DOI: 10.3724/SP.J.1003.2014.14012

Biodiversity Science (生物多样性) 2014/22:3 PP.264-276

Scratchpads 2.0:a virtual research environment for biodiversity sciences in the Internet era

We describe key features of the Scratchpads 2.0 Virtual Research Environment (VRE),which supports the creation,management and reuse of biodiversity data.This paper provides an introduction to recent developments and status of the Scratchpads 2.0 system,including its technical architecture.Key features include mechanisms to integrate individual research data and online resources,creation and management of multilingual content,license and authorization of system and data content,dynamic tracing of data editing history,research team cooperation,and methods of data paper publication.Important technical features include effective maintenance and installation of the system,ability to build distributed architecture,modularized function and development,and implementation of related information standards.These are put into a context with related biodiversity informatics tools.Scratchpads was designed with accurate role orientation,a deep understanding of taxonomic research requirements,and excellent technical solutions.All of these attributes contribute to Scratchpads’ importance to e-infrastrature in the Internet era for taxonomy,thereby providing us with a promising tool to complete ambitious projects like World Online Flora.

Key words:biodiversity informatics,data-publishing,online flora,virtual research environment

ReleaseDate:2015-03-10 13:13:17

Agosti D (2003) Encyclopedia of life: Should species description equal gene sequence? Trends in Ecology and Evolution, 18, 273.

Baker E, Rycroft S, Smith VS (2014) Linking multiple biodiversity informatics platforms with Darwin Core Archives. Biodiversity Data Journal, 2, e1039. doi: 10.3897/BDJ.2. e1039. .

Bebber DP, Carine MA, Wood JRI, Wortley AH, Harris DJ, Prance GT, Davidse G, Paige J, Pennington TD, Robson NKB, Scotland RW (2010) Herbaria are a major frontier for species discovery. Proceedings of the National Academy of Sciences, USA, 107, 22169-22171.

Benson DA, Karsch-Mizra CI, Lipman DJ, Ostell J, Sayers EW (2011) GenBank. Nucleic Acids Research, January; 39 (Database issue): D32-D37. Published online 2010 November 10. doi: 10.1093/nar/gkq1079.

Blagoderov V, Brake I, Georgiev T, Penev L, Roberts D, Rycroft S, Scott B, Agosti D, Catapano T, Smith VS (2010) Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys. ZooKeys, 50, 17-28.

Bowker GC (2000) Biodiversity datadiversity. Social Studies of Science, 30, 643-683.

Brach AR, Boufford DE (2011) Why are we still producing paper floras? Annals of the Missouri Botanical Garden, 98, 297-300.

Brake I, Duin D, Van de Velde I, Smith V, Rycroft S (2011) Who learns from whom? Supporting users and developers of a major biodiversity e-infrastructure. ZooKeys, 150, 177-192.

Chavan V, Ingwersen P (2009) Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community. BMC Bioinformatics, 10, S2.

Chavan V, Penev L (2011) The data paper: a mechanism to incentivize data publishing in biodiversity science. BMC Bioinformatics, 12, S2.

Clark BR, Godfray HCJ, Kitching IJ, Mayo SJ, Scoble MJ (2009) Taxonomy as an e-Science. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367, 953-966.

Costello MJ (2009) Motivating online publication of data. BioScience, 59, 418-427.

Costello MJ, May RM, Stork NE (2013a) Can we name Earth's species before they go extinct? Science, 339, 413-416.

Costello MJ, Michener WK, Gahegan M, Zhang Z-Q, Bourne PE (2013b) Biodiversity data should be published, cited, and peer reviewed. Trends in Ecology and Evolution, 28, 454-461.

Deans AR, Yoder MJ, Balhoff JP (2012) Time to change how we describe biodiversity. Trends in Ecology and Evolution, 27, 78-84.

Duin D, van den Besselaar P (2011) Studying the effects of virtual biodiversity research infrastructures. ZooKeys, 150, 193-210.

Erwin T, Stoev P, Georgiev T, Penev L (2011) ZooKeys 150: Three and a half years of innovative publishing and growth. ZooKeys, 150, 5-14.

Fontaine B, van Achterberg K, Alonso-Zarazaga MA, Araujo R, Asche M, Asp?ck H, Asp?ck U, Audisio P, Aukema B, Bailly N, Balsamo M, Bank RA, Belfiore C, Bogdanowicz W, Boxshall G, Burckhardt D, Chylarecki P, Deharveng L, Dubois A, Enghoff H, Fochetti R, Fontaine C, Gargominy O, Lopez MSG, Goujet D, Harvey MS, Heller K-G, van Helsdingen P, Hoch H, De Jong Y, Karsholt O, Los W, Magowski W, Massard JA, McInnes SJ, Mendes LF, Mey E, Michelsen V, Minelli A, Nafria JMN, van Nieukerken EJ, Pape T, De Prins W, Ramos M, Ricci C, Roselaar C, Rota E, Segers H, Timm T, van Tol J, Bouchet P (2012) New species in the Old World: Europe as a frontier in diodiversity exploration, a test bed for 21st century taxonomy. PLoS ONE, 7, e36881.

Frodin DG (2001) Guide to Standard Floras of the World. Cambridge University Press, Cambridge.

Godfray HCJ (2002) Challenges for taxonomy: the discipline will have to reinvent itself if it is to survive and flourish. Nature, 417, 17-19.

Godfray HCJ, Clark BR, Kitching IJ, Mayo SJ, Scoble MJ (2007) The web and the structure of taxonomy. Systematic Biology, 56, 943-955.

Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B: Biological Sciences, 270, 313-321.

Johnson NF (2012) A collaborative, integrated and electronic future for taxonomy. Invertebrate Systematics, 25, 471-475.

Knapp S (2008) Taxonomy as a team sport. In: The New Taxonomy (ed. Wheeler Q), pp. 33-53. CRC Press Taylor & Francis Group, Boca Raton, London, New York.

Kress WJ (2004) Paper floras: how long will they last? a review of flowering plants of the Neotropics. American Journal of Botany, 91, 2124-2127.

Leptin M (2012) Open access—pass the buck. Science, 335, 1279.

Li GJ (李国杰), Chen XQ (程学旗) (2012) Big Data: a significant strategic area in future science, technology, and economy development—research status and thinking of Big Data. Bulletin of the Chinese Academy of Sciences (中国科学院院刊), 27, 11.

Lynch C (2008) Big data: How do your data grow? Nature, 455, 28-29.

Maddison DR, Guralnick R, Hill A, Reysenbach A-L, McDade LA (2012) Ramping up biodiversity discovery via online quantum contributions. Trends in Ecology and Evolution, 27, 72-77.

Marhold K, Stuessy T, Agababian M, Agosti D, Alford MH, Crespo A, Crisci JV, Dorr LJ, Ferencová Z, Frodin D, Geltman DV, Kilian N, Linder HP, Lohmann LG, Oberprieler C, Penev L, Smith GF, Thomas W, Tulig M, Turland N, Zhang XC (2013) The future of botanical monography: Report from an international workshop, 12-16 March 2012, Smolenice, Slovak Republic. Taxon, 62, 4-20.

Mayo SJ (2008) Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis. Kew Bulletin, 63, 1-16.

Mitch W (2008) Big data: Wikiomics. Nature, 455, 22-25.

Moore W (2011) Biology needs cyberinfrastructure to facilitate specimen-level data acquisition for insects and other hyperdiverse groups. ZooKeys, 147, 479-486.

Parr CS, Guralnick R, Cellinese N, Page RDM (2012) Evolutionary informatics: unifying knowledge about the diversity of life. Trends in Ecology and Evolution, 27, 94-103.

Patterson DJ, Cooper J, Kirk PM, Pyle RL, Remsen DP (2010) Names are key to the big new biology. Trends in Ecology and Evolution, 25, 686-691.

Penev L, Kress WJ, Knapp S, Li DZ, Renner S (2010a) Fast, linked, and open―the future of taxonomic publishing for plants: launching the journal PhytoKeys. PhytoKeys, 1, 1-14.

Penev L, Roberts D, Smith VS, Agosti D, Erwin T (2010b) Taxonomy shifts up a gear: new publishing tools to accelerate biodiversity research. ZooKeys, 50, i-iv.

Penev L, Sharkey M, Erwin T, van Noort S, Buffington M, Seltmann K, Johnson N, Taylor M, Thompson F, Dallwitz M (2009) Data publication and dissemination of interactive keys under the open access model. ZooKeys, 21, 1-17.

Platnick NI (2013) The information content of taxon names: a reply to de Queiroz and Donoghue. Systematic Biology, 62, 175-176.

Scotland RW, Wood JRI (2012) Accelerating the pace of taxonomy. Trends in Ecology and Evolution, 27, 415-416.

Sheng YY (盛杨燕), Zhou T (周涛) (2013) Big?Data Time: A Revolution that Will Transform How We Live,?Work, and Think (大数据时代: 生活、工作与思维的大变革). Zhejiang People's Publishing House. (in Chinese).

Smith V (2009) Data publication: towards a database of everything. BMC Research Notes, 2, 113.

Smith V, Penev L (2011) Collaborative electronic infrastructures to accelerate taxonomic research. ZooKeys, 150, 1-3.

Smith V, Rycroft S, Brake I, Scott B, Baker E, Livermore L, Blagoderov V, Roberts D (2011) Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science. ZooKeys, 150, 53-70.

Smith V, Rycroft S, Harman K, Scott B, Roberts D (2009) Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life. BMC Bioinformatics, 10, S6.

Stoltzfus A, O’Meara B, Whitacre J, Mounce R, Gillespie E, Kumar S, Rosauer D, Vos R (2012) Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. BMC Research Notes, 5, 1-15.

Stuessy TF (2009) Paradigms in biological classification (1707-2007): Has anything really changed? Taxon, 58, 68-76.

Thessen A, Patterson D (2011) Data issues in the life sciences. ZooKeys, 150, 15-51.

Thomas C (2009) Biodiversity databases spread, prompting unification call. Science, 324, 1632-1633.

Thomas WW, Forzza RC, Michelangeli FA, Giulietti AM, Leitman PM (2011) Large-scale monographs and floras: the sum of local floristic research. Plant Ecology and Diversity, 5, 217-223.

Vision T (2010) Open data and the social contract of scientific publishing. BioScience, 60, 330-331.

Whitlock MC (2011) Data archiving in ecology and evolution: best practices. Trends in Ecology and Evolution, 26, 61-65.

Wieczorek J, Bloom D, Guralnick R, Blum S, D?ring M, Giovanni R, Robertson T, Vieglais D (2012) Darwin Core: an evolving community-developed biodiversity data standard. PLoS ONE, 7, e29715.

Winker K, Withrow JJ (2013) Natural history: small collections make a big impact. Nature, 493, 480.

Yesson C (2007) How Global Is the Global Biodiversity Information Facility? PLoS ONE, 2, e1124