ViBRANT 1 of 14

Virtual Biodiversity Research and Access Network for

TaxonomyViBRANT

FP7 - INFRASTRUCTURES - 2010 - 2CCPCSA

INFRA-2010-1.2.3: Virtual Research Communities

http://vbrant.eu

Currently in “negotiation”Starts 1 Dec. 2010

ViBRANT

Scratchpads

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• Hosted websites for taxonomists• Research & publication platform • Modular (Drupal) & flexible • Supports the taxonomic workflow• Bottom-up design, agile dev.• Ecosystem of communities (150+)• 2,000+ users (unpaid) from 2007• ViBRANT follow on, €4.75M

http://scratchpads.eu

ViBRANT

Objectives (in “EU-speak”)

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1. to provide sustainable services in data mobilisation, integration, publication, sharing,

use and reuse to research communities, biodiversity and conservation agencies,

national and regional authorities and the European public.

2. to connect end users of biodiversity data to networks of primary producers or to the

most appropriate research facility.

3. to provide the means for biodiversity researchers to establish and document the state

of the art in biodiversity research.

4. to identify research and development needs and gaps in the provision of support to

biodiversity researchers.

5. to provide an information centre for biodiversity research results and developments.

6. to defragment access to biodiversity data through data mining biodiversity literature.

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

Operational consortium objectives are…

ViBRANT

Practical Objectives - part 1

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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…• 4-6,000 taxonomists• 30-40,000 “pro-amateurs”• Many more citizen scientists?

Addressing the challenges of taxonomy

ViBRANT

Practical Objectives - part 2

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Addressing the challenges of biodiversity informatics

“…the field [of biodiversity informatics] appears to be growing in a void of overarching, motivating questions, effectively making it a set of technologies in search of questions to address.”

Peterson et al, Syst. & Biodiv. 2010

ViBRANT

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

Consortium partners

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• 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

ViBRANT

Macro Structure- Delivery Components

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Networking(WP3, 4, & 8)

Service(WP5 & 6)

Research(WP2 & 7)

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CP-CSA Split & Macro Organisation

Networking Activities (*1,932,641 €)

Service Activities (*1,281,893 €)

Research Activities (*1,552,707 €)

• WP3. (713,415 €) Training, outreach & community support (4)• WP4. (796,278 €) Standardisation (5)• WP8. (422,948 €) Ecological and conservation data mobilization (5)

• WP5. (1,013,430 €) Interaction and data services (5)• WP6. (268,463 €) Scholarly Publishing (2)

• WP2. (908,416 €) Technical architecture (2)• WP7. (644,291 €) Biodiversity literature data access & data mining (4)

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• WP1. (*424,532 €) Management, coordination & administration (7 partners)

* Pre-negotiation figures

ViBRANT

Networking Activities• WP3. (713,415 €), 4 partners Training, outreach & community support

• WP4. (796,278 €), 5 partners Standardisation

• WP8. (422,948 €), 5 partners Ecological and conservation data mobilization

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ViBRANT

Networking Activities• WP3. (713,415 €), 4 partners Training, outreach & community support

• WP4. (796,278 €), 5 partners Standardisation

• WP8. (422,948 €), 5 partners Ecological and conservation data mobilization

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ViBRANT

Networking Activities• WP3. (713,415 €), 4 partners Training, outreach & community support

• WP4. (796,278 €), 5 partners Standardisation

• WP8. (422,948 €), 5 partners Ecological and conservation data mobilization

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ViBRANT

Service Activities• WP5. (1,013,430 €), 5 partners Interaction and data services

• WP6. (268,463 €), 2 partners Scholarly Publishing

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ViBRANT

Service Activities• WP5. (1,013,430 €), 5 partners Interaction and data services

• WP6. (268,463 €), 2 partners Scholarly Publishing

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ViBRANT

Research Activities

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• WP2. (908,416 €), 2 partners Technical architecture

• WP7. (644,291 €), 4 partners Biodiversity literature data access & data mining

ViBRANT

Research Activities

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• WP2. (908,416 €), 2 partners Technical architecture

• WP7. (644,291 €), 4 partners Biodiversity literature data access & data mining

ViBRANT

Practical issues

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• Starts 1 Dec. 2010 - finishes 30 Nov. 2013• Kick off meeting - 20-21st Jan., 2011, Paris• Maximise synergies with EDIT (closes 28 Feb. 2011)• Agile project development (we make it up as we go along)• Metrics of success are user engagement (linear growth)

Key facts

• Project lead (VS coordinator, DR project manager & WP1 lead, SR WP2 lead)• Running WP1+2• 2 developer posts (inc. SR), 1 admin post (GR), +VS, DR, CL, SK (+ eMonocot posts)• Promoting a shared vision for the project• Sustainability beyond ViBRANT

NHM Role

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Value Added (“EU-Speak”)

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1. A direct route by which a wide range of stakeholders can access multi-level biodiversity

information and data.

2. Dramatically increase the efficiency and capacity of European stakeholders to monitor

and manage information on ecosystems, biodiversity and natural resources.

3. Support the emergence of virtual research communities of European and international

dimension, providing a framework for uniting national initiatives across the ERA.

4. Provide data management, analysis and publication tools in a self-governed, standards

based framework, ensuring that data can be integrated into the biodiversity information

and support services needed by society.

5. Has to potential to deliver social change that goes far beyond earlier “name and fact

recording” initiatives (which are the foundation of this infrastructure).

“defragment & integrate the stakeholders of biodiversity data”

ViBRANT

Practical Value Added

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1. More reliable (e.g., distribute the servers)

2. More functional (e.g., phylogenetic & publication services)

3. Easier to use (better workflows)

4. Prettier (better graphical design - more intuitive)

5. More integrated (for data stored inside & outside the Scratchpad framework)

6. More sustainable (simple administration, distribute developers, development sandbox)

“making the Scratchpads better”

1. Easier to compile, manage and reuse your data

2. Easier to find and reuse other peoples data

3. Promoting your data inside & outside the taxonomic community

4. Getting people to work for you (crowdsourcing)

“making taxonomy better”

ViBRANT

Practical Value Added - an example“get published through your Scratchpad”

Write the title & abstract

ViBRANT

Practical Value Added - an example“get published through your Scratchpad”

Define who you want to see / coauthor the manuscript

ViBRANT

Practical Value Added - an example“get published through your Scratchpad”

Define the structure of the paper

ViBRANT

Practical Value Added - an example

drag-&-drop the content

ViBRANT

Practical Value Added - an example

Preview the manuscript

ViBRANT

Practical Value Added - an example

Submit the manuscript for review (sent as XML)

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Practical Value Added - an example

Get published after peer review

PD

FH

TM

LX

ML

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Practical Value Added - an example

Zookeys special issue

Questions?

ViBRANT

Practical Value Added - an example

• 15 genera, 55 species• Lower Cretaceous – Recent• Types are located• Rare in collections – often

overlooked• Diversity should be higher

EDIT IRG: “Streamlining Fungus Gnat taxonomy”