an introduction to scratchpads: making your data work for you laurence livermore natural history...
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An Introduction to Scratchpads:Making your data work for you
Laurence LivermoreNatural History Museum, London
Joinville, BrazilNovember, 2012
What are Scratchpads?
• Hosted websites for biodiversity data
• Virtual research & publication platform
• Completely open access & open source
• Modular & flexible
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What Scratchpads are not!
• A single biodiversity database
• Restricted thematically, geographically or taxonomically
• A tool just for taxonomists
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How are Scratchpads funded?
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2007 2011 2014
ViBRANTVirtual Biodiversity Research
&
Examples of usage:
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Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,
genotypic & morphometric datasets, keys, phylogenies)
ProjectsConservation Regions Societies
Who uses Scratchpads?
• Total Sites: 400+
• Total Users: 7,000+
• Active Users: 5,500+ (273 w / 759
m)
• Content: 430,000+
Site
s Use
rs
ViBRANT SP 2
• Professional scientists
• Amateur naturalists
• Citizen scientists
• Individuals, groups & societies
eMonocot Scratchpads
• 15 sites and growing
• 40+ international users
• Scratchpads / eMonocot Portal
now active!
Site list: http://about.e-monocot.org/list-emonocot-scratchpads
Why Scratchpads?
Science is global
• It needs global standards
• Global workflows
• Cooperation of large
institutes and organisations
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Why Scratchpads?
Science is carried out “locally”
• By local scientists
• Involvement with local infrastructures
• Funded locally
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Why Scratchpads?
This leads to:
• A complex, fragmented & hard to navigate landscape
• Dispersed data sources
• Difficulties for collecting information for research
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Why should we change?
The problems with traditional published data:
• Most descriptions are under copyright (~1923)
• Limited Open Access and accessibility
• No mechanism for updates & corrections
• Little or no data integration (except citations)
• No mechanism for community engagement
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Why should we change?
This results in:
• Vast amounts of unpublished taxonomic “knowledge”
• The knowledge that is published cannot be mobilised
• Low scientific impact (but long half-life)
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The Scratchpad Concept
A Scratchpad is a website that holds data for you and your community
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Your data External data & services
What can Scratchpads do?
• Taxon pages (generated from tagged content)
• Distribution maps (from specimens and TDWG regional
distributions - Brummitt, 2001)
• Specimen records
• Character matrixes
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Example Taxon Page
Example regional distribution
What can Scratchpads do?
• Bibliography management
• Images, video and sound (bulk import)
• Excel spreadsheet import
Example Literature
What can Scratchpads do?
• Tabular data editing
• Custom content
• User management
• Custom webforms
• Analytics
Analytics
What can Scratchpads do?
• Darwin Core Archive export
(links to eMonocot Portal and EOL)
• EOL data import (taxonomy,
species information)
• GBIF Map integration
Getting data in and out of Scratchpads
What new features are coming soon?
• Matrix-based keys using the character project
• Publication tool - submit manuscripts through your site via Phytokeys
or the new Biodiversity Data Journal
• Checklists, multiple language support and more!
Testing screenshots of the publishing tool
ID Keypreview
Multi-figure plates Plate layout
ID Keybuilder
Manuscript preview
Help & Support
• In-site Support- One click help within your site
• Wiki- Training manuals, videos & glossary
• Training Courses (12 in 2012)- UK (6), Sweden, (2) Greece (1),
Bulgaria (1), South Africa (1), Brazil (1)
• Ambassadors Programme- Enthusiastic experienced users- Local support
• Embedded Issues Queue- Bug reports- Feature requests
• Sandbox Site- http://sandbox.scratchpad.eu
http://scratchpad.eu/help
• Scratchpad technical development- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton
• Scratchpad outreach- Irina Brake & Dimitris Koureas
• E-Monocot - Paul Wilkin & the Kew team, Charles Godfray & the Oxford team
• ViBRANT- Vince Smith, Dave Roberts & Lucy Reeve
• Our 7,000+ users
Acknowledgements
Security & Backups
• Nightly backups of database and files
• Off-site tape backup
• Whole-site archives available upon request
• Berlin mirror
Technical Infrastructure
• LAMP (standard open source setup)
• Multiple virtual servers (scaleable)
• Aegir hosting system (multisite management)