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Integrating data publishing with workflows in biodiversity research, Potsdam 2013


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  • 1. Integrating data publishing with workflows in biodiversity research Lyubomir Penev, Teodor Georgiev, Pavel Stoev, Jordan Biserkov, Laurence Livermore, Jeremy Miller, David Roberts, Vincent Smith, Daniel Mietchen ViBRANT 43rd Annual Meeting of the Ecological Society of Germany, Austria and Switzerland, Potsdam, September 9-13, 2013
  • 2. Think about a dataset...
  • 3. ...and how it came to be...
  • 4. ...what it means to you...
  • 5. ...what it could enable...
  • 6. ...who knows about it...
  • 7. they got to know about it...
  • 8. ...who actually uses it...
  • 9. ...and how we can improve that...
  • 10. The “Publishing Bottleneck in Biodiversity”? What is that?
  • 11. Massive sampling/data gathering
  • 12. ‘Dark Taxa’ increase dramatically! Rod Page, iPhylo blogspot, 12 April 2011
  • 13. The paper/PDF impediment
  • 14. … the burden of OCR, double-keying and markup of paper/PDF literature
  • 15. Low uptake of open data publishing/sharing
  • 16. The “impact factor” pressure
  • 17. The “peer review” pressure
  • 18. The solution?
  • 19. Launch date http://biodiversitydatajournal. com
  • 20. Novel concepts Authoring, reviewing and publishing in one place, for the first time! Upfront markup! “Small” data imported in and downloadable from text Large datasets published as data papers Text stored and treated as data Community peer-reviewed and community owned interoperable data Text and data integrated publishing!
  • 21. How does BDJ do that? Community peer-review (options for public and Open review) ALL ONLINE! Collaborative ARTICLE AUTHORING (PENSOFT WRITING TOOL) MANUSCRIPT published XML text + data Authors, Reviewers, Editors, Mentors, Copyeditors Automated submission Revisions online ARTICLES Occurr- ence data Taxon namesTaxon treatments Plazi Wiki COL Biblio- graphies
  • 22. Novel work flows Authoring Peer-review Publishing and dissemination
  • 23. Article templates
  • 24. DwC terms visible in text
  • 25. Compose plates
  • 26. Pick up a reference
  • 27. Cite a reference
  • 28. No author guidelines! The tool will guide you!
  • 29. Authors do not need to markup or hyperlink anything! It is done by the tool!
  • 30. No layout stage!
  • 31. Novel work flows Authoring Peer-review Publishing and dissemination
  • 32. Penso Wri ng Tool (PWT) Collabora ve onlinewri ng Authors Penso Journal System (PJS) Editor Public Community Closed Review requests Peer-reviewop ons All reviewsassembledintoa singleonlineversion Review Review Review Nominatedreviewers Publicreviewers Panel reviewers Editorial decision&feedback Onlineedi ng Author’srevised manuscript Publica on& dissemina onOnlineedi ng Community and public peer-review
  • 33. Now imagine…
  • 34. Consolidated Reviewers’ Version
  • 35. Novel work flow Authoring Peer-review Publishing and dissemination
  • 36. Article metadata
  • 37. Download data
  • 38. Map localities
  • 39. Taxa and their usages
  • 40. Taxon profile
  • 41. Taxon profile
  • 42. Tables and Figures
  • 43. References
  • 44. Possible solution for “dark” taxa Pwt – collaborative article authoring toolDark taxon sequenced Bdj – peer-review Automated submission to Pensoft Writing Tool MANUSCRIPT PUBLISHED BOLD Metadata: voucher specimen, images, locality, etc. manuscript finalization & SUBMISSION Automated update of bibliographic metadata, taxon names, Zoobank records, etc.
  • 45. Automated pre-publication registration of new taxon names Manuscript SUBMISSION MANUSCRIPT ACCEPTED XML Response ARTICLE PUBLISHED Taxon name available/valid (effectively published) XML article metadata XML Query Peer review
  • 46. Unified marked up final output Taxon treatments, keys, images, localities, references PROSPECTIVE PUBLISHING | HISTORICAL LITERATURE Re-publishing of legacy literature Content management systems & repositories (SCRATCHPADS, CDM, etc.) PENSOFT WRITING TOOL 2nd DIGITAL EDITION semantically enhanced HTML and XML archiving Species-ID, Wikispecies Wikipedia Indexing (IPNI, ZooBank, Myco- Bank, GNA) Aggregators (EOL, GBIF) Electronic archives; Data Centers END USERS OCR, re-typing, markup, extracting images , tables XML IMPORT
  • 47. What will BDJ publish? Single taxon treatments and acts Local/regional and habitat checklists, sampling reports, N2K inventories Ecological and biological observations on species and communities Identification keys Data papers describing data Descriptions of software tools and work flows Recruiting editors! Editor Application Form
  • 48. Implementation in other domains welcome!
  • 49. Now what about your dataset?
  • 50. Why publish in BDJ? Not just a journal Even not just a data journal! A work flow and infrastructure to mobilize, review, publish, store, disseminate, make interoperable, collate and re-use data through the act of publishing!
  • 51. LOW COST!
  • 52. I Open Access! and…. ViBRANT PLAZI
  • 53. Drawings:
  • 54. Classifications
  • 55. Import co-author’s profile
  • 56. Describe new taxon
  • 57. Structure of the checklist filed External links
  • 58. External links
  • 59. DwC Template
  • 60. DwC Template
  • 61. DwC Template
  • 62. Key preview