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Scratchpads Publication Module

Scratchpads Publication Module. - A paradigm shift in publishing. RBG Kew, Seminar, 17-04-2013. Our current taxonomic data production. 15-20k new spp. described annually (2M total) 1 30k nomenclatural acts (12M total) 1 20k phylogenies (750k total) 2 31k taxa sequenced (360k taxa total) 3

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Scratchpads Publication Module

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  1. ScratchpadsPublication Module - A paradigm shift in publishing RBG Kew, Seminar, 17-04-2013

  2. Our current taxonomic data production • 15-20k new spp. described annually (2M total)1 • 30k nomenclatural acts (12M total) 1 • 20k phylogenies (750k total)2 • 31k taxa sequenced (360k taxa total)3 • 800k BioMed papers (40M total pp. of taxonomy) 4 • Countless specimens, images, maps, keys and datasets Typically generated by small communities for “local” research projects Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

  3. On the other hand: Estimates of 7.5 million species still undescribed1 1How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127

  4. Expected volume of taxonomicandbiodiversity data Need of extracting, aggregatingandlinkingdataon a global level

  5. The four nodes of data workflow 1. We collect and generatedata 2.We curate, link and structure data 3.We analysedata 4.We publishdata

  6. The four nodes of data workflow What are the bottlenecks in the workflow? Data collection & generation Data publishing Data curation Data analysis

  7. What we need is… a seamless workflow Data collection & generation Data publishing Data curation Data analysis

  8. To achieve this… • This requires data, information & knowledge to be… • Digital • Not printed paper • Openly accessible • Not behind barriers (e.g. paywalls) • Linked-up • Not in silos “Link together evolutionary data… by developing analytical tools and proper documentation and then use this framework to conduct comparative analyses, studies of evolutionary process and biodiversity analyses” Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001

  9. ScratchpadsVirtual Research Environments Making taxonomy digital, open & linked

  10. What are Scratchpads? Hosted websites for biodiversity data Virtual research & publication platform Completely open access & open source Modular & flexible

  11. The main features The Publication module Open-access journal

  12. How do Scratchpads and BDJ interact?

  13. Working in a single environment Allowsubmission of datasets for publication without reformattingand restructuring based on standardised XML schema

  14. Assembling a manuscript

  15. Submitting your data Author names and affiliations Taxon descriptions Specimen data Figures and Tables XML References Manuscript text

  16. Previewing your manuscript

  17. Submission & enhanced peer review • Manuscript data validation • One-click submission to BDJ • Traditional peer review and optional panel/public review

  18. What will BDJ publish? • Single taxon treatments and nomenclatural acts • Local or regional checklists • Sampling reports and occasional inventories • Habitat-based checklists and inventories • Ecological and biological observations of species and communities? • Single identification keys • biodiversity-related databases, including genomic, ecological and environmental data (data papers) • Biodiversity-related software tools

  19. The data workflow XML submission PENSOFT JOURNAL SYSTEM (PJS 2.0) Scratchpads Community MANUSCRIPT published (XML, PDF) Archive datasets Occurrence data Taxon treatments Taxon names Wiki Plazi

  20. Upcoming features • Additional manuscript types (checklists, keys & data) • Post-publication Scratchpad data feedback • Publish directly in Phytokeys, Zookeysetc

  21. Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomicworkflow in asinglevirtualenvironment

  22. Launch Date: May 2013 Currently accepting manuscripts from Scratchpads or via the online Pensoft Writing Tool

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