swiss orchid foundation scratchpads and vibrant overview

Ed BakerNatural History Museum, London, UK

Virtual BiodiversityViBRANT

Why Scratchpads?


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


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


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


Goal

“a scholarly communication systemthat is intertwined with the pursuit ofnatural history, rather than an after-

thought or annex”


Your data1

“Published” & reviewedon your site

3Uploaded &

tagged

2

Fast Intuitive Fit for use

What is a Scratchpad?A website for you & your community


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


Scratchpad Application FormFree to any individual or community


Categories of Scratchpads

Taxa(Classifications, taxon profiles, specimens, literature, images, maps, phenotypic,

genotypic & morphometric datasets, keys, phylogenies)

ProjectsConservation Regions Societies


Flexible Template SiteWith easy navigation


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.


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


ScratchpadTechnicalOverview


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


Scratchpad Developers Site

http://dev.scratchpads.eu/


ScratchpadFunctionality

Summary


Taxonomy

Taxonomy import,management and

navigation


Bibliographic data

Reference manager /Endnote support forbibliographies


Images

Image galleries,image upload &annotation


Character Matricies

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


Mapping

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


Specimens & locations

Specimen & locationrecords (DwC)


Pages, Forums, Blogs


Mass Import

Import from Excel file to any content type


Administration


Putting itall together

- an example site


Scratchpad structure

Taxonomybiblio

Content typesimage page

taxon page view

term 1

term 2

term 3node view

list view

custom view


Home page


Scratchpad 2 faceted search

• Rapid content discovery• Systematic browsing• Content specific facet

display (e.g. biblo, media)• Slickgrid filters for other

content types


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

Vimeo


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


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


User Support


Getting help

http://scratchpads.eu/help


The Sandbox


Built in help, the FAQ & issues queue

swiss orchid foundation scratchpads and vibrant overview

Technology

virtual research communities

research database

data data set

users unpaid

local scientists

eu fp7

eu fp6

example site