Scratchpad virtualresearch environments:
sharing, linking and publishingbiodiversity data the ViBRANT way
Vince Smith1, Dave Roberts1 & Lyubomir Penev2
1. Natural History Museum, London2. Pensoft Publishers, Sofia, Bulgaria
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
Our informatics grand challenge…
Cyndy Parr, Rob Guralnick, Nico Cellinese and Rod Page. TREE. doi:10.1016/j.tree.2011.11.001
This requires data, information & knowledge to be…
• Digital Not printed paper
• Openly accessible Not behind barriers
• Linked-up Not in silos
“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”
• 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…
Most of our output is not digital, open or linked
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.
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Magic
Your data Your web site
A website for you & your community
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
• Hosted websites for biodiversity data
• Virtual research & publication platform
• Completely open access & open source
• Modular & flexible
What are Scratchpads?
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
• A single biodiversity database
• Restricted thematically, geographically or taxonomically
• A tool just for taxonomists
• Owned or controlled by anyone other than the data creator
What Scratchpads are not!
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
How are Scratchpads funded?
2007 2011 2014
Virtual BiodiversityViBRANT
&
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Taxonomy & LiteratureLice, mosquitos, freeloader flies, ...
(rapid upload and management of names, synonyms & bibliographic data)
Freeloader Flies, fungus gnats, ...(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)
Taxon descriptions & Publications
European Mosquito Bulletin, Phasmid Studies, ...(submission, review & dissemination of articles)
eJournals
Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)
Characters, Phylogeny & Specimens
Image GalleriesDragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...
(rapid upload, annotation & display of images)
ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...(space for data collection, services, discussion & organisation)
Societies, Organisations & Projects
SitesUsers
2007 2008 2009 2010 2011 2012
Active Users
Site
s
Use
rs
ViBRANTScratchpads 2
500
1000
2000
3000
4000500060007000
20
50
100
200
300400
Scratchpadsbiodiversity online
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
ViBRANT Goals
VisionConnecting the people, data & science of biodiversity
PositionOpen & sustainable development of a federated network of biodiversity informatics infrastructures
MissionFacilitate the mobalisation, sharing, reuse and publication of biodiversity data
http://vbrant.eu
ScratchpadsVirtual Research
Environment
Bioclimaticmodelling
Manuscript publishing
Sustainability
Data mining
Citizen science
Field recording
Sociology
Support services
Training& outreach
Data standards
Visualisation
Controlled vocabulary
Data aggregation
GBIF integration
Scratchpad hosting
Software inte-gration
Matrix data editor
Data publishing
Communal literature
Literature mark up
Phylogeny tools
Identification tools
NetworkingTraining
StandardsMobilisation
ServiceData
Publishing
ResearchArchitecture
Literature
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Nexus
DwCA
CSV/tab
Newick
EoL Transfer schema (SPM) XML
SDD, Lucid, Nexus
RDF
Taxonomic Concept Schema XML
Excel file
CSV, XLS, Microsoft Word .DOC, TXT
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
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
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
http://www.comber.hcmr.gr
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Oxford Batch Operations Enginehttps://oboe.oerc.ox.ac.uk/
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
BDJThe Biodiversity Data Journal
Making small data big!
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
B iodiversity D ata Journal
1t2011
ISSN 1314-2828 (online) ISSN 1314-2836 (print)
Launched to accelerate biodiversity data journal
http://www.pensoft.net/biodiversitydata
A peer-reviewed open-access journal
Editor-in-Chief: VINCENT SMITH Natural History Museum, London, UK
Plazi
I . P . N . I
1. Define the publication
2. Enter metadata
3. Select taxa & content
4. Organise manuscript
5. Submit to journal
Articles
Bibliographies
Occurrence
Taxon treatments
Taxon names
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
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
Virtual BiodiversityViBRANT
-infrastructureSEVENTH FRAMEWORK PROGRAMME
Thank you for yourattention.
Any questionse-mail: [email protected]
e-mail: [email protected]
http://vbrant.eu http://scratchpads.eu
Top Related