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 .

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. ...how 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

19. The “peer review” pressure

20. The solution?

23. Launch date
http://biodiversitydatajournal.
com

24. 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!

25. 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

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

27. Article
templates

28. DwC terms
visible in text

29. Compose plates

31. Pick up a reference

32. Cite a reference

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

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

36. No layout stage!

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

38. 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

41. Now imagine…

42. Consolidated Reviewers’
Version

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

45. Article metadata

46. Download data

47. Map localities

48. Taxa and their usages

49. Taxon profile

50. Taxon profile

51. Tables and Figures

52. References

55. 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.

56. 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

57. 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

58. 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

59. Implementation in other domains
welcome!

60. Now what about your
dataset?

61. 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!

62. LOW COST!

64. I Open Access!
and….
ViBRANT
PLAZI

65. Drawings: slavenapeneva.com

66. Classifications

67. Import co-author’s profile

68. Describe new taxon

69. Structure of the checklist filed
External links

70. External links

71. DwC Template

72. DwC Template

73. DwC Template

74. Key preview