Presented by Vince Smith at the iEvoBio 2013 meeting in Snowbird, Utah, USA on 25th June, 2013. The presentation coauthors are Alice Heaton, Laurence Livermore, Simon Rycroft and Ben Scott from the Natural History Museum, London, and Lyubomir Penev from Pensoft Publishing, Bulgaria.

1. Don’t make me think
Biodiversity data publishing made easy
Vince Smith, Alice Heaton, Laurence Livermore,
Simon Rycroft, Ben Scott & Lyubomir Penev*
The Natural History Museum London
Pensoft Publishing*, Bulgaria

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

3. • Hosted websites for
biodiversity data
• Virtual research
environments
• Completely open
access & open source
• Modular & flexible
• Running since 2007
• Making taxonomy
digital, open & linked
Scratchpads (http://Scratchpads.eu)

4. 65,000
unique visitors/month
Per month unique visitors to Scratchpad sites
512Scratchpad Communities
by 6,500active registered users
covering 73,444taxa
in 515,189 pages.
Scratchpad usage metrics
81 paper citations in 2012
In total more than
1,300,000 visitors

5. Taxa
(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic
& morphometric datasets, keys, phylogenies)
ProjectsConservation Regions Societies
Examples of Scratchpad use

6. Data
curation
Data publishing via Scratchpads
Data
collection &
generation
Data
analysis
Data
publishing
No kudos, credit
or citation of data
in Scratchpads

7. Structured data
Publish, cite,
disseminate &
archive data
EOL
Dryad
GBIF
Wiki Species-Id
PubMed
Plazi
Select,
describe &
annotate data
Publication module

8. Biodiversity Data Journal
• New, Open Access data journal
• Launches Mid-2013
• Supports the full life cycle of a
manuscript
• Writing, submission, review,
publication & dissemination
• Structured, reusable,
standardized data
• Linked to Scratchpads via
publishing module
http://biodiversitydatajournal.com/

9. The publication module
Scratchpad templates for publishing...
• Taxon treatments
• Nomenclatural acts
• Checklists / inventories
• Identification keys and trees
• Metadata descriptions of databases
• Descriptions of software tools
Easy & intuitive
• Draws on data from your site
• Pre-submission validation
• Submitted as structured XML
• No reformatting

10. Assembling a manuscript
1. Add article level metadata...
• Choose authors, select template
• Add context (title, abstract)
2. Select data
• Taxon descriptions
• Specimens
• Datasets
• Figures & tables
• Keys & trees
3. Describe data
• Intro., methods, conclusions
• Auto-compile references
4. Submit
• Preview manuscript
• Validate

11. After submission

12. More information
Scratchpads (GPLv2 License)
• http://scratchpads.eu/ (Scratchpad project)
• http://scratchpads.eu/develop/repository (Developer resources)
• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree (Git repository)
Scratchpad Publication Module (also GPLv2)
• https://git.scratchpads.eu/v/scratchpads-2.0.git/tree/
HEAD:/sites/all/modules/custom/publication
Biodiversity Data Journal
• http://biodiversitydatajournal.com/
Credits
• Alice Heaton, Simon Rycroft, Ben Scott (programming)
• Laurence Livermore (user testing & support)
• Lyubomir Penev & the Pensoft team (Biodiversity Data Journal)
Funding
• EU FP7 Infrastrastructures (ViBRANT), UK NERC (e-Monocot)