Don’t make me thinkBiodiversity data publishing made easy
Vince Smith, Alice Heaton, Laurence Livermore, Simon Rycroft, Ben Scott & Lyubomir Penev*
The Natural History Museum LondonPensoft Publishing*, Bulgaria
Data curation
Data publishing
What we need is…
Data collection &generation
aseamless
workflow
Data analysis
• 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)
65,000 unique visitors/month
Per month unique visitors to Scratchpad sites
512 Scratchpad Communities
by 6,500 active registered users
covering 73,444 taxa
in 515,189 pages.
Scratchpad usage metrics
81 paper citations in 2012
In total more than
1,300,000 visitors
Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic, genotypic
& morphometric datasets, keys, phylogenies)
ProjectsConservation Regions Societies
Examples of Scratchpad use
Data curation
Data publishing via Scratchpads
Data collection &generation
Data analysis
Data publishing
No kudos, credit
or citation of data in Scratchpads
Structured data
Publish, cite,disseminate & archive data
EOLDryad GBIFWiki Species-IdPubMed Plazi
Select, describe &
annotate dataPublication module
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 modulehttp://biodiversitydatajournal.com/
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
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
After submission
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)
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