Volume 2013

2013

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EISSN 1758-0463

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Volume 2013, 2013

Original Articles

RefPrimeCouch—a reference gene primer CouchApp

Jascha Silbermann, Catrin Wernicke, Heike Pospisil, Marcus Frohme

Database, Volume 2013, 2013, bat081, https://doi.org/10.1093/database/bat081

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A CTD–Pfizer collaboration: manual curation of 88 000 scientific articles text mined for drug–disease and drug–phenotype interactions

Allan Peter Davis, Thomas C. Wiegers, Phoebe M. Roberts, Benjamin L. King, Jean M. Lay, Kelley Lennon-Hopkins, Daniela Sciaky, Robin Johnson, Heather Keating, Nigel Greene, Robert Hernandez, Kevin J. McConnell, Ahmed E. Enayetallah, Carolyn J. Mattingly

Database, Volume 2013, 2013, bat080, https://doi.org/10.1093/database/bat080

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

Jasmine Y. Young, Zukang Feng, Dimitris Dimitropoulos, Raul Sala, John Westbrook, Marina Zhuravleva, Chenghua Shao, Martha Quesada, Ezra Peisach, Helen M. Berman

Database, Volume 2013, 2013, bat079, https://doi.org/10.1093/database/bat079

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Addition of a breeding database in the Genome Database for Rosaceae

Kate Evans, Sook Jung, Taein Lee, Lisa Brutcher, Ilhyung Cho, Cameron Peace, Dorrie Main

Database, Volume 2013, 2013, bat078, https://doi.org/10.1093/database/bat078

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CoIN: a network analysis for document triage

Yi-Yu Hsu, Hung-Yu Kao

Database, Volume 2013, 2013, bat076, https://doi.org/10.1093/database/bat076

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HypoxiaDB: a database of hypoxia-regulated proteins

Pankaj Khurana, Ragumani Sugadev, Jaspreet Jain, Shashi Bala Singh

Database, Volume 2013, 2013, bat074, https://doi.org/10.1093/database/bat074

Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases

Lacey-Anne Sanderson, Stephen P. Ficklin, Chun-Huai Cheng, Sook Jung, Frank A. Feltus, Kirstin E. Bett, Dorrie Main

Database, Volume 2013, 2013, bat075, https://doi.org/10.1093/database/bat075

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RAvariome: a genetic risk variants database for rheumatoid arthritis based on assessment of reproducibility between or within human populations

Yoko Nagai, Tadashi Imanishi

Database, Volume 2013, 2013, bat073, https://doi.org/10.1093/database/bat073

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HTS-DB: an online resource to publish and query data from functional genomics high-throughput siRNA screening projects

Rebecca E. Saunders, Rachael Instrell, Rossella Rispoli, Ming Jiang, Michael Howell

Database, Volume 2013, 2013, bat072, https://doi.org/10.1093/database/bat072

Ureidoglycolate hydrolase, amidohydrolase, lyase: how errors in biological databases are incorporated in scientific papers and vice versa

Riccardo Percudani, Davide Carnevali, Vincenzo Puggioni

Database, Volume 2013, 2013, bat071, https://doi.org/10.1093/database/bat071

yApoptosis: yeast apoptosis database

Kwanjeera Wanichthanarak, Marija Cvijovic, Andrea Molt, Dina Petranovic

Database, Volume 2013, 2013, bat068, https://doi.org/10.1093/database/bat068

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Capturing cooperative interactions with the PSI-MI format

Kim Van Roey, Sandra Orchard, Samuel Kerrien, Marine Dumousseau, Sylvie Ricard-Blum, Henning Hermjakob, Toby J. Gibson

Database, Volume 2013, 2013, bat066, https://doi.org/10.1093/database/bat066

BioC: a minimalist approach to interoperability for biomedical text processing

Donald C. Comeau, Rezarta Islamaj Doğan, 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

Database, Volume 2013, 2013, bat064, https://doi.org/10.1093/database/bat064

Groups: knowledge spreadsheets for symbolic biocomputing

Michael Travers, Suzanne M. Paley, Jeff Shrager, Timothy A. Holland, Peter D. Karp

Database, Volume 2013, 2013, bat061, https://doi.org/10.1093/database/bat061

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IQdb: an intelligence quotient score-associated gene resource for human intelligence

Lei Kong, Lu Cheng, Li-ya Fan, Min Zhao, Hong Qu

Database, Volume 2013, 2013, bat063, https://doi.org/10.1093/database/bat063

Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort

Sushil Tripathi, Karen R. Christie, Rama Balakrishnan, Rachael Huntley, David P. Hill, Liv Thommesen, Judith A. Blake, Martin Kuiper, Astrid Lægreid

Database, Volume 2013, 2013, bat062, https://doi.org/10.1093/database/bat062

metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research

Mike Lyne, Richard N Smith, Rachel Lyne, Jelena Aleksic, Fengyuan Hu, Alex Kalderimis, Radek Stepan, Gos Micklem

Database, Volume 2013, 2013, bat060, https://doi.org/10.1093/database/bat060

BGDB: a database of bivalent genes

Qingyan Li, Shuabin Lian, Zhiming Dai, Qian Xiang, Xianhua Dai

Database, Volume 2013, 2013, bat057, https://doi.org/10.1093/database/bat057

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists

Laura K. Wiley, R. Michael Sivley, William S. Bush

Database, Volume 2013, 2013, bat056, https://doi.org/10.1093/database/bat056

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BmTEdb: a collective database of transposable elements in the silkworm genome

Hong-En Xu, Hua-Hao Zhang, Tian Xia, Min-Jin Han, Yi-Hong Shen, Ze Zhang

Database, Volume 2013, 2013, bat055, https://doi.org/10.1093/database/bat055

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JBioWH: an open-source Java framework for bioinformatics data integration

Roberto Vera, Yasset Perez-Riverol, Sonia Perez, Balázs Ligeti, Attila Kertész-Farkas, Sándor Pongor

Database, Volume 2013, 2013, bat051, https://doi.org/10.1093/database/bat051

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DoSA: Database of Structural Alignments

Swapnil Mahajan, Garima Agarwal, Mohammed Iftekhar, Bernard Offmann, Alexandre G. de Brevern, Narayanaswamy Srinivasan

Database, Volume 2013, 2013, bat048, https://doi.org/10.1093/database/bat048

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

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

Database, Volume 2013, 2013, bat034, https://doi.org/10.1093/database/bat034

A guide to best practices for Gene Ontology (GO) manual annotation

Rama Balakrishnan, Midori A. Harris, Rachael Huntley, Kimberly Van Auken, J. Michael Cherry

Database, Volume 2013, 2013, bat054, https://doi.org/10.1093/database/bat054

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DBATE: database of alternative transcripts expression

Valerio Bianchi, Alessio Colantoni, Alberto Calderone, Gabriele Ausiello, Fabrizio Ferrè, Manuela Helmer-Citterich

Database, Volume 2013, 2013, bat050, https://doi.org/10.1093/database/bat050

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Managing the data deluge: data-driven GO category assignment improves while complexity of functional annotation increases

Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch

Database, Volume 2013, 2013, bat041, https://doi.org/10.1093/database/bat041

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Analysis of disease-associated objects at the Rat Genome Database

Shur-Jen Wang, Stanley J. F. Laulederkind, G. T. Hayman, Jennifer R. Smith, Victoria Petri, Timothy F. Lowry, Rajni Nigam, Melinda R. Dwinell, Elizabeth A. Worthey, Diane H. Munzenmaier, Mary Shimoyama, Howard J. Jacob

Database, Volume 2013, 2013, bat046, https://doi.org/10.1093/database/bat046

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor R. Lemischka, Avi Ma'ayan

Database, Volume 2013, 2013, bat045, https://doi.org/10.1093/database/bat045

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The CARLSBAD Database: A Confederated Database of Chemical Bioactivities

Stephen L. Mathias, Jarrett Hines-Kay, Jeremy J. Yang, Gergely Zahoransky-Kohalmi, Cristian G. Bologa, Oleg Ursu, Tudor I. Oprea

Database, Volume 2013, 2013, bat044, https://doi.org/10.1093/database/bat044

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Construction of protein phosphorylation networks by data mining, text mining and ontology integration: analysis of the spindle checkpoint

Karen E. Ross, Cecilia N. Arighi, Jia Ren, Hongzhan Huang, Cathy H. Wu

Database, Volume 2013, 2013, bat038, https://doi.org/10.1093/database/bat038

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UMD-MLH1/MSH2/MSH6 databases: description and analysis of genetic variations in French Lynch syndrome families

Philippe Grandval, Aurélie J. Fabre, Pascaline Gaildrat, Stéphanie Baert-Desurmont, Marie-Pierre Buisine, Anthony Ferrari, Qing Wang, Christophe Béroud, Sylviane Olschwang

Database, Volume 2013, 2013, bat036, https://doi.org/10.1093/database/bat036

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The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes

Charles A. Steward, Jose M. Gonzalez, Steve Trevanion, Dan Sheppard, Giselle Kerry, James G. R. Gilbert, Linda S. Wicker, Jane Rogers, Jennifer L. Harrow

Database, Volume 2013, 2013, bat032, https://doi.org/10.1093/database/bat032

The Banana Genome Hub

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

Database, Volume 2013, 2013, bat035, https://doi.org/10.1093/database/bat035

Cataloging the biomedical world of pain through semi-automated curation of molecular interactions

Daniel G. Jamieson, Phoebe M. Roberts, David L. Robertson, Ben Sidders, Goran Nenadic

Database, Volume 2013, 2013, bat033, https://doi.org/10.1093/database/bat033

From manual curation to visualization of gene families and networks across Solanaceae plant species

Anuradha Pujar, Naama Menda, Aureliano Bombarely, Jeremy D. Edwards, Susan R. Strickler, Lukas A. Mueller

Database, Volume 2013, 2013, bat028, https://doi.org/10.1093/database/bat028

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The PhosphoGRID Saccharomyces cerevisiae protein phosphorylation site database: version 2.0 update

Ivan Sadowski, Bobby-Joe Breitkreutz, Chris Stark, Ting-Cheng Su, Matthew Dahabieh, Sheetal Raithatha, Wendy Bernhard, Rose Oughtred, Kara Dolinski, Kris Barreto, Mike Tyers

Database, Volume 2013, 2013, bat026, https://doi.org/10.1093/database/bat026

RiceSRTFDB: A database of rice transcription factors containing comprehensive expression, cis-regulatory element and mutant information to facilitate gene function analysis

Pushp Priya, Mukesh Jain

Database, Volume 2013, 2013, bat027, https://doi.org/10.1093/database/bat027

PhenoDigm: analyzing curated annotations to associate animal models with human diseases

Damian Smedley, Anika Oellrich, Sebastian Köhler, Barbara Ruef, Sanger Mouse Genetics Project, Monte Westerfield, Peter Robinson, Suzanna Lewis, Christopher Mungall

Database, Volume 2013, 2013, bat025, https://doi.org/10.1093/database/bat025

PCorral—interactive mining of protein interactions from MEDLINE

Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, Dietrich Rebholz-Schuhmann

Database, Volume 2013, 2013, bat030, https://doi.org/10.1093/database/bat030

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The MetaboLights repository: curation challenges in metabolomics

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

Database, Volume 2013, 2013, bat029, https://doi.org/10.1093/database/bat029

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The Protein Model Portal—a comprehensive resource for protein structure and model information

Juergen Haas, Steven Roth, Konstantin Arnold, Florian Kiefer, Tobias Schmidt, Lorenza Bordoli, Torsten Schwede

Database, Volume 2013, 2013, bat031, https://doi.org/10.1093/database/bat031

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The challenge of increasing Pfam coverage of the human proteome

Jaina Mistry, Penny Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta

Database, Volume 2013, 2013, bat023, https://doi.org/10.1093/database/bat023

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PhenoMiner: quantitative phenotype curation at the rat genome database

Stanley J F Laulederkind, Weisong Liu, Jennifer R Smith, G Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy F Lowry, Jeff de Pons, Melinda R Dwinell, Mary Shimoyama

Database, Volume 2013, 2013, bat015, https://doi.org/10.1093/database/bat015

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Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

Mariana Neves, Alexander Damaschun, Nancy Mah, Fritz Lekschas, Stefanie Seltmann, Harald Stachelscheid, Jean-Fred Fontaine, Andreas Kurtz, Ulf Leser

Database, Volume 2013, 2013, bat020, https://doi.org/10.1093/database/bat020

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Sequencing and comparative analysis of the gorilla MHC genomic sequence

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

Database, Volume 2013, 2013, bat011, https://doi.org/10.1093/database/bat011

hLGDB: a database of human lysosomal genes and their regulation

Alessandro Brozzi, Lorena Urbanelli, Pierre Luc Germain, Alessandro Magini, Carla Emiliani

Database, Volume 2013, 2013, bat024, https://doi.org/10.1093/database/bat024

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Identification and prioritization of novel uncharacterized peptidases for biochemical characterization

Neil D. Rawlings

Database, Volume 2013, 2013, bat022, https://doi.org/10.1093/database/bat022

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A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations

Louise Y. C. Takeshita, Faviel F. Gonzalez-Galarza, Eduardo J. M. dos Santos, Maria Helena T. Maia, Mushome M. Rahman, Syed M. S. Zain, Derek Middleton, Andrew R. Jones

Database, Volume 2013, 2013, bat021, https://doi.org/10.1093/database/bat021

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Annotating the biomedical literature for the human variome

Karin Verspoor, Antonio Jimeno Yepes, Lawrence Cavedon, Tara McIntosh, Asha Herten-Crabb, Zoë Thomas, John-Paul Plazzer

Database, Volume 2013, 2013, bat019, https://doi.org/10.1093/database/bat019

MalaCards: an integrated compendium for diseases and their annotation

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

Database, Volume 2013, 2013, bat018, https://doi.org/10.1093/database/bat018

Towards the Collaborative Curation of the Registry underlying identifiers.org

Nick Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe

Database, Volume 2013, 2013, bat017, https://doi.org/10.1093/database/bat017

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Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

Andrew T Oberlin, Dominika A Jurkovic, Mitchell F Balish, Iddo Friedberg

Database, Volume 2013, 2013, bat016, https://doi.org/10.1093/database/bat016

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curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome

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

Database, Volume 2013, 2013, bat013, https://doi.org/10.1093/database/bat013

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The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database

Stacia R. Engel, J. Michael Cherry

Database, Volume 2013, 2013, bat012, https://doi.org/10.1093/database/bat012

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Uncovering hidden duplicated content in public transcriptomics data

Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, Frederic B. Bastian

Database, Volume 2013, 2013, bat010, https://doi.org/10.1093/database/bat010

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary

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 Orchard, Juan Antonio Vizcaíno, Henning Hermjakob, Christian Stephan, Helmut E. Meyer, Martin Eisenacher

Database, Volume 2013, 2013, bat009, https://doi.org/10.1093/database/bat009

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YY1TargetDB: an integral information resource for Yin Yang 1 target loci

Andy M. Guo, Kun Sun, Xiaoxi Su, Huating Wang, Hao Sun

Database, Volume 2013, 2013, bat007, https://doi.org/10.1093/database/bat007

T-HOD: a literature-based candidate gene database for hypertension, obesity and diabetes

Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan, Wen-Lian Hsu

Database, Volume 2013, 2013, bas061, https://doi.org/10.1093/database/bas061

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Using the OntoGene pipeline for the triage task of BioCreative 2012

Fabio Rinaldi, Simon Clematide, Simon Hafner, Gerold Schneider, Gintarė Grigonytė, Martin Romacker, Therese Vachon

Database, Volume 2013, 2013, bas053, https://doi.org/10.1093/database/bas053

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The YeastGenome app: the Saccharomyces Genome Database at your fingertips

Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, J. Michael Cherry

Database, Volume 2013, 2013, bat004, https://doi.org/10.1093/database/bat004

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CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes

Marialva Sinigaglia, Dinler Amaral Antunes, Maurício Menegatti Rigo, José Artur Bogo Chies, Gustavo Fioravanti Vieira

Database, Volume 2013, 2013, bat002, https://doi.org/10.1093/database/bat002

‘What’s in the NIDDK CDR?’—public query tools for the NIDDK central data repository

Huaqin Pan, Mary-Anne Ardini, Vesselina 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 … Philip C. Cooley

Database, Volume 2013, 2013, bas058, https://doi.org/10.1093/database/bas058

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Evidence classification of high-throughput protocols and confidence integration in RegulonDB

Verena Weiss, Alejandra Medina-Rivera, Araceli M. Huerta, Alberto Santos-Zavaleta, Heladia Salgado, Enrique Morett, Julio Collado-Vides

Database, Volume 2013, 2013, bas059, https://doi.org/10.1093/database/bas059

Use of Gene Ontology Annotation to understand the peroxisome proteome in humans

Prudence Mutowo-Meullenet, Rachael P. Huntley, Emily C. Dimmer, Yasmin Alam-Faruque, Tony Sawford, Maria Jesus Martin, Claire O’Donovan, Rolf Apweiler

Database, Volume 2013, 2013, bas062, https://doi.org/10.1093/database/bas062

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Cecilia N. Arighi, Ben Carterette, K. Bretonnel Cohen, Martin Krallinger, W. John Wilbur, Petra Fey, Robert Dodson, Laurel Cooper, Ceri E. Van Slyke, Wasila Dahdul, Paula Mabee, Donghui Li, Bethany Harris, Marc Gillespie, Silvia Jimenez, Phoebe Roberts, Lisa Matthews, Kevin Becker, Harold Drabkin … Cathy Wu

Database, Volume 2013, 2013, bas056, https://doi.org/10.1093/database/bas056

PPInterFinder—a mining tool for extracting causal relations on human proteins from literature

Kalpana Raja, Suresh Subramani, Jeyakumar Natarajan

Database, Volume 2013, 2013, bas052, https://doi.org/10.1093/database/bas052

The Xenbase literature curation process

Jeff B. Bowes, Kevin A. Snyder, Christina James-Zorn, Virgilio G. Ponferrada, Chris J. Jarabek, Kevin A. Burns, Bishnu Bhattacharyya, Aaron M. Zorn, Peter D. Vize

Database, Volume 2013, 2013, bas046, https://doi.org/10.1093/database/bas046

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Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment

Matthew A. Bertone, István Mikó, Matthew J. Yoder, Katja C. Seltmann, James P. Balhoff, Andrew R. Deans

Database, Volume 2013, 2013, bas057, https://doi.org/10.1093/database/bas057

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Database Tool

Nencki Genomics Database—Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs

Izabella Krystkowiak, Jakub Lenart, Konrad Debski, Piotr Kuterba, Michal Petas, Bozena Kaminska, Michal Dabrowski

Database, Volume 2013, 2013, bat069, https://doi.org/10.1093/database/bat069

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BBGRE: brain and body genetic resource exchange

Joo Wook Ahn, Abhishek Dixit, Caroline Johnston, Caroline M. Ogilvie, David A. Collier, Sarah Curran, Richard J. B. Dobson

Database, Volume 2013, 2013, bat067, https://doi.org/10.1093/database/bat067

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SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Piero Fariselli, Luca Fontanesi, Rita Casadio

Database, Volume 2013, 2013, bat065, https://doi.org/10.1093/database/bat065

GnpIS: an information system to integrate genetic and genomic data from plants and fungi

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

Database, Volume 2013, 2013, bat058, https://doi.org/10.1093/database/bat058

CREDO: a structural interactomics database for drug discovery

Adrian M. Schreyer, Tom L. Blundell

Database, Volume 2013, 2013, bat049, https://doi.org/10.1093/database/bat049

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MisPred: a resource for identification of erroneous protein sequences in public databases

Alinda Nagy, László Patthy

Database, Volume 2013, 2013, bat053, https://doi.org/10.1093/database/bat053

T2D@ZJU: a knowledgebase integrating heterogeneous connections associated with type 2 diabetes mellitus

Zhenzhong Yang, Jihong Yang, Wei Liu, Leihong Wu, Li Xing, Yi Wang, Xiaohui Fan, Yiyu Cheng

Database, Volume 2013, 2013, bat052, https://doi.org/10.1093/database/bat052

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CHD@ZJU: a knowledgebase providing network-based research platform on coronary heart disease

Leihong Wu, Xiang Li, Jihong Yang, Yufeng Liu, Xiaohui Fan, Yiyu Cheng

Database, Volume 2013, 2013, bat047, https://doi.org/10.1093/database/bat047

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GoSynthetic database tool to analyse natural and engineered molecular processes

Chunguang Liang, Beate Krüger, Thomas Dandekar

Database, Volume 2013, 2013, bat043, https://doi.org/10.1093/database/bat043

eFG: an electronic resource for Fusarium graminearum

Xiaoping Liu, Xiaodong Zhang, Wei-Hua Tang, Luonan Chen, Xing-Ming Zhao

Database, Volume 2013, 2013, bat042, https://doi.org/10.1093/database/bat042

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FSRD: fungal stress response database

Zsolt Karányi, Imre Holb, László Hornok, István Pócsi, Márton Miskei

Database, Volume 2013, 2013, bat037, https://doi.org/10.1093/database/bat037

dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts

Jonathan Vincent, Zhanwu Dai, Catherine Ravel, Frédéric Choulet, Said Mouzeyar, M. Fouad Bouzidi, Marie Agier, Pierre Martre

Database, Volume 2013, 2013, bat014, https://doi.org/10.1093/database/bat014

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The Eimeria Transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria

Luiz Thibério Rangel, Jeniffer Novaes, Alan M. Durham, Alda Maria B. N. Madeira, Arthur Gruber

Database, Volume 2013, 2013, bat006, https://doi.org/10.1093/database/bat006

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pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes

Wen-Ling Chan, Wen-Kuang Yang, Hsien-Da Huang, Jan-Gowth Chang

Database, Volume 2013, 2013, bat001, https://doi.org/10.1093/database/bat001

PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome

Sarika, Vasu Arora, M. A. Iquebal, Anil Rai, Dinesh Kumar

Database, Volume 2013, 2013, bas054, https://doi.org/10.1093/database/bas054

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bc-GenExMiner 3.0: new mining module computes breast cancer gene expression correlation analyses

Pascal Jézéquel, Jean-Sébastien Frénel, Loïc Campion, Catherine Guérin-Charbonnel, Wilfried Gouraud, Gabriel Ricolleau, Mario Campone

Database, Volume 2013, 2013, bas060, https://doi.org/10.1093/database/bas060

Database Update

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

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

Database, Volume 2013, 2013, bat070, https://doi.org/10.1093/database/bat070

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Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

Benjamin D. Heavner, Kieran Smallbone, Nathan D. Price, Larry P. Walker

Database, Volume 2013, 2013, bat059, https://doi.org/10.1093/database/bat059

TIMBAL v2: update of a database holding small molecules modulating protein–protein interactions

Alicia P. Higueruelo, Harry Jubb, Tom L. Blundell

Database, Volume 2013, 2013, bat039, https://doi.org/10.1093/database/bat039

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TIARA genome database: update 2013

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

Database, Volume 2013, 2013, bat003, https://doi.org/10.1093/database/bat003

Tetrahymena Functional Genomics Database (TetraFGD): an integrated resource for Tetrahymena functional genomics

Jie Xiong, Yuming Lu, Jinmei Feng, Dongxia Yuan, Miao Tian, Yue Chang, Chengjie Fu, Guangying Wang, Honghui Zeng, Wei Miao

Database, Volume 2013, 2013, bat008, https://doi.org/10.1093/database/bat008

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The Annotation-enriched non-redundant patent sequence databases

Weizhong Li, Bartosz Kondratowicz, Hamish McWilliam, Stephane Nauche, Rodrigo Lopez

Database, Volume 2013, 2013, bat005, https://doi.org/10.1093/database/bat005

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Letter to the Editor

DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration

Pascale Gaudet, Monica Munoz-Torres, Marc Robinson-Rechavi, Teresa Attwood, Alex Bateman, J. Michael Cherry, Renate Kania, Claire O'Donovan, Chisato Yamasaki

Database, Volume 2013, 2013, bat077, https://doi.org/10.1093/database/bat077