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Database - The Journal of Biological Databases and Curation, Volume 2011

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Volume 2011, 2011

Editorial

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Arek Kasprzyk:
BioMart: driving a paradigm change in biological data management.
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Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. 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, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases.

Original article

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Jie Zheng, Julia Stoyanovich, Elisabetta Manduchi, Junmin Liu, Christian J. Stoeckert Jr.:
AnnotCompute: annotation-based exploration and meta-analysis of genomics experiments.
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  - journals/biodb/TsafnatCP11
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Guy Tsafnat, Joseph Copty, Sally R. Partridge:
RAC: Repository of Antibiotic resistance Cassettes.
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Yipeng Du, Nanfang Xu, Ming Lu, Tingting Li:
hUbiquitome: a database of experimentally verified ubiquitination cascades in humans.
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  - journals/biodb/HamiltonNAPTLLB11
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John P. Hamilton, Eric C. Neeno-Eckwall, Bishwo N. Adhikari, Nicole T. Perna, Ned Tisserat, Jan Leach, C. André Lévesque, C. Robin Buell:
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.
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Satoko Yamamoto, Noriko Sakai, Hiromi Nakamura, Hiroshi Fukagawa, Ken Fukuda, Toshihisa Takagi:
INOH: ontology-based highly structured database of signal transduction pathways.
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  - journals/biodb/GenovaAZGMI11
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Alex Di Génova, Andrés Aravena, Luis Zapata, Mauricio Gonzalez, Alejandro Maass, Patricia Iturra:
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.
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  - journals/biodb/HatanoCMTNYTTF11
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Akiko Hatano, Hirokazu Chiba, Harry Amri Moesa, Takeaki Taniguchi, Satoshi Nagaie, Koji Yamanegi, Takako Takai-Igarashi, Hiroshi Tanaka, Wataru Fujibuchi:
CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses.
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Nelson Ndegwa, Richard G. Côté, David Ovelleiro, Peter D'Eustachio, Henning Hermjakob, Juan Antonio Vizcaíno, David Croft:
Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.
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Robin Haw, David Croft, Christina K. Yung, Nelson Ndegwa, Peter D'Eustachio, Henning Hermjakob, Lincoln D. Stein:
The Reactome BioMart.
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  - journals/biodb/TurnerPSABBCCDEGLLLPPQRRRRRSTWC11
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Charles F. Turner, Huaqin (Helen) Pan, Gregg W. Silk, Mary-Anne Ardini, Vesselina D. Bakalov, Stephanie Bryant, Susanna Cantor, Kungyen Chang, Michael DeLatte, Paul Eggers, Laxminarayana Ganapathi, Sujatha Lakshmikanthan, Joshua Levy, Sheping Li, Joseph Pratt, Norma Pugh, Ying Qin, Rebekah Rasooly, Helen Ray, Jean E. Richardson, Amanda Flynn Riley, Susan M. Rogers, Charlotte Scheper, Sylvia Tan, Stacie White, Philip C. Cooley:
The NIDDK Central Repository at 8 years - Ambition, Revision, Use and Impact.
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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, Srinivas Manda Srikanth, Gajanan J. Sathe, Sartaj Ahmad, Sandip N. Chavan, Ghantasala S. Sameer Kumar, Arivusudar Marimuthu, T. S. Keshava Prasad, H. C. Harsha, B. Abdul Rahiman, Osamu Ohara, Gary D. Bader, S. Sujatha Mohan, William P. Schiemann, Akhilesh Pandey:
NetSlim: high-confidence curated signaling maps.
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Junjun Zhang, Syed Haider, Joachim Baran, Anthony Cros, Jonathan M. Guberman, Jack Hsu, Yong Liang, Long Yao, Arek Kasprzyk:
BioMart: a data federation framework for large collaborative projects.
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Jonathan M. Guberman, Jiye Ai, Olivier Arnaiz, Joachim Baran, Andrew Blake, Richard A. Baldock, Claude Chelala, David Croft, Anthony Cros, Rosalind J. Cutts, Alex Di Génova, Simon A. Forbes, Takatomo Fujisawa, Emanuela Gadaleta, David M. Goodstein, Gunes Gundem, Bernard Haggarty, Syed Haider, Matthew Hall, Todd W. Harris, Robin Haw, Shen Hu, Simon J. Hubbard, Jack Hsu, Vivek Iyer, Philip Jones, Toshiaki Katayama, Rhoda Kinsella, Lei Kong, Daniel Lawson, Yong Liang, Núria López-Bigas, Jie Luo, Michael J. Lush, Jeremy C. Mason, François Moreews, Nelson Ndegwa, Darren J. Oakley, Christian Perez-Llamas, Michael Primig, Elena Rivkin, Steven Rosanoff, Rebecca Shepherd, Reinhard Simon, William C. Skarnes, Damian Smedley, Linda Sperling, William Spooner, Peter Stevenson, Kevin R. Stone, Jon W. Teague, Jun Wang, Jianxin Wang, Brett Whitty, David Tai Wai Wong, Marie Wong-Erasmus, Long Yao, Ken Youens-Clark, Christina K. Yung, Junjun Zhang, Arek Kasprzyk:
BioMart Central Portal: an open database network for the biological community.
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Lee S. Katz, Jay C. Humphrey, Andrew B. Conley, Viswateja Nelakuditi, Andrey Kislyuk, Sonia Agrawal, Pushkala Jayaraman, Brian H. Harcourt, Melissa A. Olsen-Rasmussen, Michael Frace, Nitya V. Sharma, Leonard W. Mayer, I. King Jordan:
Neisseria Base: a comparative genomics database for Neisseria meningitidis.
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Peter Stevenson, Lorna J. Richardson, Shanmugasundaram Venkataraman, Yiya Yang, Richard A. Baldock:
The BioMart interface to the eMouseAtlas gene expression database EMAGE.
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Darren J. Oakley, Vivek Iyer, William C. Skarnes, Damian Smedley:
BioMart as an integration solution for the International Knockout Mouse Consortium.
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Junjun Zhang, Joachim Baran, Anthony Cros, Jonathan M. Guberman, Syed Haider, Jack Hsu, Yong Liang, Elena Rivkin, Jianxin Wang, Brett Whitty, Marie Wong-Erasmus, Long Yao, Arek Kasprzyk:
International Cancer Genome Consortium Data Portal - a one-stop shop for cancer genomics data.
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  - journals/biodb/MoreewsRDK11
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François Moreews, Gaelle Rauffet, Patrice Déhais, Christophe Klopp:
SigReannot-mart: a query environment for expression microarray probe re-annotations.
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Carine Gubelmann, Alexandre Gattiker, Andreas Massouras, Korneel Hens, Fabrice P. A. David, Frederik Decouttere, Jacques Rougemont, Bart Deplancke:
GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.
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  - journals/biodb/Perez-LlamasGL11
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Christian Perez-Llamas, Gunes Gundem, Núria López-Bigas:
Integrative Cancer Genomics (IntOGen) in Biomart.
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  - journals/biodb/WashingtonSPRCSZLCLKMMSL11
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Nicole L. Washington, E. O. Stinson, Marc D. Perry, Peter Ruzanov, Sergio Contrino, Richard N. Smith, Zheng Zha, Rachel Lyne, Adrian Carr, Paul Lloyd, Ellen T. Kephart, Sheldon J. McKay, Gos Micklem, Lincoln D. Stein, Suzanna E. Lewis:
The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.
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Philip Jones, David Binns, Conor McMenamin, Craig McAnulla, Sarah Hunter:
The InterPro BioMart: federated query and web service access to the InterPro Resource.
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  - journals/biodb/KinsellaKHZPSASDKKF11
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Rhoda Kinsella, Andreas Kähäri, Syed Haider, Jorge Zamora, Glenn Proctor, Giulietta Spudich, Jeff Almeida-King, Daniel M. Staines, Paul S. Derwent, Arnaud Kerhornou, Paul J. Kersey, Paul Flicek:
Ensembl BioMarts: a hub for data retrieval across taxonomic space.
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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:
A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway.
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  - journals/biodb/FischerABGHKPTKRS11
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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 Jr.:
The strategies WDK: a graphical search interface and web development kit for functional genomics databases.
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  - journals/biodb/CuttsGLC11
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Rosalind J. Cutts, Emanuela Gadaleta, Nicholas R. Lemoine, Claude Chelala:
Using BioMart as a framework to manage and query pancreatic cancer data.
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  - journals/biodb/SchaefferHGACCSL11
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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:
MaizeGDB: curation and outreach go hand-in-hand.
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  - journals/biodb/MurphyPWBT11
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Caitlin Murphy, Justin Powlowski, Min Wu, Greg Butler, Adrian Tsang:
Curation of characterized glycoside hydrolases of Fungal origin.
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  - journals/biodb/ShepherdFBBCWBGJKLMBTCSF11
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Rebecca Shepherd, Simon A. Forbes, David Beare, Sally Bamford, Charlotte 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:
Data mining using the Catalogue of Somatic Mutations in Cancer BioMart.
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  - journals/biodb/HishigakiK11
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Haretsugu Hishigaki, Satoru Kuhara:
hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds.
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  - journals/biodb/GreenHSLS11
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Jason M. Green, Jaturon Harnsomburana, Mary L. Schaeffer, Carolyn J. Lawrence, Chi-Ren Shyu:
Multi-source and ontology-based retrieval engine for maize mutant phenotypes.
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  - journals/biodb/HarperSTGACCBBLS11
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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:
The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.
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  - journals/biodb/VisendiNBBOV11
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Paul Visendi, Wanjiku Ng'ang'a, Wallace Bulimo, Richard Bishop, James Ochanda, Etienne Pierre de Villiers:
TparvaDB: a database to support Theileria parva vaccine development.
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  - journals/biodb/WilliamsDRBOS11
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Gary Williams, Paul Davis, Anthony Rogers, Tamberlyn Bieri, Philip Ozersky, John Spieth:
Methods and strategies for gene structure curation in WormBase.
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  - journals/biodb/BlankenbergCKTN11
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Daniel J. Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko:
Integrating diverse databases into an unified analysis framework: a Galaxy approach.
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  - journals/biodb/YamamotoYBT11
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Yasunori Yamamoto, Atsuko Yamaguchi, Hidemasa Bono, Toshihisa Takagi:
Allie: a database and a search service of abbreviations and long forms.
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  - journals/biodb/Sirim0WSP11
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Demet Sirim, Florian Wagner, Lei Wang, Rolf D. Schmid, Jürgen Pleiss:
The Laccase Engineering Database: a classification and analysis system for laccases and related multicopper oxidases.
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  - journals/biodb/LiWQB11
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Xin Li, Fan Wu, Feng Qi, Daniel A. Beard:
A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway.
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  - journals/biodb/PetriSHSTPDMTJ11
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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:
The Rat Genome Database Pathway Portal.
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  - journals/biodb/VellozoVBHCFCRDGSCC11
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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:
CycADS: an annotation database system to ease the development and update of BioCyc databases.
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  - journals/biodb/Magrane11
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Michele Magrane:
UniProt Knowledgebase: a hub of integrated protein data.
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  - journals/biodb/CostanzoPBCH11
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Maria C. Costanzo, Julie Park, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong:
Using computational predictions to improve literature-based Gene Ontology annotations: a feasibility study.
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  - journals/biodb/BluhmBBDPQRSYYBB11
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Wolfgang Bluhm, Bojan Beran, Chunxiao Bi, Dimitris Dimitropoulos, Andreas Prlic, Greg B. Quinn, Peter W. Rose, Chaitali Shah, Jasmine Young, Benjamin T. Yukich, Helen M. Berman, Philip E. Bourne:
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
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  - journals/biodb/LaulederkindSHLNPSWPKLRMDTJ11
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Stanley J. F. Laulederkind, Mary Shimoyama, G. Thomas Hayman, Timothy 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:
The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data.
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  - journals/biodb/LumM11
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Gengkon Lum, Xiang Jia Min:
FunSecKB: the Fungal Secretome KnowledgeBase.
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  - journals/biodb/Milc0BP11
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Justyna Milc, Antonio Sala, Sonia Bergamaschi, Nicola Pecchioni:
A genotypic and phenotypic information source for marker-assisted selection of cereals: the CEREALAB database.
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  - journals/biodb/IsserlinBB11
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  - https://dblp.org/rec/journals/biodb/IsserlinBB11
Ruth Isserlin, Rashad Badrawi, Gary D. Bader:
The Biomolecular Interaction Network Database in PSI-MI 2.5.
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  - journals/biodb/HarbiKH11
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Djamel Harbi, Manish Kumar, Paul M. Harrison:
LPS-annotate: complete annotation of compositionally biased regions in the protein knowledgebase.

Database tool

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  dblp key:
  - journals/biodb/JungMRBFBSLLMBCCMM11
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Sook Jung, Naama Menda, Seth Redmond, Robert M. Buels, Maren Friesen, Yuri R. Bendaña, Lacey-Anne Sanderson, Hilmar Lapp, Taein Lee, Bob MacCallum, Kirstin E. Bett, Scott Cain, Dave Clements, Lukas A. Mueller, Dorrie Main:
The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.
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  - journals/biodb/SmitaLKJPB11
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Shuchi Smita, Sangram Keshari Lenka, Amit Katiyar, Pankaj Jaiswal, Justin Preece, Kailash Chander Bansal:
QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice.
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  dblp key:
  - journals/biodb/FicklinSCSLCJBM11
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Stephen P. Ficklin, Lacey-Anne Sanderson, Chun-Huai Cheng, Margaret Staton, Taein Lee, Ilhyung Cho, Sook Jung, Kirstin E. Bett, Doreen Main:
Tripal: a construction toolkit for online genome databases.
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  dblp key:
  - journals/biodb/ShameerSMKPS11
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Khader Shameer, Prashant Shingate, S. C. P. Manjunath, M. Karthika, Ganesan Pugalenthi, Ramanathan Sowdhamini:
3DSwap: curated knowledgebase of proteins involved in 3D domain swapping.
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  dblp key:
  - journals/biodb/DavisWMM11
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  - https://dblp.org/rec/journals/biodb/DavisWMM11
Allan Peter Davis, Thomas C. Wiegers, Cynthia G. Murphy, Carolyn J. Mattingly:
The curation paradigm and application tool used for manual curation of the scientific literature at the Comparative Toxicogenomics Database.
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  dblp key:
  - journals/biodb/StojmirovicY11
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Aleksandar Stojmirovic, Yi-Kuo Yu:
ppiTrim: constructing non-redundant and up-to-date interactomes.
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  - journals/biodb/HuangHVSMMABBN11
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Yu S. Huang, Matthew Horton, Bjarni J. Vilhjálmsson, Ümit Seren, Dazhe Meng, Christopher Meyer, Muhammad Ali Amer, Justin O. Borevitz, Joy Bergelson, Magnus Nordborg:
Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.
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  dblp key:
  - journals/biodb/TaccioliMTGAELGS11
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Cristian Taccioli, Vincenza Maselli, Jesper Tegnér, David Gomez-Cabrero, Gioia Altobelli, Warren Emmett, Francesco Lescai, Stefano Gustincich, Elia Stupka:
ParkDB: a Parkinson's disease gene expression database.
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  - journals/biodb/SridharaMBG11
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Viswanadham Sridhara, Aron Marchler-Bauer, Stephen H. Bryant, Lewis Y. Geer:
Automatic annotation of experimentally derived, evolutionarily conserved post-translational modifications onto multiple genomes.

Review

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  - journals/biodb/Lu11
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Zhiyong Lu:
PubMed and beyond: a survey of web tools for searching biomedical literature.

Database Updates

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  - journals/biodb/Marino-RamirezLMZMBL11
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Leonardo Mariño-Ramírez, Kevin M. Levine, Mario Morales, Suiyuan Zhang, Travis Moreland, Andreas D. Baxevanis, David Landsman:
The Histone Database: an integrated resource for histones and histone fold-containing proteins.

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