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Biocuration Virtual Issue

DATABASE is pleased to have published the following articles originating from International Biocuration conferences. The articles were subject to the journal’s normal peer review process, and are collected together here as a ‘virtual issue’.

The goal of the Biocurator Conferences is ‘to create a forum for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research’. Visit http://www.biocurator.org/conferences.shtml for more information.

Biocuration 2014, the Seventh International Biocuration Conference, University of Toronto in Toronto, Canada, April 6-9, 2014 (papers submitted to and selected by DATABASE)

Small molecule annotation for the Protein Data Bank
Sanchayita Sen, Jasmine Young, John M. Berrisford, Minyu Chen, Matthew J. Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P. Hudson, Reiko Igarashi, Yumiko Kengaku, Yuhe Liang, Ezra Peisach, Irina Persikova, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Gaurav Sahni, Junko Sato, Monica Sekharan, Chenghua Shao, Lihua Tan, and Marina A. Zhuravleva
Database Vol. 2014, bau116 doi: 10.1093/database/bau116
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The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, and Pål Sætrom
Database Vol. 2014, bau02;7 doi: 10.1093/database/bau027
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Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data
Sylvain Poux, Michele Magrane, Cecilia N. Arighi, Alan Bridge, Claire O’Donovan, Kati Laiho, and The UniProt Consortium
Database 2014: bau016 doi:10.1093/database/bau016
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Linking tissues to phenotypes using gene expression profiles
Anika Oellrich, Sanger Mouse Genetics Project, and Damian Smedley
http://database.oxfordjournals.org/content/2014/bau016.full
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A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, and Raja Mazumder
Database 2014: bau022 doi:10.1093/database/bau022
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GigaDB: promoting data dissemination and reproducibility
Tam P. Sneddon, Xiao Si Zhe, Scott C. Edmunds, Peter Li, Laurie Goodman, and Christopher I. Hunter
Database 2014: bau018 doi:10.1093/database/bau018
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Biocuration 2013, the Sixth International Biocuration Conference, Churchill College, Cambridge, UK, April 7–10, 2013 (papers submitted to and selected by DATABASE)

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, and Mary Shimoyama
Database Vol. 2013, bat015; doi:10.1093/database/bat015
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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, and Doron Lancet
Database Vol. 2013, bat018; doi:10.1093/database/bat018
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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, and Martin Eisenacher
Database Vol. 2013, bat009; doi:10.1093/database/bat009
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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, and John-Paul Plazzer
Database Vol. 2013, bat019; doi:10.1093/database/bat019
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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, and Andrew R. Jones
Database Vol. 2013, bat021; doi:10.1093/database/bat021
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Identification and prioritization of novel uncharacterized peptidases for biochemical characterization
Neil D. Rawlings
Database Vol. 2013, bat022; doi:10.1093/database/bat022
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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, and Iddo Friedberg
Database Vol. 2013, bat016; doi:10.1093/database/bat016
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Uncovering hidden duplicated content in public transcriptomics data
Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, and Frederic B. Bastian
Database Vol. 2013, bat010; doi:10.1093/database/bat010
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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, and Christoph Steinbeck
Database Vol. 2013, bat029; doi:10.1093/database/bat029
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Towards the Collaborative Curation of the Registry underlying identifiers.org
Nick Juty, Nicolas Le Novère, Henning Hermjakob, and Camille Laibe
Database Vol. 2013, bat017; doi:10.1093/database/bat017
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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, and Christopher Mungall
Database Vol. 2013, bat025; doi:10.1093/database/bat025
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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, and Marco Punta
Database Vol. 2013, bat023; doi:10.1093/database/bat023
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PCorral—interactive mining of protein interactions from MEDLINE
Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, and Dietrich Rebholz-Schuhmann
Database Vol. 2013, bat030; doi:10.1093/database/bat030
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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, and J. Michael Cherry
Database Vol. 2013, bat004; doi:10.1093/database/bat004
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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 and J. Michael Cherry
Database Vol. 2013, bat012; doi:10.1093/database/bat012
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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, and Torsten Schwede
Database Vol. 2013, bat031; doi:10.1093/database/bat031
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Biocuration 2012, the Fifth International Biocuration Conference, Washington, DC, April 2–4, 2012 (papers submitted to and selected by DATABASE)

Editorial: Biocuration Virtual Issue 2012
Pascale Gaudet and Raja Mazumder
Database Vol. 2012, bas011; doi:10.1093/database/bas011
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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, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul Schofield, Granger Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy Wu, Jasmine Young, and Raja Mazumder
Database Vol. 2012, bas036; doi:10.1093/database/bas036
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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 and the North East Bioinformatics Collaborative Curation Team
Database Vol. 2012, bar064; doi: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 and Aron Marchler-Bauer
Database Vol. 2012, bar058; doi: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. Mu¨ ller, P. W. Sternberg, P. Ciccarese, T. Clark, L. Marenco, R. Wang, V. Astakhov, J. S. Grethe and M. E. Martone
Database Vol. 2012, bas005; doi: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 and Henning Hermjakob
Database Vol. 2012, bas004; doi: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 and J. Michael Cherry
Database Vol. 2012, bar062; doi:10.1093/database/bar062
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Argo: an integrative, interactive, text mining-based workbench supporting curation
Rafal Rak, Andrew Rowley, William Black and Sophia Ananiadou
Database Vol. 2012, bas010; doi: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 and Theodore G. Clark
Database Vol. 2012, bas007; doi: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 and Eurie L. Hong
Database Vol. 2012, bas001; doi:10.1093/database/bas001
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Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio and Andrew I. Su
Database Vol. 2012, bar060; doi: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 and Janan T. Eppig
Database Vol. 2012, bar063; doi:10.1093/database/bar063
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Community gene annotation in practice
Jane E. Loveland, James G.R. Gilbert, Ed Griffiths and Jennifer L. Harrow
Database Vol. 2012, bas009; doi: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 and Kim D. Pruitt
Database Vol. 2012, bas008; doi: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 and Michel Dumontier
Database Vol. 2012, bas006; doi:10.1093/database/bas006
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The mouse–human anatomy ontology mapping project
Terry F. Hayamizu, Sherri de Coronado, Gilberto Fragoso, Nicholas Sioutos, James A. Kadin and Martin Ringwald
Database Vol. 2012, bar066; doi: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 and Carolyn J. Mattingly
Database Vol. 2012, bar065; doi: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 and J. Michael Cherry
Database Vol. 2012, bar057; doi: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 and Alex Bateman
Database Vol. 2012, bas003; doi: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 and Melissa Haendel
Database Vol. 2012, bar067; doi: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, Ioannis Xenarios and Pascale Gaudet
Database Vol. 2012, bar059; doi:10.1093/database/bar059
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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 and Howard J. Jacob
Database Vol. 2012, bas016; doi:10.1093/database/bas016
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The importance of identifying alternative splicing in vertebrate genome annotation
Adam Frankish, Jonathan M. Mudge, Mark Thomas and Jennifer Harrow
Database Vol. 2012, bas014; doi:10.1093/database/bas014
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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, and Andrew Chatr-aryamontri
Database Vol. 2012, bas017; doi:10.1093/database/bas017
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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, and Andrew G. Winter
Database Vol. 2012, bas020; doi:10.1093/database/bas020
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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, and Russ B. Altman
Database Vol. 2012, bas021; doi:10.1093/database/bas021
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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, and David L. Robertson
Database Vol. 2012, bas023; doi:10.1093/database/bas023
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Third International Biocurator Conference, Berlin, Germany, April 16–19, 2009 (papers submitted to and selected by DATABASE)

Meeting report: a workshop on Best Practices in Genome Annotation
Ramana Madupu, Lauren M. Brinkac, Jennifer Harrow, Laurens G. Wilming, Ulrike Böhme, Philippe Lamesch, and Linda I. Hannick
Database Vol. 2010, baq001; doi:10.1093/database/baq001
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MicroScope: a platform for microbial genome annotation and comparative genomics.
D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, and C. Médigue
Database Vol. 2009, bap021; doi:10.1093/database/bap021
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Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase
P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C. de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau, U. Hinz, C. Hulo, J. James, S. Jimenez, F. Jungo, G. Keller, P. Lemercier, D. Lieberherr, M. Moinat, A. Nikolskaya, I. Pedruzzi, C. Rivoire, B. Roechert, M. Schneider, E. Stanley, M. Tognolli, K. Sjölander, L. Bougueleret, R.L. Chisholm, and A. Bairoch
Database Vol. 2009, bap016; doi:10.1093/database/bap016
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Integrating text mining into the MGI biocuration workflow
K.G. Dowell, M.S. McAndrews-Hill, D.P. Hill, H.J. Drabkin, and J.A. Blake
Database Vol. 2009, bap019; doi:10.1093/database/bap019
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QuickGO: A user tutorial for the web-based Gene Ontology browser
Rachael P. Huntley, David Binns, Emily Dimmer, Daniel Barrell, Claire O’Donovan, and Rolf Apweiler
Database Vol. 2009, bap010; doi:10.1093/database/bap010
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A large and accurate collection of peptidase cleavages in the MEROPS database
Neil D. Rawlings
Database Vol. 2009, bap015; doi:10.1093/database/bap015
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PDBWiki: added value through community annotation of the Protein Data Bank
Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, and Dan M. Bolser
Database Vol. 2010, baq009; doi:10.1093/database/baq009
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