals/biodb/HaasRAKSBS13
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Juergen Haas, Steven Roth, Konstantin Arnold, Florian Kiefer, Tobias Schmidt, Lorenza Bordoli, Torsten Schwede:
The Protein Model Portal - a comprehensive resource for protein structure and model information.
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  - journals/biodb/MistryCEDGFBP13
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Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome.
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  - journals/biodb/LaulederkindLSHWNPLPDS13
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Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy Lowry, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
PhenoMiner: quantitative phenotype curation at the rat genome database.
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  - journals/biodb/NevesDMLSSFKL13
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Mariana L. Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz, Ulf Leser:
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.
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  - journals/biodb/WilmingHCHGCJLPSWWBH13
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Laurens G. Wilming, Elizabeth A. Hart, Penny C. Coggill, Roger Horton, James G. R. Gilbert, Chris Clee, Matt Jones, Christine Lloyd, Sophie Palmer, Sarah Sims, Siobhan Whitehead, David Wiley, Stephan Beck, Jennifer L. Harrow:
Sequencing and comparative analysis of the gorilla MHC genomic sequence.
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  - journals/biodb/BrozziUGME13
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Alessandro Brozzi, Lorena Urbanelli, Pierre-Luc Germain, Alessandro Magini, Carla Emiliani:
hLGDB: a database of human lysosomal genes and their regulation.
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  - journals/biodb/Rawlings13
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Neil D. Rawlings:
Identification and prioritization of novel uncharacterized peptidases for biochemical characterization.
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  - journals/biodb/TakeshitaGSMRZMJ13
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Louise Y. C. Takeshita, Faviel F. Gonzalez-Galarza, Eduardo José Melo dos Santos, Maria Helena Thomaz Maia, Mushome M. Rahman, Syed M. S. Zain, Derek Middleton, Andrew R. Jones:
A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations.
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  - journals/biodb/VerspoorJCMHTP13
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Karin Verspoor, Antonio Jimeno-Yepes, Lawrence Cavedon, Tara McIntosh, Asha Herten-Crabb, Zoë Thomas, John-Paul Plazzer:
Annotating the biomedical literature for the human variome.
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  - journals/biodb/RappaportNSTGSBBMSL13
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Noa Rappaport, Noam Nativ, Gil Stelzer, Michal Twik, Yaron Guan-Golan, Tsippi Iny Stein, Iris Bahir, Frida Belinky, C. Paul Morrey, Marilyn Safran, Doron Lancet:
MalaCards: an integrated compendium for diseases and their annotation.
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  - journals/biodb/JutyNHL13
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Nick S. Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe:
Towards the Collaborative Curation of the Registry underlying identifiers.org.
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  - journals/biodb/OberlinJBF13
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Andrew Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg:
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information.
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  - journals/biodb/GanzfriedRHRTJWABPHW13
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Benjamin Frederick Ganzfried, Markus Riester, Benjamin Haibe-Kains, Thomas Risch, Svitlana Tyekucheva, Ina Jazic, Xin Victoria Wang, Mahnaz Ahmadifar, Michael J. Birrer, Giovanni Parmigiani, Curtis Huttenhower, Levi Waldron:
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome.
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  - journals/biodb/EngelC13
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Stacia R. Engel, J. Michael Cherry:
The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database.
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Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, Frederic B. Bastian:
Uncovering hidden duplicated content in public transcriptomics data.
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Gerhard Mayer, Luisa Montecchi-Palazzi, David Ovelleiro, Andrew R. Jones, Pierre-Alain Binz, Eric W. Deutsch, Matthew Chambers, Marius Kallhardt, Fredrik Levander, James Shofstahl, Sandra E. Orchard, Juan Antonio Vizcaíno, Henning Hermjakob, Christian Stephan, Helmut E. Meyer, Martin Eisenacher:
The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.
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Andy M. Guo, Kun Sun, Xiaoxi Su, Huating Wang, Hao Sun:
YY1TargetDB: an integral information resource for Yin Yang 1 target loci.
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Hong-Jie Dai, Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan, Wen-Lian Hsu:
T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes.
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Fabio Rinaldi, Simon Clematide, Simon Hafner, Gerold Schneider, Gintare Grigonyte, Martin Romacker, Thérèse Vachon:
Using the OntoGene pipeline for the triage task of BioCreative 2012.
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Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry:
The YeastGenome app: the Saccharomyces Genome Database at your fingertips.
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Marialva Sinigaglia, Dinler Amaral Antunes, Maurício Menegatti Rigo, José Artur Bogo Chies, Gustavo Fioravanti Vieira:
CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes.
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Huaqin (Helen) Pan, Mary-Anne Ardini, Vesselina D. Bakalov, Michael DeLatte, Paul Eggers, Laxminarayana Ganapathi, Craig R. Hollingsworth, Joshua Levy, Sheping Li, Joseph Pratt, Norma Pugh, Ying Qin, Rebekah Rasooly, Helen Ray, Jean E. Richardson, Amanda Flynn Riley, Susan M. Rogers, Sylvia Tan, Charles F. Turner, Stacie White, Philip C. Cooley:
'What's in the NIDDK CDR?' - public query tools for the NIDDK central data repository.
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Verena Weiss, Alejandra Medina-Rivera, Araceli M. Huerta, Alberto Santos-Zavaleta, Heladia Salgado, Enrique Morett, Julio Collado-Vides:
Evidence classification of high-throughput protocols and confidence integration in RegulonDB.
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Prudence Mutowo-Meullenet, Rachael P. Huntley, Emily C. Dimmer, Yasmin Alam-Faruque, Tony Sawford, Maria Jesus Martin, Claire O'Donovan, Rolf Apweiler:
Use of Gene Ontology Annotation to understand the peroxisome proteome in humans.
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Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert J. Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila M. Dahdul, Paula M. Mabee, Donghui Li, Bethany R. Harris, Marc Gillespie, Silvia Jimenez, Phoebe M. Roberts, Lisa Matthews, Kevin G. Becker, Harold J. Drabkin, Susan M. Bello, Luana Licata, Andrew Chatr-aryamontri, Mary L. Schaeffer, Julie Park, Melissa A. Haendel, Kimberly Van Auken, Yuling Li, Juancarlos Chan, Hans-Michael Müller, Hong Cui, James P. Balhoff, Chi-Yang Wu, Zhiyong Lu, Chih-Hsuan Wei, Catalina O. Tudor, Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan, Juan Miguel Cejuela, Pratibha Dubey, Cathy H. Wu:
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
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Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan:
PPInterFinder - a mining tool for extracting causal relations on human proteins from literature.
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  - journals/biodb/BowesSJPJBBZV13
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Jeff B. Bowes, Kevin A. Snyder, Christina James-Zorn, Virgilio G. Ponferrada, Chris Jarabek, Kevin A. Burns, Bishnu Bhattacharyya, Aaron M. Zorn, Peter D. Vize:
The Xenbase literature curation process.
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Matthew A. Bertone, István Mikó, Matthew J. Yoder, Katja C. Seltmann, James P. Balhoff, Andrew R. Deans:
Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.

Database Tool

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Izabella Krystkowiak, Jakub Lenart, Konrad J. Debski, Piotr Kuterba, Michal Petas, Bozena Kaminska, Michal Dabrowski:
Nencki Genomics Database - Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs.
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Joo Wook Ahn, Abhishek Dixit, Caroline E. Johnston, Caroline M. Ogilvie, David A. Collier, Sarah Curran, Richard J. B. Dobson:
BBGRE: brain and body genetic resource exchange.
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Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio:
SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.
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Delphine Steinbach, Michael Alaux, Joelle Amselem, Nathalie Choisne, Sophie Durand, Raphaël Flores, Aminah-Olivia Keliet, Erik Kimmel, Nicolas Lapalu, Isabelle Luyten, Célia Michotey, Nacer Mohellibi, Cyril Pommier, Sébastien Reboux, Dorothée Valdenaire, Daphné Verdelet, Hadi Quesneville:
GnpIS: an information system to integrate genetic and genomic data from plants and fungi.
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Adrian Schreyer, Tom L. Blundell:
CREDO: a structural interactomics database for drug discovery.
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Alinda Nagy, László Patthy:
MisPred: a resource for identification of erroneous protein sequences in public databases.
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Zhenzhong Yang, Jihong Yang, Wei Liu, Leihong Wu, Li Xing, Yi Wang, Xiaohui Fan, Yiyu Cheng:
T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus.
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Leihong Wu, Xiang Li, Jihong Yang, Yufeng Liu, Xiaohui Fan, Yiyu Cheng:
CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease.
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Chunguang Liang, Beate Krüger, Thomas Dandekar:
GoSynthetic database tool to analyse natural and engineered molecular processes.
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Xiaoping Liu, Xiaodong Zhang, Weihua Tang, Luonan Chen, Xing-Ming Zhao:
eFG: an electronic resource for Fusarium graminearum.
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  - journals/biodb/KaranyiHHPM13
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Zsolt Karányi, Imre Holb, László Hornok, István Pócsi, Márton Miskei:
FSRD: fungal stress response database.
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  - journals/biodb/VincentDRCMBAM13
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Jonathan Vincent, Zhanwu Dai, Catherine Ravel, Frédéric Choulet, Said Mouzeyar, M. Fouad Bouzidi, Marie Agier, Pierre Martre:
dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts.
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  - journals/biodb/RangelNDMG13
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Luiz Thibério Rangel, Jeniffer Novaes, Alan M. Durham, Alda Maria B. N. Madeira, Arthur Gruber:
The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria.
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  - journals/biodb/ChanYHC13
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Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang, Jan-Gowth Chang:
pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.
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  - journals/biodb/SarikaAIRK13
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Sarika Jaiswal, Vasu Arora, Mir Asif Iquebal, Anil Rai, Dinesh Kumar:
PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome.
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Pascal Jézéquel, Jean-Sébastien Frénel, Loïc Campion, Catherine Guérin-Charbonnel, Wilfried Gouraud, Gabriel Ricolleau, Mario Campone:
bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses.

Database Update

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Joseph A. Rothwell, Jara Perez-Jimenez, Vanessa Neveu, Alexander Medina-Remón, Nouha M'Hiri, Paula García-Lobato, Claudine Manach, Craig Knox, Roman Eisner, David S. Wishart, Augustin Scalbert:
Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content.
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  - journals/biodb/HeavnerSPW13
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Benjamin D. Heavner, Kieran Smallbone, Nathan D. Price, Larry P. Walker:
Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance.
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  - journals/biodb/HiguerueloJB13
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Alicia P. Higueruelo, Harry Jubb, Tom L. Blundell:
TIMBAL v2: update of a database holding small molecules modulating protein-protein interactions.
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  - journals/biodb/HongLBJJYKPKS13
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Dongwan Hong, Jongkeun Lee, Thomas Bleazard, Hyunchul Jung, Young Seok Ju, Saet-Byeol Yu, Sujung Kim, Sung-Soo Park, Jong-Il Kim, Jeong-Sun Seo:
TIARA genome database: update 2013.
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  - journals/biodb/XiongLFYTCFWZM13
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Jie Xiong, Yuming Lu, Jinmei Feng, Dong-Xia Yuan, Miao Tian, Yue Chang, Chengjie Fu, Guangying Wang, Honghui Zeng, Wei Miao:
Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics.
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  - journals/biodb/LiKMNL13
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Weizhong Li, Bartosz Kondratowicz, Hamish McWilliam, Stephane Nauche, Rodrigo Lopez:
The Annotation-enriched non-redundant patent sequence databases.

Letter to the Editor

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Pascale Gaudet, Monica C. Munoz-Torres, Marc Robinson-Rechavi, Teresa K. Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki:
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration.

Corrigendum

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Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta:
The challenge of increasing Pfam coverage of the human proteome.

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