Presented by V. Smith at the 2013 iEvoBio Conference. Part of Evolution 2013, the joint annual meeting of the Society for the Study of Evolution (SSE), the Society of Systematic Biologists (SSB), and the American Society of Naturalists (ASN). June 21-26, 2013, Snowbird Alpine Village, Utah, USA.

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

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

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

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

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

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

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)