ViBRANT Project Overview

Virtual BiodiversityViBRANT

Virtual Biodiversity Research and Access Network for Taxonomy:

Project Overview

Vince SmithNatural History Museum, London

[email protected]

ViBRANTVirtual Biodiversity

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Outline

• Some background / why ViBRANT?

• Goals / what makes ViBRANT different

• What ViBRANT will do

• Logistics & collaboration

• Measures of success

• Longer term vision


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• 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…• 4-8,000 taxonomists• 30-40,000 “pro-amateurs”• Many more citizen scientists?

Our problemThe challenge of 21st Century taxonomy

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A solutionThe transformative role of the internet & the World Wide Web

You arehere

• Built of links• 1 trillion pages• 2 billion users

from Hobbes’ Internet timeline (http://bit.ly/dtBJ2i)

The 1st Internet4-node ARPAnet - 1969

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The web applied to taxonomyBiodiversity informatics

663 projects(Jan. 2011)

TDWG Projects Database

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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

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• Hosted websites for taxonomists• Research & publication platform • Modular (Drupal) & flexible • Supports the taxonomic workflow• 2,500 users (unpaid) from 2007• Ecosystem of communities (~200)

Scratchpadshttp://scratchpads.eu

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Goals of ViBRANT

Connecting people…ViBRANT connects people studying biodiversity regardless of their location. Each community website (Scratchpad) contains tools and services that enable users to study biodiversity in all its different facets.

Connecting data…Information about biodiversity is scattered in a myriad of different places. ViBRANT helps defragment this information providing a window on the natural world that can be filtered according to users needs.

Connecting science…ViBRANT bridges the gap between the producers & consumers of taxonomic information, providing the tools to help explain & predict the distribution of life on Earth.

To set up the means, tools and infrastructure to produce a more rational and a more effective framework for European Biodiversity research.

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What we will do

• 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.

E-Infrastructure products

ViBRANT is primarily a tool, secondarily a data provider

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Creating the best Virtual Research Environmentfor the taxonomic & systematic research community

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

• The Natural History Museum, London (NHM) - Scratchpad VRE development & management

• Hellenic Center for Marine Research, Crete (HCMR) - Extension into ecol.,con. & citizen science, esp. marine biodiversity

• Royal Belgian Institute of Natural Sciences (RBINS) - Training, outreach & community support

• Oxford e-Research Centre (UOXF.E9) - Mol. ID tools, services and data analysis

• Vrije Universiteit Amsterdam (VU) - User studies (sociological studies of user practices)

• Julius Kühn-Institute (JKI) - Data integration via controlled vocabularies & ontologies

• Museum für Naturkunde, Berlin (MFN) - Biodiversity inventorying & monitoring (mobile devices)

• University of Amsterdam (UvA) - Standards development (PESI)

• The Open University (OU) - Data mining and bibliographies (BHL)

• Karlsruher Institut für Technologie (KIT) - Document Markup & natural language text processing

• Vizzuality (Vizz) - Data visualisation & analysis (data layers)

• Pensoft Publishers (PENSOFT) - Push-button manuscript submission from the Scratchpad VRE

• Université Pierre et Marie Curie-Paris 6 (UPMC) - Morphological identification keys and services (Xper2)

• Global Biodiversity Information Facility (GBIF) - Controlled vocab. dev. & userbase expansion via GBIF nodes

• Freie Universität Berlin (BGBM) - Data aggregation portal via CDM

• Université de la Réunion (UdlR) - Mathematics & HCI of taxonomic identification keys

• University of Trieste - Key2Nature integration & outreach

Who is doing it

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What makes ViBRANT different

ViBRANT is driven by its users (old & new)Its is about audiences

Re-writing our deliverables is one of the deliverables!Our work program is flexible

The perpetual beta - like taxonomyViBRANT is agile

We do things simply & cheaply, such that we can maintain themViBRANT is sustainable

ViBRANT is primarily about tools & servicesIts (mostly) not research

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Outline

• Some background / why ViBRANT







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Networking Activities (1,805,885 €)

Service Activities (1,025,578 €)

Research Activities (1,483,411 €)

• WP3. (683,242 €) Training, outreach & community support (4)• WP4. (713,784 €) Standardisation (5)• WP8. (408,859 €) Ecological and conservation data mobilization (5)

• WP5. (755,913 €) Interaction and data services (5)• WP6. (269,665 €) Scholarly Publishing (2)

• WP2. (858,495 €) Technical architecture (2)• WP7. (624,916 €) Biodiversity literature data access & data mining (4)

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• WP1. (435,125 €) Management, coordination & administration (7 partners)

Macro Organisation (CP-CSA)

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SERVICEWP5. Data

WP6. Publishing

WP4. StandardsWP8. Mobilisation

RESEARCHWP2. Architecture

WP7. Literature

NETWORKINGWP3. Training

ViBRANT Project planThe “chromosome”

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ViBRANT logistics• Started 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 (not just EU)…• 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

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Short term success metrics

Networking (tools and collaboration)• How many people are using our tools• How deep is their engagement with these tools• How are these tools changing what they would otherwise do

User engagement as a measure of success*

Services (data & processing data)• How much internal data is being called from outside the system• How much external data is being called from inside the system• How much are our services being used to add value

Research (discovery of new information or approaches)• Traditional academic metrics (publications, presentations, blogs etc)• Uptake within ViBRANT & outside the consortium

both quantitative & qualitative (WP3)*

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Longer term success metrics

Persistence & sustainability• Maintaining what we do (perhaps without money)• If its valued, it will endure• Not everything will persist!

Once ViBRANT project is over

Finding new audiences• ViBRANT is primarily about taxonomy & taxonomists• Engage more people as “taxonomists” (e.g. citizen scientists)• Reach out to other sectors e.g. conservation & ecology

Embed our products outside the consortium• Take up by other initiatives, especially outside the EU• E.g. LifeWatch service centre, GBIF Nodes, publishers, CBoL, EoL

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(My) Longer term vision

Defragmenting our output• Tools that support technical & social workflows of taxonomy• Provide the means to (loosely) aggregate that content

Taxonomy’s three problems, & my view of how we fix them

Speeding up out output• Digitising collections• Increasing our workforce (engaging non-professionals)• Coordinated & standardised programs for new kinds of output

Improved labeling & findability• Simple & persistent identifiers on defined concepts of everything• Simplifying how we define (publish) concepts

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Where taxonomy is nowAnd where we might like to be…

You arehere

• Built of links• 1 trillion pages• 2 billion users

from Hobbes’ Internet timeline (http://bit.ly/dtBJ2i)

The 1st Internet4-node ARPAnet - 1969

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Documents

ViBRANT Project Overview