TDWG_ ViBRANT_301013

Virtual BiodiversityViBRANT

SEVENTH FRAMEWORK PROGRAMME -infrastructure

ViBRANT: progress towards an integrated framework

Vince Smith & Dave Roberts


-infrastructureSEVENTH FRAMEWORK PROGRAMME

ViBRANTs contribution

Interoperability, workflows, services, information modeling & user support

17 partners in 9 countries(universities, museums & SMEs)



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



ViBRANT OutputsE-Infrastructure

Products (extra-network activities because of the infrastructure)

• A Virtual Research Environment (Scratchpads) where users can safely store, share and manage data.

• Analytical services for users to build identification keys and phylogenetic trees.• A publication platform for users to automatically compile manuscripts from their research

database.• A portal for users to centrally access publicly accessible biodiversity research

information and literature.• Training, support & sociological study, helping research communities to use these tools

and services.• A standards compliant technical architecture that can be sustained by biodiversity

research community.

• Content: eBooks, eJournals, Con. assessments, flora and faunal studies, long term data repositories, community vocabulariers, id. guides, citizen science projects.

• Code: Drupal modules, OBOE services• New sectors of interest: agriculture, education



Knowledge Organization System GBIF Service migrated to GBIF Secretariat (hosting) TDWD VoMaG task group installed (governance) Species-ID Semantic Media Wiki Integrated with GBIF-KOS system

Scratchpad Common Access pointCDM <–> Scratchpad and CDM <–> Xper2 pipelines Pipelines further defined via DwC-A extensions & SDD

Improved data interfaces & API New vocabularies supported (e.g. Audubon Core) Development of APIs on the CDM

Liaise with major initiatives TDWG, EOL, EU-BON, & LifeWatch



Users

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Tasks

Oxford Batch Operations Engine https://oboe.oerc.ox.ac.uk/



http://biblife.org

more nodes coming soon ....

Citations growing at about 5,000 / month

Currently holds about 210,000 references

http://zoobank.org/RefBankRefBank nodes



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2008 2009 2010 2011 2012

Number of Citations Papers mentioning a Scratchpad Site

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2008 2009 2010 2011 2012

Number of Citations Papers mentioning the Scratchpad Project

600

SitesUsers

2007 2008 2009 2010 2011 2012 2013

Active Users

Site

s

Use

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ViBRANT Scratchpads 2

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irtual Biodiversity

http://www.comber.hcmr.gr



An example site at http://nptstartup.gbif.org

The code is available at https://git.scratchpads.eu/git/scratchpads-2.0.git as a branch “gbif-npt-startup”

Import the checklist requested separately by writing to [email protected]

Finish the setup with initial news and textual contents

The target audience:

The approach:

The result:

Nodes that have limited web presence.

Using the country checklist generated from the GBIF mediated data to dynamically retrieve biodiversity information from GBIF & EOL.

A web portal that is easy to set up, customise, and enables joint development.

http://links.gbif.org/npt



Plazi

I . P . N . I

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All Author Title

Start a manuscript

How it works

Articles About

Journal features

Focus and Scope

Globally unique innovations

Criteria for publication

Peer review

For authors

Data publication

Publication fees

Licenses and Copyright

Frequently Asked Questions(FAQ)

Contacts

Editorial team

Follow us

Most visited papers

This work is licensed under theCreative Commons Attribution 3.0

(CC-BY).

Making “small” data big

No lower/upper limit ofmanuscript size

Publish all kinds of biodiversityrelated data

Reduced page chargesaffordable by all

More than just datajournal!

Integrated text and datapublishing

Completely online revisions andediting

Community ownership of data

Community peer-review

7 weeks from submission todecision

3 days from acceptance topublication

Public peer-review on author’schoice

Free of charge in launch phase

Resolving the publishingResolving the publishingResolving the publishingbottleneck forbiodiversity

Science is a combination of gatheringScience is a combination of gatheringfacts and making theories; neither canfacts and making theories; neither canprogress on its own. In the history ofprogress on its own. In the history ofscience, the laborious accumulation ofscience, the laborious accumulation offacts is the dominant mode, not afacts is the dominant mode, not anovelty.novelty.

Peter Norvig

Citable publication Increase collaboration

Re-use and multiply effect Establish scientific priority

Link data to a biggernetwork

Respond to fundingrequirements

Why publish my data?Why publish my data?

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

PWT or Scratchpads

Editor-in-Chief: VINCENT SMITHNatural History Museum, London, UK



Lessons

Market your products!!!

Deliver an immediate benefit to users

Have a Champion

Be agile

Users need

TDWG_ ViBRANT_301013

Technology

infrastructure content

framework programme0https

gbif mediated data

biodiversity information

gbif eol

research communities

research database

branch gbifnpt