This document discusses the challenges of modern taxonomy and proposes Scratchpads as a solution. Scratchpads are customizable, modular websites that allow taxonomists to store, share, and publish their research online. They provide taxonomy tools, multimedia galleries, mapping, and more. The ViBRANT project aims to develop and support Scratchpads further to help taxonomists collaborate globally on biodiversity research.

1. Ed Baker
Natural History Museum, London, UK

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Why Scratchpads?

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21st Century taxonomy
The challenge for modern taxonomists
Goal…
• Inventory the Earth’s species
• Document their relationships
• “Publish” & apply these data
Data set…
• 1.8 M described spp. (10M names)
• 300M pages (over last 250 years)
• 1.5-3B specimens
People…
• 4-6,000 scientists
• 30-40,000 “pro-amateurs”
• Many more citizen scientists?

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The problem
Science is global
• It needs global standards
• Global workflows
• Cooperation of global players
Science is carried out “locally”
• By local scientists
• Being part of local infrastructures
• Having local funders

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Towards a solution
The European Distributed Institute of Taxonomy
• A Network of Excellence (NoE)
• 29 leading European, North American,
& Russian natural history collections-based
institutions
• Circa 12M !, funded under EU FP6
• March 2006 - February 2011
Products…
• Funding
• Training & outreach
• Websites
• Integrated scientific activities
• Inventories
• Computer tools

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Goal
“a scholarly communication system
that is intertwined with the pursuit of
natural history, rather than an after-
thought or annex”

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What is a Scratchpad?
A website for you & your community
1 2 3
Your data Uploaded & “Published” & reviewed
tagged on your site
Fast Intuitive Fit for use

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Scratchpads
Overview
• Hosted websites for taxonomists
• Research & publication platform
• Modular (Drupal) & flexible
• Supports the taxonomic workflow
• Bottom-up design, agile dev.
• Ecosystem of communities (330+)
• 7,350+ users (unpaid) from 2007

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Scratchpad Application Form
Free to any individual or community

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Categories of Scratchpads
Taxa
(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,
genotypic & morphometric datasets, keys, phylogenies)
Conservation Projects Regions Societies

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Flexible Template Site
With easy navigation

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Sustaining Scratchpads
ViBRANT: Building on EDIT & the Scratchpads
“To set up the means, tools and infrastructure to produce a more rational
and a more effective framework for European Biodiversity research”
• A Virtual Research Environment (Scratchpads) where users can safely
store, share and manage their research information.
• Analytical services for users to build identification keys and
phylogenetic trees.
• A publication platform for users to automatically compile taxonomic
manuscripts from their research database.
• A portal for users to centrally access publicly accessible biodiversity
research information and literature.
• Training, support & sociological study, helping research communities to
use these tools and services.
• A standards compliant technical architecture that can be sustained by
the biodiversity research community.

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ViBRANT logistics
• Starts December 2010 (36 months)
• Project website (http://vbrant.eu)
• Virtual Research Communities, CP-CSA, EU FP7
• !6.2M Euros (EU Contribution !4.75M)
• 17 Partners in 9 countries, 603 person months
Collaboration…
• ESFRI Projects: LifeWatch, ELIXIR & EMBRC
• GBIF - controlled vocabularies, nodes & observational data recording
• PESI, 4D4Life & related EU projects
• Encyclopedia of Life, Barcode of Life & Biodiversity Heritage Library
• South African National Biodiversity Institute & Atlas of living Australia

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Scratchpad
Technical
Overview

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Scratchpad management
Scalable & sustainable technology
Hardware, software & user support
One virtual machine, open-source, self-archiving, backed-up, multi-site configuration
(easy to move & upgrade, secure & reliable, low admin., low marginal costs)

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Scratchpad Developers Site
http://dev.scratchpads.eu/

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Scratchpad
Functionality
Summary

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Taxonomy
Taxonomy import,
management and
navigation

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Bibliographic data
Reference manager /
Endnote support for
bibliographies

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Images
Image galleries,
image upload &
annotation

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Character Matricies
Molecular & morphological character matricies
(discrete, morphometric and text characters)

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Mapping
• Point & TDWG region maps
• Flexible polygon maps & annotations
• GBIF point imports
• Edit point location & metadata

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Specimens & locations
Specimen & location
records (DwC)

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Pages, Forums, Blogs

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Mass Import
Import from Excel file to any content type

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Administration

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Putting it
all together
- an example site

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Scratchpad structure
list view
Content types
image biblio page
Taxonomy
taxon page view
term 1
term 2
custom view
node view
term 3

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Home page

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Scratchpad 2 faceted search
• Rapid content discovery
• Systematic browsing
• Content specific facet
display (e.g. biblo, media)
• Slickgrid filters for other
content types

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Scratchpad 2 multimedia gallery
• New look
• Video support
• Faceted search & browse
• Embed YouTube &
Vimeo

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Scratchpad 2 taxon pages
• Easy publishing to EOL
• Better content control
• Direct editing
• Parent-child data inheritance
• Inspired by Natural History Guides

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Scratchpad 2 “publication” options
Taxon descriptions
• Manuscripts from Scratchpads to ZooKeys & PhytoKeys
• Produced directly from the database
• Three exemplar papers produced via SP1
• Comprehensive new data structure in SP2
1. Define the 2. Enter 3. Select taxa 4. Organise 5. Submit to
publication metadata & content manuscript journal

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User Support

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Getting help
http://scratchpads.eu/help

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The Sandbox

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Built in help, the FAQ & issues queue