Kimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Muller, Rex Chisholm, Eva Huala, Paul W. Sternberg

Database, Volume 2012, 2012, bas040, https://doi.org/10.1093/database/bas040

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Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts

Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu

Database, Volume 2012, 2012, bas041, https://doi.org/10.1093/database/bas041

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Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information

Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur

Database, Volume 2012, 2012, bas042, https://doi.org/10.1093/database/bas042

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Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II

Zhiyong Lu, Lynette Hirschman

Database, Volume 2012, 2012, bas043, https://doi.org/10.1093/database/bas043

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Strategies for annotation and curation of translational databases: the eTUMOUR project

Margarida Julià-Sapé, Miguel Lurgi, Mariola Mier, Francesc Estanyol, Xavier Rafael, Ana Paula Candiota, Anna Barceló, Alina García, M. Carmen Martínez-Bisbal, Rubén Ferrer-Luna, Àngel Moreno-Torres, Bernardo Celda, Carles Arús

Database, Volume 2012, 2012, bas035, https://doi.org/10.1093/database/bas035

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference

Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Michael J. Cherry, Peter D’Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O’Donovan, Francis Ouellette, Kim D. Pruitt … Raja Mazumder

Database, Volume 2012, 2012, bas036, https://doi.org/10.1093/database/bas036

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DFVF: database of fungal virulence factors

Tao Lu, Bo Yao, Chi Zhang

Database, Volume 2012, 2012, bas032, https://doi.org/10.1093/database/bas032

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The Units Ontology: a tool for integrating units of measurement in science

Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf

Database, Volume 2012, 2012, bas033, https://doi.org/10.1093/database/bas033

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Assessment of community-submitted ontology annotations from a novel database-journal partnership

Tanya Z. Berardini, Donghui Li, Robert Muller, Raymond Chetty, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala

Database, Volume 2012, 2012, bas030, https://doi.org/10.1093/database/bas030

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CreZOO—the European virtual repository of Cre and other targeted conditional driver strains

Christina Chandras, Michael Zouberakis, Ekaterina Salimova, Damian Smedley, Nadia Rosenthal, Vassilis Aidinis

Database, Volume 2012, 2012, bas029, https://doi.org/10.1093/database/bas029

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MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes

Andreas Braun, Bettina Halwachs, Martina Geier, Katrin Weinhandl, Michael Guggemos, Jan Marienhagen, Anna J. Ruff, Ulrich Schwaneberg, Vincent Rabin, Daniel E. Torres Pazmiño, Gerhard G. Thallinger, Anton Glieder

Database, Volume 2012, 2012, bas028, https://doi.org/10.1093/database/bas028

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Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE

Aurélie Névéol, W. John Wilbur, Zhiyong Lu

Database, Volume 2012, 2012, bas026, https://doi.org/10.1093/database/bas026

Directly e-mailing authors of newly published papers encourages community curation

Stephanie M. Bunt, Gary B. Grumbling, Helen I. Field, Steven J. Marygold, Nicholas H. Brown, Gillian H. Millburn, the FlyBase Consortium

Database, Volume 2012, 2012, bas024, https://doi.org/10.1093/database/bas024

Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database

Daniel G. Jamieson, Martin Gerner, Farzaneh Sarafraz, Goran Nenadic, David L. Robertson

Database, Volume 2012, 2012, bas023, https://doi.org/10.1093/database/bas023

Using ODIN for a PharmGKB revalidation experiment

Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman

Database, Volume 2012, 2012, bas021, https://doi.org/10.1093/database/bas021

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Text mining for the biocuration workflow

Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, Andrew G. Winter

Database, Volume 2012, 2012, bas020, https://doi.org/10.1093/database/bas020

The PRINTS database: a fine-grained protein sequence annotation and analysis resource—its status in 2012

Teresa K. Attwood, Alain Coletta, Gareth Muirhead, Athanasia Pavlopoulou, Peter B. Philippou, Ivan Popov, Carlos Romá-Mateo, Athina Theodosiou, Alex L. Mitchell

Database, Volume 2012, 2012, bas019, https://doi.org/10.1093/database/bas019

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Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa

Ambarish Nag, Tatiana V. Karpinets, Christopher H. Chang, Maor Bar-Peled

Database, Volume 2012, 2012, bas013, https://doi.org/10.1093/database/bas013

How to link ontologies and protein–protein interactions to literature: text-mining approaches and the BioCreative experience

Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri

Database, Volume 2012, 2012, bas017, https://doi.org/10.1093/database/bas017

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GrameneMart: the BioMart data portal for the Gramene project

William Spooner, Ken Youens-Clark, Daniel Staines, Doreen Ware

Database, Volume 2012, 2012, bar056, https://doi.org/10.1093/database/bar056

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The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes

Sudheer Tumu, Ashish Patil, William Towns, Madhu Dyavaiah, Thomas J. Begley

Database, Volume 2012, 2012, bas002, https://doi.org/10.1093/database/bas002

dbPTB: a database for preterm birth

Alper Uzun, Alyse Laliberte, Jeremy Parker, Caroline Andrew, Emily Winterrowd, Surendra Sharma, Sorin Istrail, James F. Padbury

Database, Volume 2012, 2012, bar069, https://doi.org/10.1093/database/bar069

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

Sarah Burge, Elizabeth Kelly, David Lonsdale, Prudence Mutowo-Muellenet, Craig McAnulla, Alex Mitchell, Amaia Sangrador-Vegas, Siew-Yit Yong, Nicola Mulder, Sarah Hunter

Database, Volume 2012, 2012, bar068, https://doi.org/10.1093/database/bar068

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The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species

Kevin L. Childs, Kranti Konganti, C. Robin Buell

Database, Volume 2012, 2012, bar061, https://doi.org/10.1093/database/bar061

The importance of identifying alternative splicing in vertebrate genome annotation

Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer Harrow

Database, Volume 2012, 2012, bas014, https://doi.org/10.1093/database/bas014

Ontology searching and browsing at the Rat Genome Database

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

Database, Volume 2012, 2012, bas016, https://doi.org/10.1093/database/bas016

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Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees

Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnum Rendino, William Kelley Thomas, Daniel W. Udwary, Cathy H. Wu, the North East Bioinformatics Collaborative Curation Team

Database, Volume 2012, 2012, bar064, https://doi.org/10.1093/database/bar064

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Annotation of functional sites with the Conserved Domain Database

Myra K. Derbyshire, Christopher J. Lanczycki, Stephen H. Bryant, Aron Marchler-Bauer

Database, Volume 2012, 2012, bar058, https://doi.org/10.1093/database/bar058

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A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework

A. E. Bandrowski, J. Cachat, Y. Li, H. M. Müller, P. W. Sternberg, P. Ciccarese, T. Clark, L. Marenco, R. Wang, V. Astakhov, J. S. Grethe, M. E. Martone

Database, Volume 2012, 2012, bas005, https://doi.org/10.1093/database/bas005

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PRIDE: Quality control in a proteomics data repository

Attila Csordas, David Ovelleiro, Rui Wang, Joseph M. Foster, Daniel Ríos, Juan Antonio Vizcaíno, Henning Hermjakob

Database, Volume 2012, 2012, bas004, https://doi.org/10.1093/database/bas004

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YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie Sullivan, Gos Micklem, J. Michael Cherry

Database, Volume 2012, 2012, bar062, https://doi.org/10.1093/database/bar062

Argo: an integrative, interactive, text mining-based workbench supporting curation

Rafal Rak, Andrew Rowley, William Black, Sophia Ananiadou

Database, Volume 2012, 2012, bas010, https://doi.org/10.1093/database/bas010

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Tetrahymena genome database Wiki: a community-maintained model organism database

Nicholas A. Stover, Ravinder S. Punia, Michael S. Bowen, Steven B. Dolins, Theodore G. Clark

Database, Volume 2012, 2012, bas007, https://doi.org/10.1093/database/bas007

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CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations

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

Database, Volume 2012, 2012, bas001, https://doi.org/10.1093/database/bas001

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su

Database, Volume 2012, 2012, bar060, https://doi.org/10.1093/database/bar060

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Disease model curation improvements at Mouse Genome Informatics

Susan M. Bello, Joel E. Richardson, Allan P. Davis, Thomas C. Wiegers, Carolyn J. Mattingly, Mary E. Dolan, Cynthia L. Smith, Judith A. Blake, Janan T. Eppig

Database, Volume 2012, 2012, bar063, https://doi.org/10.1093/database/bar063

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Community gene annotation in practice

Jane E. Loveland, James G.R. Gilbert, Ed Griffiths, Jennifer L. Harrow

Database, Volume 2012, 2012, bas009, https://doi.org/10.1093/database/bas009

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Tracking and coordinating an international curation effort for the CCDS Project

Rachel A. Harte, Catherine M. Farrell, Jane E. Loveland, Marie-Marthe Suner, Laurens Wilming, Bronwen Aken, Daniel Barrell, Adam Frankish, Craig Wallin, Steve Searle, Mark Diekhans, Jennifer Harrow, Kim D. Pruitt

Database, Volume 2012, 2012, bas008, https://doi.org/10.1093/database/bas008

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Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

Jose Cruz-Toledo, Maureen McKeague, Xueru Zhang, Amanda Giamberardino, Erin McConnell, Tariq Francis, Maria C. DeRosa, Michel Dumontier

Database, Volume 2012, 2012, bas006, https://doi.org/10.1093/database/bas006

The mouse–human anatomy ontology mapping project

Terry F. Hayamizu, Sherri de Coronado, Gilberto Fragoso, Nicholas Sioutos, James A. Kadin, Martin Ringwald

Database, Volume 2012, 2012, bar066, https://doi.org/10.1093/database/bar066

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MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database

Allan Peter Davis, Thomas C. Wiegers, Michael C. Rosenstein, Carolyn J. Mattingly

Database, Volume 2012, 2012, bar065, https://doi.org/10.1093/database/bar065

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Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report

Esther T. Chan, J. Michael Cherry

Database, Volume 2012, 2012, bar057, https://doi.org/10.1093/database/bar057

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AntiFam: a tool to help identify spurious ORFs in protein annotation

Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Martin, Claire O'Donovan, Alex Bateman

Database, Volume 2012, 2012, bas003, https://doi.org/10.1093/database/bas003

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Research resources: curating the new eagle-i discovery system

Nicole Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson, Melissa Haendel

Database, Volume 2012, 2012, bar067, https://doi.org/10.1093/database/bar067

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Biocurators and Biocuration: surveying the 21st century challenges

Sarah Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, Michael Cherry, Claire O'Donovan, loannis Xenarios, Pascale Gaudet

Database, Volume 2012, 2012, bar059, https://doi.org/10.1093/database/bar059

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Database Update

Dr. PIAS 2.0: an update of a database of predicted druggable protein–protein interactions

Nobuyoshi Sugaya, Satoru Kanai, Toshio Furuya

Database, Volume 2012, 2012, bas034, https://doi.org/10.1093/database/bas034

Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals

Joseph A. Rothwell, Mireia Urpi-Sarda, Maria Boto-Ordoñez, Craig Knox, Rafael Llorach, Roman Eisner, Joseph Cruz, Vanessa Neveu, David Wishart, Claudine Manach, Cristina Andres-Lacueva, Augustin Scalbert

Database, Volume 2012, 2012, bas031, https://doi.org/10.1093/database/bas031

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Database Tool

CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data

Julia Feichtinger, Ramsay J. McFarlane, Lee D. Larcombe

Database, Volume 2012, 2012, bas055, https://doi.org/10.1093/database/bas055

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species

Victor Zeng, Cassandra G. Extavour

Database, Volume 2012, 2012, bas048, https://doi.org/10.1093/database/bas048

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RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity

Sławek Mazur, Gabor Csucs, Karol Kozak

Database, Volume 2012, 2012, bas027, https://doi.org/10.1093/database/bas027

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HAltORF: a database of predicted out-of-frame alternative open reading frames in human

Benoît Vanderperre, Jean-François Lucier, Xavier Roucou

Database, Volume 2012, 2012, bas025, https://doi.org/10.1093/database/bas025

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ScreenTroll: a searchable database to compare genome-wide yeast screens

Peter H. Thorpe, John C. Dittmar, Rodney Rothstein

Database, Volume 2012, 2012, bas022, https://doi.org/10.1093/database/bas022

MSV3d: database of human MisSense variants mapped to 3D protein structure

Tien-Dao Luu, Alin-Mihai Rusu, Vincent Walter, Raymond Ripp, Luc Moulinier, Jean Muller, Thierry Toursel, Julie D. Thompson, Olivier Poch, Hoan Nguyen

Database, Volume 2012, 2012, bas018, https://doi.org/10.1093/database/bas018

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CPPsite: a curated database of cell penetrating peptides

Ankur Gautam, Harinder Singh, Atul Tyagi, Kumardeep Chaudhary, Rahul Kumar, Pallavi Kapoor, G. P. S. Raghava

Database, Volume 2012, 2012, bas015, https://doi.org/10.1093/database/bas015

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Corrigendum

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

Database, Volume 2012, 2012, bas012, https://doi.org/10.1093/database/bas012

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Editorial

BioCreative-2012 Virtual Issue

Cathy H. Wu, Cecilia N. Arighi, Kevin B. Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur

Database, Volume 2012, 2012, bas049, https://doi.org/10.1093/database/bas049