This document discusses scratchpad virtual research environments for sharing, linking, and publishing biodiversity data. It notes that most biodiversity data like new species descriptions, nomenclatural acts, phylogenies, taxon sequences, and literature are currently generated in small communities for local projects and are often not digital, open, or linked. Scratchpads are presented as a solution, providing hosted websites for biodiversity data, serving as a virtual research and publication platform that is open access, open source, modular, and flexible. Funding has come from the ViBRANT project as well as growth in sites, users, and features offered over time.

1. Scratchpad virtual
research environments:
sharing, linking and publishing
biodiversity data the ViBRANT way
Vince Smith1, Dave Roberts1 & Lyubomir Penev2
1. Natural History Museum, London
2. Pensoft Publishers, Sofia, Bulgaria

2. Our informatics grand challenge…
“Link together evolutionary
data… by developing
analytical tools and proper
documentation and then
use this framework to
conduct comparative
analyses, studies of
evolutionary process and
biodiversity analyses”
Cyndy Parr, Rob Guralnick, Nico
Cellinese and Rod Page. TREE.
doi:10.1016/j.tree.2011.11.001

3. Our informatics grand challenge…
“Link together evolutionary This requires data, information
data… by developing & knowledge to be…
analytical tools and proper
documentation and then • Digital
use this framework to Not printed paper
conduct comparative • Openly accessible
analyses, studies of
evolutionary process and Not behind barriers
biodiversity analyses” • Linked-up
Not in silos
Cyndy Parr, Rob Guralnick, Nico
Cellinese and Rod Page. TREE.
doi:10.1016/j.tree.2011.11.001

4. Most of our output is not digital, open or linked
• 15-20k new spp. described annually (2M total)1
• 30k nomenclatural acts (12M total) 1
• 20k phylogenies (750k total)2
• 31k taxa sequenced (360k taxa total)3
• 800k BioMed papers (40M total pp. of taxonomy) 4
• Countless specimens, images, maps, keys…
Typically generated by small
communities for “local” research
projects
Figures from 1) Zhang, Zootaxa 2011 4, 1-4; 2) Web-of-Science; 3) Genbank and 4) PubMed.

5. ViBRANT
Virtual Biodiversity
A website for you & your community
Magic
Your data Your web site
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

6. ViBRANT
Virtual Biodiversity
What are Scratchpads?
• Hosted websites for biodiversity data
• Virtual research & publication platform
• Completely open access & open source
• Modular & flexible
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

7. ViBRANT
Virtual Biodiversity
What Scratchpads are not!
• A single biodiversity database
• Restricted thematically, geographically or taxonomically
• A tool just for taxonomists
• Owned or controlled by anyone other than the data creator
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

8. ViBRANT
Virtual Biodiversity
How are Scratchpads funded?
2007 2011 2014
ViBRANT
Virtual Biodiversity
&
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

9. ViBRANT
Virtual Biodiversity
Taxonomy & Literature
Lice, mosquitos, freeloader flies, ...
Scratchpads Characters, Phylogeny & Specimens
Termites, bryozoa, ...
(character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)
biodiversity online
(rapid upload and management of names, synonyms & bibliographic data)
7000
6000
Sites
5000
Users 4000
400
300
Active Users
3000
200
2000
100
Taxon descriptions & Publications Image Galleries
Freeloader Flies, fungus gnats, ...
1000 Dragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...
(rapid upload, annotation & display of images)
(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)
50
500
20
Users
2007 2008 2009 2010 2011 2012
Sites
ViBRANT
Scratchpads 2
eJournals Societies, Organisations & Projects
European Mosquito Bulletin, Phasmid Studies, ... ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...
(submission, review & dissemination of articles) (space for data collection, services, discussion & organisation)
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

10. ViBRANT
Virtual Biodiversity
Training Data
ViBRANT Goals & outreach standards
Support Controlled
services vocabulary
Vision Networking
Connecting the people, data & science of Sociology
Training
Standards
Data
aggregation
Mobilisation
biodiversity GBIF
Field
recording integration
Citizen Visualisation
Position science
Scratchpads
Open & sustainable development of a Virtual Research
Environment
federated network of biodiversity Phylogeny
tools
Scratchpad
hosting
informatics infrastructures
Bioclimatic Software inte-
modelling gration
Mission Identification Sustainability
tools
Facilitate the mobalisation, sharing, Matrix data
editor
Communal
literature
reuse and publication of biodiversity data
Data Literature
publishing Service Research mark up
Data Architecture
Publishing Literature
http://vbrant.eu Manuscript
publishing
Data mining
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

11. ViBRANT
Virtual Biodiversity
Taxonomic Concept Nexus
Schema XML Newick
CSV/tab Excel file
EoL Transfer schema (SPM) XML
SDD, Lucid, CSV, XLS,
DwCA RDF
Nexus Microsoft Word
.DOC, TXT
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

12. ViBRANT
Virtual Biodiversity
What can Scratchpads do?
• Taxon pages (generated from tagged content)
• Distribution maps (from specimens and TDWG regional distributions - Brummitt, 2001)
• Specimen records
• Bibliography management
• Images, video and sound (bulk import)
• Excel spreadsheet import
• Tabular data editing & Character matrixes
• Custom content
• User management
• Custom webforms
• Analytics
• Darwin Core Archive export (links to eMonocot Portal and EOL)
• EOL data import (taxonomy, species information)
• GBIF Map integration
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

13. ViBRANT
Virtual Biodiversity
http://www.comber.hcmr.gr
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

14. ViBRANT
Virtual Biodiversity
Oxford Batch Operations Engine
https://oboe.oerc.ox.ac.uk/
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

15. ViBRANT
Virtual Biodiversity
BDJ
The Biodiversity Data Journal
Making small data big!
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

16. ViBRANT
Virtual Biodiversity
ISSN 1314-2828 (online) ISSN 1314-2836 (print)
1. Define the A peer-reviewed open-access journal
publication Biodiversity Articles
D ata Journal
Launched to accelerate biodiversity data journal
Bibliographies
2. Enter
metadata
Occurrence
3. Select taxa Taxon
& content 1t 2011 treatments Plazi
http://www.pensoft.net/biodiversitydata
4. Organise Taxon
manuscript Editor-in-Chief: VINCENT SMITH
Natural History Museum, London, UK
names
5. Submit to
journal
I . P . N . I
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

17. ViBRANT
Virtual Biodiversity
Acknowledgements
• Scratchpad technical development
- Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton
• Scratchpad outreach
- Laurence Livermore & 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
SEVENTH FRAMEWORK
PROGRAMME -infrastructure

18. ViBRANT
Virtual Biodiversity
Thank you for your
attention.
Any questions
e-mail: enquiries@vbrant.eu
e-mail: scratchpad@nhm.ac.uk
http://vbrant.eu http://scratchpads.eu
SEVENTH FRAMEWORK
PROGRAMME -infrastructure