An introduction to ViBRANT: Virtual Biodiversity Research and Access Network for Taxonomy

1 of 14 Virtual Biodiversity Research and Access Network for Taxonomy ViBRANT INFRA-2010-1.2.3: Virtual Research Communities http://vbrant.eu Currently in “negotiation” Starts 1 Dec. 2010 FP7 - INFRASTRUCTURES - 2010 - 2 CCPCSA

Scratchpads 2 of 14
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

Objectives (in “EU-speak”) 3 of 14
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.
to connect end users of biodiversity data to networks of primary producers or to the most appropriate research facility.
to provide the means for biodiversity researchers to establish and document the state of the art in biodiversity research.
to identify research and development needs and gaps in the provision of support to biodiversity researchers.
to provide an information centre for biodiversity research results and developments.
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…

Practical Objectives - part 1 4 of 14
Inventory the Earth’s species
Document their relationships
“ Publish” & apply these data
Goal… Addressing the challenges of taxonomy
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?

Practical Objectives - part 2 5 of 14 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

17 partners in 9 countries (universities, museums & SMEs) Consortium partners 6 of 14
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 (Xper 2 )
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 R é union (UdlR)
- Mathematics & HCI of taxonomic identification keys
University of Trieste
- Key2Nature integration & outreach

Macro Structure - Delivery Components 7 of 14 Networking (WP3, 4, & 8) Service (WP5 & 6) Research (WP2 & 7)

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)
8 of 14
WP1. (* 424,532 € ) Management, coordination & administration (7 partners)
* Pre-negotiation figures

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
9 of 14

Service Activities
WP5. (1,013,430 €), 5 partners
Interaction and data services
WP6. (268,463 €), 2 partners
Scholarly Publishing
10 of 14

Research Activities 11 of 14
WP2. (908,416 €), 2 partners
Technical architecture
WP7. (644,291 €), 4 partners
Biodiversity literature data access & data mining

Practical issues 12 of 14
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

Value Added (“EU-Speak”) 13 of 14
A direct route by which a wide range of stakeholders can access multi-level biodiversity information and data.
Dramatically increase the efficiency and capacity of European stakeholders to monitor and manage information on ecosystems, biodiversity and natural resources.
Support the emergence of virtual research communities of European and international dimension, providing a framework for uniting national initiatives across the ERA.
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.
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”

Practical Value Added 14 of 14
More reliable (e.g., distribute the servers)
More functional (e.g., phylogenetic & publication services)
Easier to use (better workflows)
Prettier (better graphical design - more intuitive)
More integrated (for data stored inside & outside the Scratchpad framework)
More sustainable (simple administration, distribute developers, development sandbox)
“ making the Scratchpads better”
Easier to compile, manage and reuse your data
Easier to find and reuse other peoples data
Promoting your data inside & outside the taxonomic community
Getting people to work for you (crowdsourcing)
“ making taxonomy better”

Practical Value Added - an example “ get published through your Scratchpad” Write the title & abstract

Practical Value Added - an example “ get published through your Scratchpad” Define who you want to see / coauthor the manuscript

Practical Value Added - an example “ get published through your Scratchpad” Define the structure of the paper

Practical Value Added - an example drag-&-drop the content

Practical Value Added - an example Preview the manuscript

Practical Value Added - an example Submit the manuscript for review (sent as XML)

Practical Value Added - an example Get published after peer review PDF HTML XML

Practical Value Added - an example Zookeys special issue

Questions?

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”

An introduction to ViBRANT: Virtual Biodiversity Research and Access Network for Taxonomy

by Vincent Smith

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