Integrating data publishing with workflows in biodiversity research, Potsdam 2013

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My talk at http://gfoe-2013.de/ about http://biodiversitydatajournal.com/ and http://pwt.pensoft.net/ .
Based on http://www.slideshare.net/pensoft/revolution-in-publishing-bio-horizon-rome-2013 .

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Integrating data publishing with workflows in biodiversity research, Potsdam 2013

  1. 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. 2. Think about a dataset...
  3. 3. ...and how it came to be...
  4. 4. ...what it means to you...
  5. 5. ...what it could enable...
  6. 6. ...who knows about it...
  7. 7. ...how they got to know about it...
  8. 8. ...who actually uses it...
  9. 9. ...and how we can improve that...
  10. 10. The “Publishing Bottleneck in Biodiversity”? What is that?
  11. 11. Massive sampling/data gathering
  12. 12. ‘Dark Taxa’ increase dramatically! Rod Page, iPhylo blogspot, 12 April 2011
  13. 13. The paper/PDF impediment
  14. 14. … the burden of OCR, double-keying and markup of paper/PDF literature
  15. 15. Low uptake of open data publishing/sharing
  16. 16. The “impact factor” pressure
  17. 17. The “peer review” pressure
  18. 18. The solution?
  19. 19. Launch date http://biodiversitydatajournal. com
  20. 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. 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. 22. Novel work flows Authoring Peer-review Publishing and dissemination
  23. 23. Article templates
  24. 24. DwC terms visible in text
  25. 25. Compose plates
  26. 26. Pick up a reference
  27. 27. Cite a reference
  28. 28. No author guidelines! The tool will guide you!
  29. 29. Authors do not need to markup or hyperlink anything! It is done by the tool!
  30. 30. No layout stage!
  31. 31. Novel work flows Authoring Peer-review Publishing and dissemination
  32. 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. 33. Now imagine…
  34. 34. Consolidated Reviewers’ Version
  35. 35. Novel work flow Authoring Peer-review Publishing and dissemination
  36. 36. Article metadata
  37. 37. Download data
  38. 38. Map localities
  39. 39. Taxa and their usages
  40. 40. Taxon profile
  41. 41. Taxon profile
  42. 42. Tables and Figures
  43. 43. References
  44. 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. 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. 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. 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 http://pensoft.net/journals/bdj/editor_form.html
  48. 48. Implementation in other domains welcome!
  49. 49. Now what about your dataset?
  50. 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. 51. LOW COST!
  52. 52. I Open Access! and…. ViBRANT PLAZI
  53. 53. Drawings: slavenapeneva.com
  54. 54. Classifications
  55. 55. Import co-author’s profile
  56. 56. Describe new taxon
  57. 57. Structure of the checklist filed External links
  58. 58. External links
  59. 59. DwC Template
  60. 60. DwC Template
  61. 61. DwC Template
  62. 62. Key preview

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