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. Revolution?
Again??

3. …but if there is
a bottleneck,
then expect
a revolution!

4. The “Publishing Bottleneck
in Biodiversity”?
What is that?

5. Massive sampling/data gathering

6. „Dark Taxa‟ increase
dramatically!
Rod Page, iPhylo blogspot, 12 April 2011

7. The paper/PDF impediment

8. … the burden or OCR, double-keying and
markup of paper/PDF literature

9. Low uptake of open data publishing/sharing

10. The “impact factor” pressure

13. The “peer review” pressure

14. The solution?

17. Launch date
http://biodiversitydatajournal.com

18. 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!

19. 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

20. Novel work flows
Authoring
Peer-review
Publishing and dissemination

21. Article
templates

22. Classifications

23. Import co-author’s profile

24. Describe new taxon

25. Structure of the checklist filed
External links

26. External links

27. DwC Template

28. DwC Template

29. DwC Template

30. DwC terms
visible in text

31. Compose plates

33. Pick up a reference

34. Cite a reference

35. Construction
of keys

36. Key preview

38. No author guidelines!
The tool will guide
you!

39. Authors do not need
to markup or
hyperlink anything!
It is done by the tool!

40. No layout stage!

41. Novel work flows
Authoring
Peer-review
Publishing and dissemination

42. 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

45. Now imagine…

46. Consolidated Reviewers‟ Version

47. Novel work flow
Authoring
Peer-review
Publishing and dissemination

49. Article metadata

50. Download data

51. Map localities

52. Taxa and their usages

53. Taxon profile

54. Taxon profile

55. Tables and Figures

56. References

59. 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.

60. 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

61. 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

62. 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

63. 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

64. Implementation in other domains
welcome!

65. LOW COST!

67. I Open Access!
and….
ViBRANT
PLAZI

68. Drawings: slavenapeneva.com