Sharing, linking and publishing biodiversity data the ViBRANT way

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



• Hosted websites for biodiversity data

• Virtual research & publication platform

• Completely open access & open source

• Modular & flexible

What are Scratchpads?



• 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!



How are Scratchpads funded?

2007 2011 2014


&



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

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300400

Scratchpadsbiodiversity online



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



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



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



http://www.comber.hcmr.gr



Oxford Batch Operations Enginehttps://oboe.oerc.ox.ac.uk/



BDJThe Biodiversity Data Journal

Making small data big!



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



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



Thank you for yourattention.

Any questionse-mail: [email protected]

e-mail: [email protected]

http://vbrant.eu http://scratchpads.eu

Sharing, linking and publishing biodiversity data the ViBRANT way

Technology

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