This talk was given during the BioSyst.eu 2013 conference in Vienna.

1. Publishing Biodiversity:
The interplay between Scratchpads and
the new Biodiversity Data Journal
Koureas D.N.1, Rycroft S. 1, Baker E. 1, Livermore L. 1, Scott B. 1,
Heaton A.1, Bouton K.1, Penev L.2, Roberts D.1 and Smith V.S.1
1
The Natural History Museum London
2
Pensoft Publishers

2. Our current taxonomic data production
• 15-20k new spp. described annually (2M total)1
• 30k nomenclatural acts (12M total) 1
• 20k phylogenies (750k total)2
• 31k taxa sequenced (360k taxa total)3
• 800k BioMed papers (40M total pp. of taxonomy) 4
• Countless specimens, images, maps, keys and datasets
Typically generated by small communities for
“local” research projects
Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

3. The four nodes of data workflow
1. We collect and generate data
2. We curate, link and structure data
3. We analyse data
4. We publish data

4. The four nodes of data workflow
What are the
bottlenecks
in the workflow? Data
Data
collection &
collection &
generation
generation
bottleneck
Data
Data Data
Data
publishing
publishing curation
curation
bottleneck
Data
Data
analysis
analysis

5. What we need is…
a
seamless
workflow Data
Data
collection &
collection &
generation
generation
Data
Data Data
Data
publishing
publishing curation
curation
Data
Data
analysis
analysis

6. To achieve this…
This requires data, information & knowledge
Link together
“ to be…
evolutionary •Digital
data… by developing Not printed paper
•Openly accessible
analytical tools and Not behind barriers (e.g. paywalls)
proper •Linked-up
documentation and Not in silos
then use this framework to
conduct comparative analyses,
studies of evolutionary process Global Systematics
and biodiversity analyses”
Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001

7. Scratchpads
Virtual Research Environments
Making taxonomy digital, open & linked

8. so…
what are
the
Scratchpads?

9. What are Scratchpads?
• Hosted websites for biodiversity data
• Virtual research & publication platform
• Completely open access & open source
• Modular & flexible

10. What are Scratchpads?
facilitate
development of online research communities
through
standardized environment of entering and curating data
that allow
sharing and interlinking
and
dissemination of research products

11. The Scratchpads concept
A Scratchpad is a website that holds data for you and your community
Your data External data & services

12. Examples of use:
Taxa
(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic
& morphometric datasets, keys, phylogenies)
Conservation Projects Regions Societies

13. Are Scratchpads sustainable?
464 Scratchpads Communities
by 6,407 active registered users
In total more than
covering 52,661 taxa
in 559,488 pages. 1,200,000 visitors
Per month unique visitors to Scratchpads sites
65000
unique visitors/month

14. Are Scratchpads sustainable?
2007 2011 2014
ViBRANT
Virtual Biodiversity Research
& &
Other grants in the pipeline
Proposals?

15. the main
features

16. The main features
Dynamic Biological Classifications
Manually entered or imported
Auto generated

17. The main features
Taxon pages
Overview of data related to taxon
Generated from tagged content

18. The main features
Bibliography management
An inbuilt Bibliography manager
Faceted browsing
Taxon tagging and free keywords
Import from and export to all major formats

19. The main features
Specimen/Observation data
Annotated full specimen/observation records
Linked to images and georeferenced

20. The main features
Distribution maps
Google maps based
Data layers
Occurrence data
Distribution data
TDWG regions
GBIF data

21. The main features
Character matrices – Key construction
Quantitative or qualitative characters
Auto generation of keys
Taxon based matrices
[Specimens based character matrices]

22. The main features
Media handling
Bulk upload
Metadata (incl. EXIF)
Media galleries

23. The main features
Generation of custom pages
Tagged or not
External RSS
Twitter feeds
Media files

24. The main features
Enhanced communication tools
Working groups
Forums
Blog entries
Webforms
Newsletters
RSS syndication
Inbuilt comments

25. The main features
analytical
tools
OBOE service
i.a.
Ecological informatics,
Phylogenetics,
Sequence alignment

26. The main features
data
mobilisation
more on the way…

27. The main features
The
Publication
module
Open-access
journal

28. What will BDJ publish?
• Single taxon treatments and
nomenclatural acts
• Local or regional checklists
• Sampling reports and occasional
inventories
• Habitat-based checklists and inventories
• Ecological and biological observations of
species and communities?
• Single identification keys
• biodiversity-related databases, including
genomic, ecological and environmental
data (data papers)
• Biodiversity-related software tools

29. How do
Scratchpads
and
BDJ
interact?

30. Working in a single environment
Allow submission of
datasets
for publication
without
reformatting and restructuring
based on standardised XML schema

31. The publication module
Data included in manuscript in a structured annotated format
Author names and affiliations

32. The publication module
Taxon descriptions

33. The publication module
Specimen data

34. The publication module
Author names and affiliations
Taxon descriptions
Specimen data
Figures and Tables
XML
XML
Keys
References
Texts

35. The data workflow
XML
Community
submission
PENSOFT JOURNAL SYSTEM
SCRATCHPADS
(PJS 2.0)
MANUSCRIPT PUBLISHED
MANUSCRIPT PUBLISHED
(XML, PDF)
(XML, PDF)
Archive datasets Occurrence data Taxon treatments Taxon names
Plazi Wiki

36. The editorial workflow
Scratchpads Penso Peer-review op ons
Journal Public
Community
System Closed
(PJS)
Review
Review
Nominated reviewers
requests
Review
Editor
Collabora ve Panel reviewers
online wri ng Online edi ng
Review
Editorial
decision & feedback Public reviewers
Authors
Publica on & All reviews assembled into a
Online edi ng dissemina on single online version
Author’s revised
manuscript

37. Example papers via Scratchpads…
Blagoderov V, Hippa H, Nel A (2010). ZooKeys 50: 79–90. Faulwetter S, Chatzigeorgiou G, Galil BS, Nicolaidou A, Brake I, von Tschirnhaus M (2010). ZooKeys 50: 91–96.
doi: 10.3897/zookeys.50.506 Arvanitidis C (2011. ZooKeys 150: 327–345. doi: doi: 10.3897/zookeys.50.505
10.3897/zookeys.150.1877
http://sciaroidea.info/node/44428 http://polychaetes.marbigen.org/node/35 http://milichiidae.info/node/14995
Live (updated) versions of these papers

39. Acknowledgements
Scratchpads technical development
- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Bouton
Scratchpads outreach
- Laurence Livermore, Isa van deVelde & Dimitris Koureas
e-Monocot
- Paul Wilkin & the Kew team, Charles Godfray & the Oxford team
ViBRANT
- Vince Smith, Dave Roberts & Lucy Reeve
Pensoft
- Lyobomir Penev and the team
Our 7000 users

40. Data
Data
collection &
collection &
generation
generation
Data Data
Data
Data
publishing
publishing Thank you curation
curation
Data
Data
analysis
analysis

42. Authors and Contributors
Contributors
(mentor, linguis c editor, copy editor,
poten al reviewer, colleague/friend) Con
trib
u
ng
ite
Inv
Manuscript ready to submit
Taxon treatment
Template-
based Interac ve key
manuscript Checklist
Authoring
Lead author crea on
Data paper
Inv
ite
ing
hor
Aut
Co-authors