Upload
edward-baker
View
466
Download
1
Tags:
Embed Size (px)
Citation preview
Ed BakerNatural History Museum, London, UK
Virtual BiodiversityViBRANT
Why Scratchpads?
Virtual BiodiversityViBRANT
21st Century taxonomy
• Inventory the Earth’s species• Document their relationships• “Publish” & apply these data
Goal…
• 1.8 M described spp. (10M names)• 300M pages (over last 250 years)• 1.5-3B specimens
Data set…
People…• 4-6,000 scientists• 30-40,000 “pro-amateurs”• Many more citizen scientists?
The challenge for modern taxonomists
Virtual BiodiversityViBRANT
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
Virtual BiodiversityViBRANT
Towards a solutionThe 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
Virtual BiodiversityViBRANT
Goal
“a scholarly communication systemthat is intertwined with the pursuit ofnatural history, rather than an after-
thought or annex”
Virtual BiodiversityViBRANT
Your data1
“Published” & reviewedon your site
3Uploaded &
tagged
2
Fast Intuitive Fit for use
What is a Scratchpad?A website for you & your community
Virtual BiodiversityViBRANT
ScratchpadsOverview
• 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
Virtual BiodiversityViBRANT
Scratchpad Application FormFree to any individual or community
Virtual BiodiversityViBRANT
Categories of Scratchpads
Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,
genotypic & morphometric datasets, keys, phylogenies)
ProjectsConservation Regions Societies
Virtual BiodiversityViBRANT
Flexible Template SiteWith easy navigation
Virtual BiodiversityViBRANT
Virtual BiodiversityViBRANT
Sustaining ScratchpadsViBRANT: Building on EDIT & the Scratchpads
“To set up the means, tools and infrastructure to produce a more rationaland a more effective framework for European Biodiversity research”
• A Virtual Research Environment (Scratchpads) where users can safelystore, share and manage their research information.
• Analytical services for users to build identification keys andphylogenetic trees.
• A publication platform for users to automatically compile taxonomicmanuscripts from their research database.
• A portal for users to centrally access publicly accessible biodiversityresearch information and literature.
• Training, support & sociological study, helping research communities touse these tools and services.
• A standards compliant technical architecture that can be sustained bythe biodiversity research community.
Virtual BiodiversityViBRANT
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
Virtual BiodiversityViBRANT
ScratchpadTechnicalOverview
Virtual BiodiversityViBRANT
Scratchpad managementScalable & sustainable technology
One virtual machine, open-source, self-archiving, backed-up, multi-site configuration(easy to move & upgrade, secure & reliable, low admin., low marginal costs)
Hardware, software & user support
Virtual BiodiversityViBRANT
Scratchpad Developers Site
http://dev.scratchpads.eu/
Virtual BiodiversityViBRANT
ScratchpadFunctionality
Summary
Virtual BiodiversityViBRANT
Taxonomy
Taxonomy import,management and
navigation
Virtual BiodiversityViBRANT
Bibliographic data
Reference manager /Endnote support forbibliographies
Virtual BiodiversityViBRANT
Images
Image galleries,image upload &annotation
Virtual BiodiversityViBRANT
Character Matricies
Molecular & morphological character matricies(discrete, morphometric and text characters)
Virtual BiodiversityViBRANT
Mapping
• Point & TDWG region maps• Flexible polygon maps & annotations• GBIF point imports• Edit point location & metadata
Virtual BiodiversityViBRANT
Specimens & locations
Specimen & locationrecords (DwC)
Virtual BiodiversityViBRANT
Pages, Forums, Blogs
Virtual BiodiversityViBRANT
Mass Import
Import from Excel file to any content type
Virtual BiodiversityViBRANT
Administration
Virtual BiodiversityViBRANT
Putting itall together
- an example site
Virtual BiodiversityViBRANT
Scratchpad structure
Taxonomybiblio
Content typesimage page
taxon page view
term 1
term 2
term 3node view
list view
custom view
Virtual BiodiversityViBRANT
Home page
Virtual BiodiversityViBRANT
Scratchpad 2 faceted search
• Rapid content discovery• Systematic browsing• Content specific facet
display (e.g. biblo, media)• Slickgrid filters for other
content types
Virtual BiodiversityViBRANT
Scratchpad 2 multimedia gallery• New look• Video support• Faceted search & browse• Embed YouTube &
Vimeo
Virtual BiodiversityViBRANT
Scratchpad 2 taxon pages• Easy publishing to EOL• Better content control• Direct editing• Parent-child data inheritance• Inspired by Natural History Guides
Virtual BiodiversityViBRANT
Scratchpad 2 “publication” options
• Manuscripts from Scratchpads to ZooKeys & PhytoKeys• Produced directly from the database• Three exemplar papers produced via SP1• Comprehensive new data structure in SP2
Taxon descriptions
1. Define thepublication
2. Entermetadata
3. Select taxa& content
4. Organisemanuscript
5. Submit tojournal
Virtual BiodiversityViBRANT
User Support
Virtual BiodiversityViBRANT
Getting help
http://scratchpads.eu/help
Virtual BiodiversityViBRANT
The Sandbox
Virtual BiodiversityViBRANT
Built in help, the FAQ & issues queue