Volume 2011

2011

Cover image

EISSN 1758-0463

Issue navigation

< Previous Next >

Volume 2011, 2011

Editorial

BioMart: driving a paradigm change in biological data management

Arek Kasprzyk

Database, Volume 2011, 2011, bar049, https://doi.org/10.1093/database/bar049

View article

Towards BioDBcore: a community-defined information specification for biological databases

Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock … Chisato Yamasaki

Database, Volume 2011, 2011, baq027, https://doi.org/10.1093/database/baq027

View article

Original Articles

AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments

Jie Zheng, Julia Stoyanovich, Elisabetta Manduchi, Junmin Liu, Christian J. Stoeckert, Jr

Database, Volume 2011, 2011, bar045, https://doi.org/10.1093/database/bar045

View article

RAC: Repository of Antibiotic resistance Cassettes

Guy Tsafnat, Joseph Copty, Sally R. Partridge

Database, Volume 2011, 2011, bar054, https://doi.org/10.1093/database/bar054

View article

hUbiquitome: a database of experimentally verified ubiquitination cascades in humans

Yipeng Du, Nanfang Xu, Ming Lu, Tingting Li

Database, Volume 2011, 2011, bar055, https://doi.org/10.1093/database/bar055

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes

John P. Hamilton, Eric C. Neeno-Eckwall, Bishwo N. Adhikari, Nicole T. Perna, Ned Tisserat, Jan E. Leach, C. André Lévesque, C. Robin Buell

Database, Volume 2011, 2011, bar053, https://doi.org/10.1093/database/bar053

View article

INOH: ontology-based highly structured database of signal transduction pathways

Satoko Yamamoto, Noriko Sakai, Hiromi Nakamura, Hiroshi Fukagawa, Ken Fukuda, Toshihisa Takagi

Database, Volume 2011, 2011, bar052, https://doi.org/10.1093/database/bar052

View article

SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss

Alex Di Génova, Andrés Aravena, Luis Zapata, Mauricio González, Alejandro Maass, Patricia Iturra

Database, Volume 2011, 2011, bar050, https://doi.org/10.1093/database/bar050

View article

CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses

Akiko Hatano, Hirokazu Chiba, Harry Amri Moesa, Takeaki Taniguchi, Satoshi Nagaie, Koji Yamanegi, Takako Takai-Igarashi, Hiroshi Tanaka, Wataru Fujibuchi

Database, Volume 2011, 2011, bar046, https://doi.org/10.1093/database/bar046

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations

Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan A. Vizcaíno, David Croft

Database, Volume 2011, 2011, bar047, https://doi.org/10.1093/database/bar047

The Reactome BioMart

Robin A. Haw, David Croft, Christina K. Yung, Nelson Ndegwa, Peter D'Eustachio, Henning Hermjakob, Lincoln D. Stein

Database, Volume 2011, 2011, bar031, https://doi.org/10.1093/database/bar031

View article

The NIDDK Central Repository at 8 years—Ambition, Revision, Use and Impact

Charles F. Turner, Huaqin Pan, Gregg W. Silk, Mary-Anne Ardini, Vesselina Bakalov, Stephanie Bryant, Susanna Cantor, Kung-yen Chang, Michael DeLatte, Paul Eggers, Laxminarayana Ganapathi, Sujatha Lakshmikanthan, Joshua Levy, Sheping Li, Joseph Pratt, Norma Pugh, Ying Qin, Rebekah Rasooly, Helen Ray … Philip C. Cooley

Database, Volume 2011, 2011, bar043, https://doi.org/10.1093/database/bar043

View article

NetSlim: high-confidence curated signaling maps

Rajesh Raju, Vishalakshi Nanjappa, Lavanya Balakrishnan, Aneesha Radhakrishnan, Joji Kurian Thomas, Jyoti Sharma, Maozhen Tian, Shyam Mohan Palapetta, Tejaswini Subbannayya, Nirujogi Raja Sekhar, Babylakshmi Muthusamy, Renu Goel, Yashwanth Subbannayya, Deepthi Telikicherla, Mitali Bhattacharjee, Sneha M. Pinto, Nazia Syed, Manda Srinivas Srikanth, Gajanan J. Sathe … Akhilesh Pandey

Database, Volume 2011, 2011, bar032, https://doi.org/10.1093/database/bar032

View article

BioMart: a data federation framework for large collaborative projects

Junjun Zhang, Syed Haider, Joachim Baran, Anthony Cros, Jonathan M. Guberman, Jack Hsu, Yong Liang, Long Yao, Arek Kasprzyk

Database, Volume 2011, 2011, bar038, https://doi.org/10.1093/database/bar038

View article

BioMart Central Portal: an open database network for the biological community

Jonathan M. Guberman, J. Ai, O. Arnaiz, Joachim Baran, Andrew Blake, Richard Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, A. Di Génova, Simon Forbes, T. Fujisawa, E. Gadaleta, D. M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall … Arek Kasprzyk

Database, Volume 2011, 2011, bar041, https://doi.org/10.1093/database/bar041

View article

Neisseria Base: a comparative genomics database for Neisseria meningitidis

Lee S. Katz, Jay C. Humphrey, Andrew B. Conley, Viswateja Nelakuditi, Andrey O. Kislyuk, Sonia Agrawal, Pushkala Jayaraman, Brian H. Harcourt, Melissa A. Olsen-Rasmussen, Michael Frace, Nitya V. Sharma, Leonard W. Mayer, I. King Jordan

Database, Volume 2011, 2011, bar035, https://doi.org/10.1093/database/bar035

The BioMart interface to the eMouseAtlas gene expression database EMAGE

Peter Stevenson, Lorna Richardson, Shanmugasundaram Venkataraman, Yiya Yang, Richard Baldock

Database, Volume 2011, 2011, bar029, https://doi.org/10.1093/database/bar029

BioMart as an integration solution for the International Knockout Mouse Consortium

Darren J. Oakley, Vivek Iyer, William C. Skarnes, Damian Smedley

Database, Volume 2011, 2011, bar028, https://doi.org/10.1093/database/bar028

View article

International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data

Junjun Zhang, Joachim Baran, A. Cros, Jonathan M. Guberman, Syed Haider, Jack Hsu, Yong Liang, Elena Rivkin, Jianxin Wang, Brett Whitty, Marie Wong-Erasmus, Long Yao, Arek Kasprzyk

Database, Volume 2011, 2011, bar026, https://doi.org/10.1093/database/bar026

View article

SigReannot-mart: a query environment for expression microarray probe re-annotations

François Moreews, Gaelle Rauffet, Patrice Dehais, Christophe Klopp

Database, Volume 2011, 2011, bar025, https://doi.org/10.1093/database/bar025

View article

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice David, Frederik Decouttere, Jacques Rougemont, Bart Deplancke

Database, Volume 2011, 2011, bar040, https://doi.org/10.1093/database/bar040

Integrative Cancer Genomics (IntOGen) in Biomart

Christian Perez-Llamas, Gunes Gundem, Nuria Lopez-Bigas

Database, Volume 2011, 2011, bar039, https://doi.org/10.1093/database/bar039

View article

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details

Nicole L. Washington, E. O. Stinson, Marc D. Perry, Peter Ruzanov, Sergio Contrino, Richard Smith, Zheng Zha, Rachel Lyne, Adrian Carr, Paul Lloyd, Ellen Kephart, Sheldon J. McKay, Gos Micklem, Lincoln D. Stein, Suzanna E. Lewis

Database, Volume 2011, 2011, bar023, https://doi.org/10.1093/database/bar023

The InterPro BioMart: federated query and web service access to the InterPro Resource

Philip Jones, David Binns, Conor McMenamin, Craig McAnulla, Sarah Hunter

Database, Volume 2011, 2011, bar033, https://doi.org/10.1093/database/bar033

View article

Ensembl BioMarts: a hub for data retrieval across taxonomic space

Rhoda J. Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel Staines, Paul Derwent, Arnaud Kerhornou, Paul Kersey, Paul Flicek

Database, Volume 2011, 2011, bar030, https://doi.org/10.1093/database/bar030

View article

A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway

Rajesh Raju, Lavanya Balakrishnan, Vishalakshi Nanjappa, Mitali Bhattacharjee, Derese Getnet, Babylakshmi Muthusamy, Joji Kurian Thomas, Jyoti Sharma, B. Abdul Rahiman, H.C. Harsha, Subramanian Shankar, T.S. Keshava Prasad, S. Sujatha Mohan, Gary D. Bader, Mohan R. Wani, Akhilesh Pandey

Database, Volume 2011, 2011, bar021, https://doi.org/10.1093/database/bar021

View article

The strategies WDK: a graphical search interface and web development kit for functional genomics databases

Steve Fischer, Cristina Aurrecoechea, Brian P. Brunk, Xin Gao, Omar S. Harb, Eileen T. Kraemer, Cary Pennington, Charles Treatman, Jessica C. Kissinger, David S. Roos, Christian J. Stoeckert

Database, Volume 2011, 2011, bar027, https://doi.org/10.1093/database/bar027

View article

Using BioMart as a framework to manage and query pancreatic cancer data

Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine, Claude Chelala

Database, Volume 2011, 2011, bar024, https://doi.org/10.1093/database/bar024

View article

MaizeGDB: curation and outreach go hand-in-hand

Mary L. Schaeffer, Lisa C. Harper, Jack M. Gardiner, Carson M. Andorf, Darwin A. Campbell, Ethalinda K.S. Cannon, Taner Z. Sen, Carolyn J. Lawrence

Database, Volume 2011, 2011, bar022, https://doi.org/10.1093/database/bar022

View article

Curation of characterized glycoside hydrolases of Fungal origin

Caitlin Murphy, Justin Powlowski, Min Wu, Greg Butler, Adrian Tsang

Database, Volume 2011, 2011, bar020, https://doi.org/10.1093/database/bar020

View article

Data mining using the Catalogue of Somatic Mutations in Cancer BioMart

Rebecca Shepherd, Simon A. Forbes, David Beare, S. Bamford, Charlotte G. Cole, Sari Ward, Nidhi Bindal, Prasad Gunasekaran, Mingming Jia, Chai Yin Kok, Kenric Leung, Andrew Menzies, Adam P. Butler, Jon W. Teague, Peter J. Campbell, Michael R. Stratton, P. Andrew Futreal

Database, Volume 2011, 2011, bar018, https://doi.org/10.1093/database/bar018

View article

hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds

Haretsugu Hishigaki, Satoru Kuhara

Database, Volume 2011, 2011, bar017, https://doi.org/10.1093/database/bar017

View article

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

Jason M. Green, Jaturon Harnsomburana, Mary L. Schaeffer, Carolyn J. Lawrence, Chi-Ren Shyu

Database, Volume 2011, 2011, bar012, https://doi.org/10.1093/database/bar012

View article

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

Lisa C. Harper, Mary L. Schaeffer, Jordan Thistle, Jack M. Gardiner, Carson M. Andorf, Darwin A. Campbell, Ethalinda K.S. Cannon, Bremen L. Braun, Scott M. Birkett, Carolyn J. Lawrence, Taner Z. Sen

Database, Volume 2011, 2011, bar016, https://doi.org/10.1093/database/bar016

View article

TparvaDB: a database to support Theileria parva vaccine development

Paul Visendi, Wanjiku Ng'ang'a, Wallace Bulimo, Richard Bishop, James Ochanda, Etienne P. de Villiers

Database, Volume 2011, 2011, bar015, https://doi.org/10.1093/database/bar015

View article

Methods and strategies for gene structure curation in WormBase

G.W. Williams, P.A. Davis, A.S. Rogers, T. Bieri, P. Ozersky, J. Spieth

Database, Volume 2011, 2011, baq039, https://doi.org/10.1093/database/baq039

View article

Integrating diverse databases into an unified analysis framework: a Galaxy approach

Daniel Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko

Database, Volume 2011, 2011, bar011, https://doi.org/10.1093/database/bar011

View article

Allie: a database and a search service of abbreviations and long forms

Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, Toshihisa Takagi

Database, Volume 2011, 2011, bar013, https://doi.org/10.1093/database/bar013

View article

The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases

Demet Sirim, Florian Wagner, Lei Wang, Rolf D Schmid, Jürgen Pleiss

Database, Volume 2011, 2011, bar006, https://doi.org/10.1093/database/bar006

A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway

Xin Li, Fan Wu, Feng Qi, Daniel A. Beard

Database, Volume 2011, 2011, bar005, https://doi.org/10.1093/database/bar005

View article

The Rat Genome Database Pathway Portal

Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob, RGD Team

Database, Volume 2011, 2011, bar010, https://doi.org/10.1093/database/bar010

View article

CycADS: an annotation database system to ease the development and update of BioCyc databases

Augusto F. Vellozo, Amélie S. Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé, Angela E. Douglas, Toni Gabaldón, Marie-France Sagot, Hubert Charles, Stefano Colella

Database, Volume 2011, 2011, bar008, https://doi.org/10.1093/database/bar008

UniProt Knowledgebase: a hub of integrated protein data

Michele Magrane, UniProt Consortium

Database, Volume 2011, 2011, bar009, https://doi.org/10.1093/database/bar009

View article

Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study

Maria C. Costanzo, Julie Park, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong

Database, Volume 2011, 2011, bar004, https://doi.org/10.1093/database/bar004

View article

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

Wolfgang F. Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlić, Gregory B. Quinn, Peter W. Rose, Chaitali Shah, Jasmine Young, Benjamin Yukich, Helen M. Berman, Philip E. Bourne

Database, Volume 2011, 2011, bar003, https://doi.org/10.1093/database/bar003

View article

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data

Stanley J. F. Laulederkind, Mary Shimoyama, G. Thomas Hayman, Timothy F. Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, George Kowalski, Weisong Liu, Wes Rood, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob, RGD Team

Database, Volume 2011, 2011, bar002, https://doi.org/10.1093/database/bar002

View article

FunSecKB: the Fungal Secretome KnowledgeBase

Gengkon Lum, Xiang Jia Min

Database, Volume 2011, 2011, bar001, https://doi.org/10.1093/database/bar001

View article

A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database

Justyna Milc, Antonio Sala, Sonia Bergamaschi, Nicola Pecchioni

Database, Volume 2011, 2011, baq038, https://doi.org/10.1093/database/baq038

View article

The Biomolecular Interaction Network Database in PSI-MI 2.5

Ruth Isserlin, Rashad A. El-Badrawi, Gary D. Bader

Database, Volume 2011, 2011, baq037, https://doi.org/10.1093/database/baq037

LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase

Djamel Harbi, Manish Kumar, Paul M. Harrison

Database, Volume 2011, 2011, baq031, https://doi.org/10.1093/database/baq031

View article

Database Tool

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data

Sook Jung, Naama Menda, Seth Redmond, Robert M. Buels, Maren Friesen, Yuri Bendana, Lacey-Anne Sanderson, Hilmar Lapp, Taein Lee, Bob MacCallum, Kirstin E. Bett, Scott Cain, Dave Clements, Lukas A. Mueller, Dorrie Main

Database, Volume 2011, 2011, bar051, https://doi.org/10.1093/database/bar051

View article

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

Shuchi Smita, Sangram Keshari Lenka, Amit Katiyar, Pankaj Jaiswal, Justin Preece, Kailash Chander Bansal

Database, Volume 2011, 2011, bar037, https://doi.org/10.1093/database/bar037

Tripal: a construction toolkit for online genome databases

Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret E. Staton, Taein Lee, Il-Hyung Cho, Sook Jung, Kirstin E. Bett, Doreen Main

Database, Volume 2011, 2011, bar044, https://doi.org/10.1093/database/bar044

View article

3DSwap: curated knowledgebase of proteins involved in 3D domain swapping

Khader Shameer, Prashant N. Shingate, S. C. P. Manjunath, M. Karthika, Ganesan Pugalenthi, Ramanathan Sowdhamini

Database, Volume 2011, 2011, bar042, https://doi.org/10.1093/database/bar042

View article

The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database

Allan Peter Davis, Thomas C. Wiegers, Cynthia G. Murphy, Carolyn J. Mattingly

Database, Volume 2011, 2011, bar034, https://doi.org/10.1093/database/bar034

View article

ppiTrim: constructing non-redundant and up-to-date interactomes

Aleksandar Stojmirović, Yi-Kuo Yu

Database, Volume 2011, 2011, bar036, https://doi.org/10.1093/database/bar036

Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies

Yu S. Huang, Matthew Horton, Bjarni J. Vilhjálmsson, Ümit Seren, Dazhe Meng, Christopher Meyer, Muhammad Ali Amer, Justin O. Borevitz, Joy Bergelson, Magnus Nordborg

Database, Volume 2011, 2011, bar014, https://doi.org/10.1093/database/bar014

View article

ParkDB: a Parkinson’s disease gene expression database

Cristian Taccioli, Vincenza Maselli, Jesper Tegnér, David Gomez-Cabrero, Gioia Altobelli, Warren Emmett, Francesco Lescai, Stefano Gustincich, Elia Stupka

Database, Volume 2011, 2011, bar007, https://doi.org/10.1093/database/bar007