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

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Presented by Vince Smith at the iEvoBio 2013 meeting in Snowbird, Utah, USA on 25th June, 2013. The presentation coauthors are Alice Heaton, Laurence Livermore, Simon Rycroft and Ben Scott from the Natural History Museum, London, and Lyubomir Penev from Pensoft Publishing, Bulgaria.

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

  1. 1. Don’t make me thinkBiodiversity data publishing made easyVince Smith, Alice Heaton, Laurence Livermore,Simon Rycroft, Ben Scott & Lyubomir Penev*The Natural History Museum LondonPensoft Publishing*, Bulgaria
  2. 2. DatacurationDatapublishingWhat we need is…Datacollection &generationaseamlessworkflowDataanalysis
  3. 3. • Hosted websites forbiodiversity data• Virtual researchenvironments• Completely openaccess & open source• Modular & flexible• Running since 2007• Making taxonomydigital, open & linkedScratchpads (http://Scratchpads.eu)
  4. 4. 65,000unique visitors/monthPer month unique visitors to Scratchpad sites512Scratchpad Communitiesby 6,500active registered userscovering 73,444taxain 515,189 pages.Scratchpad usage metrics81 paper citations in 2012In total more than1,300,000 visitors
  5. 5. Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic& morphometric datasets, keys, phylogenies)ProjectsConservation Regions SocietiesExamples of Scratchpad use
  6. 6. DatacurationData publishing via ScratchpadsDatacollection &generationDataanalysisDatapublishingNo kudos, creditor citation of datain Scratchpads
  7. 7. Structured dataPublish, cite,disseminate &archive dataEOLDryadGBIFWiki Species-IdPubMedPlaziSelect,describe &annotate dataPublication module
  8. 8. Biodiversity Data Journal• New, Open Access data journal• Launches Mid-2013• Supports the full life cycle of amanuscript• Writing, submission, review,publication & dissemination• Structured, reusable,standardized data• Linked to Scratchpads viapublishing modulehttp://biodiversitydatajournal.com/
  9. 9. The publication moduleScratchpad templates for publishing...• Taxon treatments• Nomenclatural acts• Checklists / inventories• Identification keys and trees• Metadata descriptions of databases• Descriptions of software toolsEasy & intuitive• Draws on data from your site• Pre-submission validation• Submitted as structured XML• No reformatting
  10. 10. Assembling a manuscript1. Add article level metadata...• Choose authors, select template• Add context (title, abstract)2. Select data• Taxon descriptions• Specimens• Datasets• Figures & tables• Keys & trees3. Describe data• Intro., methods, conclusions• Auto-compile references4. Submit• Preview manuscript• Validate
  11. 11. After submission
  12. 12. More informationScratchpads (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/publicationBiodiversity 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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