View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by George Washington University: Health Sciences Research Commons (HSRC) Himmelfarb Health Sciences Library, The George Washington University Health Sciences Research Commons Biochemistry and Molecular Medicine Faculty Biochemistry and Molecular Medicine Publications 2012 Recent advances in biocuration: Meeting report from the Fifth nI ternational Biocuration Conference Pascale Gaudet International Society of Biocuration, Geneva, Switzerland Cecilia Arighi University of Delaware Frederic Bastian University of Lausanne Alex Bateman Wellcome Trust Sanger Institute, Cambs, UK Judith A. Blake Jackson Lab, Bar Harbor, ME See next page for additional authors Follow this and additional works at: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs Part of the Biochemistry, Biophysics, and Structural Biology Commons Recommended Citation Gaudet P, Arighi C, Bastian F, Bateman A, Blake JA, Mazumder, R. et al (2012). Recent advances in biocuration: meeting report from the Fifth nI ternational Biocuration Conference. Database, bas036. This Journal Article is brought to you for free and open access by the Biochemistry and Molecular Medicine at Health Sciences Research Commons. It has been accepted for inclusion in Biochemistry and Molecular Medicine Faculty Publications by an authorized administrator of Health Sciences Research Commons. For more information, please contact [email protected]. Authors Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Raja Mazumder, and +17 additional authors This journal article is available at Health Sciences Research Commons: http://hsrc.himmelfarb.gwu.edu/smhs_biochem_facpubs/92 Database, Vol. 2012, Article ID bas036, doi:10.1093/database/bas036 ............................................................................................................................................................................................................................................................................................. Original article Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference Pascale Gaudet1,*, Cecilia Arighi2, Frederic Bastian3, Alex Bateman4, Judith A. Blake5, Michael J. Cherry6, Peter D’Eustachio7, Robert Finn8, Michelle Giglio9, Lynette Hirschman10, Renate Kania11, William Klimke12, Maria Jesus Martin13, Ilene Karsch-Mizrachi12, Monica Munoz-Torres14, Darren Natale14, Claire O’Donovan13, Francis Ouellette15, Kim D. Pruitt12, Marc Robinson-Rechavi3, Susanna-Assunta Sansone16, Paul Schofield17, Granger Sutton18, Kimberly Van Auken19, Sona Vasudevan14, Cathy Wu2, Jasmine Young20 and Raja Mazumder21,* 1Chair, International Society for Biocuration and CALIPHO Group, Swiss Institute of Bioinformatics, 1 Rue Michel Servet, Geneva, Switzerland, 2University of Delaware, Newark, DE, USA, 3Swiss Institute of Bioinformatics and Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland, 4Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, UK, 5The Jackson Laboratory, Bar Harbor, ME, 6Department of Genetics, Stanford University, Stanford, CA, 7NYU School of Medicine, New York, NY, 8HHMI - Janelia Farm Research Campus, VA, 9Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 10The MITRE Corporation, Bedford, MA, USA, 11Heidelberg Institute for Theoretical Studies, Heidelberg, Germany, 12NCBI/NLM/NIH/DHHS, Bethesda, MD, USA, 13European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK, 14Georgetown University, Washington, DC, USA, 15Ontario Institute for Cancer Research and Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada, 16University of Oxford, Oxford, UK, 17Cambridge University, Cambridge, UK, 18J. Craig Venter Institute, Rockville, MD,19California Institute of Technology, Pasadena, CA, 20RCSB Protein Data Bank, Rutgers University, NJ, and 21Chair, Fifth International Biocuration conference organizing committee; Department of Biochemistry and Molecular Biology, The George Washington University, Washington, DC 20037, USA *Corresponding author: Tel: +41 22 379 49 17; Fax: +41 22 379 58 58; Email: [email protected] Correspondence may also be addressed to Raja Mazumder. Tel: +1 202 994 5951; Fax: +1 202 994 9994; Email: [email protected] Submitted 4 July 2012; Revised 13 September 2012; Accepted 19 September 2012 ............................................................................................................................................................................................................................................................................................. The 5th International Biocuration Conference brought together over 300 scientists to exchange on their work, as well as discuss issues relevant to the International Society for Biocuration’s (ISB) mission. Recurring themes this year included the creation and promotion of gold standards, the need for more ontologies, and more formal interactions with journals. The conference is an essential part of the ISB’s goal to support exchanges among members of the biocuration community. Next year’s conference will be held in Cambridge, UK, from 7 to 10 April 2013. In the meanwhile, the ISB website provides information about the society’s activities (http://biocurator.org), as well as related events of interest. ............................................................................................................................................................................................................................................................................................. scientists who have the specific expertise of creating tools Introduction and platforms for indexing, integrating, displaying and Biological databases have been a key item in the toolbox of ultimately helping understand complex biological data. life scientists for 30 years. Initially mostly focused on anno- There are a large number of biological databases, as indi- tation of sequences, a wealth of highly varied resources cated by the 2012 Nucleic Acids Research (NAR) online data- have burgeoned in the past 10 years, propelled in part by base collection that catalogued 1380 published biological the development of high-throughput techniques and the databases (1). In this context, professional biocuration is resulting acceleration in data generation. Those databases now becoming well established. The International Society are developed and maintained by biologists and computer for Biocuration (ISB, http://www.biocurator.org) is a ............................................................................................................................................................................................................................................................................................. ß The Author(s) 2012. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Page 1 of 8 (page number not for citation purposes) Original article Database, Vol. 2012, Article ID bas036, doi:10.1093/database/bas036 ............................................................................................................................................................................................................................................................................................. non-for-profit organization founded in 2009 to promote capturing biological annotations unified by the common the interests of biocurators. The ISB now counts over 300 goal of trying to engage scientists to help curate data. members from nearly 150 databases and institutions in 26 This is a topic of great interest to most databases, as well different countries. This corresponds to only a fraction of as their users, as a possible means to help increase effi- the biocuration community, as several groups such as bio- ciency of data capture. curators from commercial databases, as well as researchers, One popular way of capturing annotations from the students and post-docs who perform biocuration work as community is through the use of wikis. This approach was part of a research project are under-represented in the ISB. presented by Nicholas Stover, for the Tetrahymena genome Since 2005, the biocuration community has been holding database, as well as other ciliate genomes, namely conferences with the goals of presenting and promoting Ichthyophthirius multifiliis and Oxytricha trifallax (1). the various projects, exchanging ideas, and fostering colla- Andrew Su presented the GeneWiki project, a Wikipedia- borations among the biocuration community. Those con- based annotation tool for human genes (2). One of the key ferences have been extremely successful, and their points of using Wikipedia is the sheer number of editors popularity continues to increase. The 5th International who have produced, detailed and information-rich articles. Biocuration Conference was held in Georgetown, Furthermore, Su described how the processing of the Washington, DC, USA, from 2 to 4 April 2012. Hosted by GeneWiki annotations suggests novel Gene Ontology The Protein Information