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Don't make me think: biodiversity data publishing made easy

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Presented by V. Smith at the 2013 iEvoBio Conference. Part of Evolution 2013, the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). June 21-26, 2013, Snowbird Alpine Village, Utah, USA.

Publié dans : Technologie
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Don't make me think: biodiversity data publishing made easy

  1. 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. 2. What we need is… a seamless workflow Data collection & generation Data Data publishing curation Data analysis
  3. 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. 4. Scratchpad usage metrics 512 Scratchpad Communities by 6,500 active registered users covering 73,444 taxa in 515,189 pages. In total more than 1,300,000 visitors 81 paper citations in 2012 Per month unique visitors to Scratchpad sites 65,000 unique visitors/month
  5. 5. Examples of Scratchpad use Taxa (Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  6. 6. Data publishing via Scratchpads No kudos, credit or citation of data in Scratchpads Data collection & generation Data Data publishing curation Data analysis
  7. 7. Structured data Select, describe & annotate data Publish, cite, disseminate & archive data Publication module EOL Dryad GBIF Wiki Species-Id PubMed Plazi
  8. 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. 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. 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. 11. After submission
  12. 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)