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Don’t make me think

Don’t make me think. Biodiversity data publishing made easy. Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev* The Natural History Museum London Pensoft Publishing*, Bulgaria. What we need is…. a seamless workflow. Data collection & generation.

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Don’t make me think

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  1. Don’t make me think Biodiversity data publishing made easy Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev* The Natural History Museum London Pensoft Publishing*, Bulgaria

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

  3. Scratchpads (http://Scratchpads.eu) • Hosted websites for biodiversity data • Virtual research environments • Completely open access & open source • Modular & flexible • Running since 2007 • Making taxonomy digital, open & linked

  4. Scratchpad usage metrics 512Scratchpad Communities by 6,500 active registered users covering 73,444 taxa in 515,189 pages. In total more than1,300,000 visitors 81 paper citations in 2012 Per month unique visitors to Scratchpad sites 65,000 unique visitors/month

  5. Examples of Scratchpad use Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies

  6. Data publishing via Scratchpads No kudos, credit or citation of data in Scratchpads Data collection & generation Data publishing Data curation Data analysis

  7. Structured data Select, describe & annotate data Publication module EOL Dryad GBIF Wiki Species-Id PubMed Plazi Publish, cite, disseminate & archive data

  8. Biodiversity Data Journal • New, Open Access data journal • Launches Mid-2013 • Supports the full life cycle of a manuscript • Writing, submission, review, publication & dissemination • Structured, reusable, standardized data • Linked to Scratchpads via publishing module http://biodiversitydatajournal.com/

  9. The publication module • Scratchpad templates for publishing... • Taxon treatments • Nomenclatural acts • Checklists / inventories • Identification keys and trees • Metadata descriptions of databases • Descriptions of software tools • Easy & intuitive • Draws on data from your site • Pre-submission validation • Submitted as structured XML • No reformatting

  10. Assembling a manuscript • 1. Add article level metadata... • Choose authors, select template • Add context (title, abstract) • 2. Select data • Taxon descriptions • Specimens • Datasets • Figures & tables • Keys & trees • 3. Describe data • Intro., methods, conclusions • Auto-compile references • 4. Submit • Preview manuscript • Validate

  11. After submission

  12. More information • Scratchpads (GPLv2 License) • http://scratchpads.eu/ (Scratchpad project) • http://scratchpads.eu/develop/repository (Developer resources) • https://git.scratchpads.eu/v/scratchpads-2.0.git/tree (Git repository) • Scratchpad Publication Module (also GPLv2) • https://git.scratchpads.eu/v/scratchpads-2.0.git/tree/ • HEAD:/sites/all/modules/custom/publication • Biodiversity Data Journal • http://biodiversitydatajournal.com/ • Credits • Alice Heaton, Simon Rycroft, Ben Scott (programming) • Laurence Livermore (user testing & support) • Lyubomir Penev & the Pensoft team (Biodiversity Data Journal) • Funding • EU FP7 Infrastrastructures (ViBRANT), UK NERC (e-Monocot)

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