Revolution in publication:
Data and text publishing integrated
in the
Biodiversity Data Journal
Lyubomir Penev, Teodor Geo...
Revolution?
Again??
…but if there is
a bottleneck,
then expect
a revolution!
The “Publishing Bottleneck
in Biodiversity”?
What is that?
Massive sampling/data gathering
„Dark Taxa‟ increase
dramatically!
Rod Page, iPhylo blogspot, 12 April 2011
The paper/PDF impediment
… the burden or OCR, double-keying and
markup of paper/PDF literature
Low uptake of open data publishing/sharing
The “impact factor” pressure
The “peer review” pressure
The solution?
Launch date
http://biodiversitydatajournal.com
Novel concepts
Authoring, reviewing and publishing in one
place, for first time!
Upfront markup!
“Small” data imported in ...
How BDJ does that?
COMMUNITY PEER-REVIEW
(OPTIONS FOR PUBLIC AND
OPEN REVIEW)
ALL ONLINE!
COLLABORATIVE
ARTICLE AUTHORING
...
Novel work flows
Authoring
Peer-review
Publishing and dissemination
Article
templates
Classifications
Import co-author’s profile
Describe new taxon
Structure of the checklist filed
External links
External links
DwC Template
DwC Template
DwC Template
DwC terms
visible in text
Compose plates
Pick up a reference
Cite a reference
Construction
of keys
Key preview
No author guidelines!
The tool will guide
you!
Authors do not need
to markup or
hyperlink anything!
It is done by the tool!
No layout stage!
Novel work flows
Authoring
Peer-review
Publishing and dissemination
Penso
Wri ng
Tool
(PWT)
Collabora ve
online wri ng
Authors
Penso
Journal
System
(PJS)
Editor
Public
Community
Closed
Revie...
Now imagine…
Consolidated Reviewers‟ Version
Novel work flow
Authoring
Peer-review
Publishing and dissemination
Article metadata
Download data
Map localities
Taxa and their usages
Taxon profile
Taxon profile
Tables and Figures
References
Possible solution for “dark” taxa
PWT – COLLABORATIVE
ARTICLE AUTHORING TOOLDark taxon sequenced
BDJ – PEER-REVIEW
Automat...
Automated pre-publication
registration of new taxon names
MANUSCRIPT
SUBMISSION
MANUSCRIPT
ACCEPTED
XML
Response
ARTICLE
P...
Unified marked up final output
Taxon treatments, keys, images, localities, references
PROSPECTIVE PUBLISHING | HISTORICAL ...
What will BDJ publish?
Single taxon treatments and acts
Local/regional and habitat checklists,
sampling reports, N2K inven...
Why publish in BDJ?
Not just a journal
Even not just a data journal!
A work flow and infrastructure to
mobilize, review, p...
Implementation in other domains
welcome!
LOW COST!
I Open Access!
and….
ViBRANT
PLAZI
Drawings: slavenapeneva.com
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
Revolution in publishing bio horizon rome 2013
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Revolution in publishing bio horizon rome 2013

  1. 1. Revolution in publication: Data and text publishing integrated in the Biodiversity Data Journal Lyubomir Penev, Teodor Georgiev, Pavel Stoev, Jordan Biserkov, Laurence Livermore, Jeremy Miller, David Roberts, Vincent Smith ViBRANT Biodiversity Informatics Horizons 2020 September 3-6, 2013, Rome
  2. 2. Revolution? Again??
  3. 3. …but if there is a bottleneck, then expect a revolution!
  4. 4. The “Publishing Bottleneck in Biodiversity”? What is that?
  5. 5. Massive sampling/data gathering
  6. 6. „Dark Taxa‟ increase dramatically! Rod Page, iPhylo blogspot, 12 April 2011
  7. 7. The paper/PDF impediment
  8. 8. … the burden or OCR, double-keying and markup of paper/PDF literature
  9. 9. Low uptake of open data publishing/sharing
  10. 10. The “impact factor” pressure
  11. 11. The “peer review” pressure
  12. 12. The solution?
  13. 13. Launch date http://biodiversitydatajournal.com
  14. 14. Novel concepts Authoring, reviewing and publishing in one place, for 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!
  15. 15. How BDJ does 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
  16. 16. Novel work flows Authoring Peer-review Publishing and dissemination
  17. 17. Article templates
  18. 18. Classifications
  19. 19. Import co-author’s profile
  20. 20. Describe new taxon
  21. 21. Structure of the checklist filed External links
  22. 22. External links
  23. 23. DwC Template
  24. 24. DwC Template
  25. 25. DwC Template
  26. 26. DwC terms visible in text
  27. 27. Compose plates
  28. 28. Pick up a reference
  29. 29. Cite a reference
  30. 30. Construction of keys
  31. 31. Key preview
  32. 32. No author guidelines! The tool will guide you!
  33. 33. Authors do not need to markup or hyperlink anything! It is done by the tool!
  34. 34. No layout stage!
  35. 35. Novel work flows Authoring Peer-review Publishing and dissemination
  36. 36. Penso Wri ng Tool (PWT) Collabora ve online wri ng Authors Penso Journal System (PJS) Editor Public Community Closed Review requests Peer-review op ons All reviews assembled into a single online version Review Review Review Nominated reviewers Public reviewers Panel reviewers Editorial decision & feedback Online edi ng Author’s revised manuscript Publica on & dissemina onOnline edi ng Community and public peer-review
  37. 37. Now imagine…
  38. 38. Consolidated Reviewers‟ Version
  39. 39. Novel work flow Authoring Peer-review Publishing and dissemination
  40. 40. Article metadata
  41. 41. Download data
  42. 42. Map localities
  43. 43. Taxa and their usages
  44. 44. Taxon profile
  45. 45. Taxon profile
  46. 46. Tables and Figures
  47. 47. References
  48. 48. 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.
  49. 49. 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
  50. 50. 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
  51. 51. 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
  52. 52. 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
  53. 53. Implementation in other domains welcome!
  54. 54. LOW COST!
  55. 55. I Open Access! and…. ViBRANT PLAZI
  56. 56. Drawings: slavenapeneva.com

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