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Scratchpads training course introduction


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This is the introduction presentation for the basic Scratchpads training course

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Scratchpads training course introduction

  1. 1. An Introduction to Scratchpads:Making your data work for you Koureas D.N., Van deVelde I., Roberts D.
  2. 2. keep the discussion going@vbrant @scratchpads &@dimitriskoureasat#piblei
  3. 3. butwhat aretheScratchpads?
  4. 4. What are Scratchpads?• Hosted websites for biodiversity data• Virtual research & publication platform• Completely open access & open source• Modular & flexible
  5. 5. What are Scratchpads?Facilitate the development of online research communitiesProvide a standardized environment of entering and curating dataEnable users in sharing and interlinking their dataAccelerate publication process & dissemination of research products
  6. 6. The Scratchpads conceptA Scratchpad is a website that holds data for you and your community Your data External data & services
  7. 7. What Scratchpads are not!A single biodiversity databaseRestricted thematically, geographically or taxonomicallyA tool just for taxonomists
  8. 8. Examples of usage: Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic & morphometric datasets, keys, phylogenies) Conservation Projects Regions Societies
  9. 9. How are Scratchpads doing?464 Scratchpads Communitiesby 6,407 active registered users In total more thancovering 52,661 taxain 559,488 pages. 1,200,000 visitorsPer month unique visitors to Scratchpads sites 65000 unique visitors/month
  10. 10. How are Scratchpads funded?2007 2011 2014 ViBRANT Virtual Biodiversity Research &
  11. 11. Why Scratchpads? Our informatics grand challenge…“Link together evolutionary This requires data, information & knowledgedata… by developing analytical to be…tools and proper • Digitaldocumentation and then use Not printed paperthis framework to conduct • Openly accessiblecomparative analyses, studies Not behind barriersof evolutionary process and • Linked-upbiodiversity analyses” Not in silosCyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page.TREE. doi:10.1016/j.tree.2011.11.001
  12. 12. Why Scratchpads? 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 projectsFigures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.
  13. 13. Why Scratchpads?Vast amounts of unpublished taxonomic “knowledge” OrPublished knowledge cannot easily be mobilised
  14. 14. Why Scratchpads?This leads to:• A complex, fragmented & hard to navigate landscape• Dispersed data sources• Difficulties for collecting information for research
  15. 15. Why Scratchpads?• Science is global• It needs global standards• Global workflows• Cooperation of large institutes and organisations
  16. 16. ScratchpadsVirtual Research Environments Making taxonomy digital, open & linked
  17. 17. the mainfeatures
  18. 18. The main features Classification term oriented system Biological Non-biologicalclassifications classificationsTaxonomies Hierarchical controlled vocabularies
  19. 19. The main featuresDynamic Biological Classifications Manually entered or imported Auto generated Nomenclatural annotation
  20. 20. The main featuresTaxon pages Overview of data related to taxon Generated from tagged content
  21. 21. The main features Bibliography managementAn inbuilt Bibliography managerFaceted browsingTaxon tagging and free keywordsImport from and export to all major formats
  22. 22. The main features Specimen/Observation dataAnnotated full specimen/observation recordsLinked to images and georeferenced
  23. 23. The main featuresDistribution maps Google maps based Data layers Occurrence data Distribution data TDWG regions GBIF data
  24. 24. The main featuresExample regional distribution
  25. 25. Character matrices – Key constructionQuantitative or qualitative charactersAuto generation of keysTaxon based matrices [Specimens based character matrices]
  26. 26. Media handling Bulk upload Metadata (incl. EXIF) Media galleries
  27. 27. Enhanced communication tools Working groups Forums Blog entries Webforms Newsletters RSS syndication Inbuilt comments
  28. 28. Generation of custom pages Tagged or not External RSS Twitter feeds Media files
  29. 29. otherfeaturesMultilanguage support (Localization, Internationalization)OBOE REST service
  30. 30. otherfeaturesSEO optimization & Google AnalyticsInterface customization
  31. 31. Built to interact
  32. 32. Publishing toolManuscript preview Multi-figure plates Plate layoutID Key ID Keypreview builder
  33. 33. Scratchpads are an integrated system toEnter, Curate, Mark-up, Link and Publish data workflow taxonomic in a single virtual environment
  34. 34. Help & Support • In-site Support - One click help within your site • Wiki - Training manuals, videos & glossary • Training Courses (12 in 2012) - UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) • Ambassadors Programme - Enthusiastic experienced users - Local support • Embedded Issues Queue - Bug reports - Feature requests • Sandbox Site - http://sandbox.scratchpad.eu
  35. 35. AcknowledgementsScratchpad technical development - Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine BoutonScratchpad outreach - Isa van deVelde, Laurence Livermore & Dimitris KoureasE-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford teamViBRANT - Vince Smith, Dave Roberts & Lucy ReeveOur 7,000+ users
  36. 36. and now…hands-on timeyour training site:http://pro-ibioXX.taxon.namesome dummy data: