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

2. 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 Our current taxonomic data production 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 undescribed 1 1 How Many Species Are There on Earth and in the Ocean? Mora C et al. doi:10.1371/journal.pbio.1001127

4. Expected volume of taxonomic and biodiversity data Need of extracting, aggregating and linking data on a global level

5. The four nodes of data workflow 1. We collect and generate data 2. We curate, link and structure data 3. We analyse data 4. We publish data

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

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

8. Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001 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” To achieve this…

9. Scratchpads Virtual 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 Publication module Open-access journal The main features

12. How do Scratchpads and BDJ interact?

13. Allow submission of datasets for publication without reformatting and restructuring Working in a single environment based on standardised XML schema

14. Assembling a manuscript

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

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 MANUSCRIPT PUBLISHED (XML, PDF) MANUSCRIPT PUBLISHED (XML, PDF) PENSOFT JOURNAL SYSTEM (PJS 2.0) XML submission SCRATCHPADS Community Taxon namesOccurrence datadatasets Archive Taxon treatments Plazi Wiki

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

21. Scratchpads are an integrated system to Enter, Curate, Mark-up, Link and Publish data taxonomic workflow in a single virtual environment

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