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

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Given at an Entomology departmental meeting, at the Natural History Museum, London, UK. July 9th, 2010.

Given at an Entomology departmental meeting, at the Natural History Museum, London, UK. July 9th, 2010.

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  • In negotiation (administrative dotting on ‘I’s and crossing of ‘t’s). Funded from FP7 Infratructures. Starts 1 Dec. 2010.
  • Builds on the Scratchpad project, funded under EDIT.
  • Overall objectives (written in EU-speak).
  • Objectives translated into English. 2 parts. Part 1 - Address the problems of taxonomy.
  • Part 2. Address the problems of biodiversity informatics. This is a your field, growing up in a vacume, isolated from practical scientific questions. Lots of Whizz-bang tools, but often with little practical use. ViBRANT’S goal is to bridge the gap between the informatics and the user community. Its about making technology usable and useful for taxonomists in the first instance, and secondly to make taxonomic data more useful and usable.
  • These are the people involved. As far-flung as the Reunion Islands.
  • What we are going to do (as a Chromosome) I’ll break this down later). Two key points. One - all roads lead to the Scratchpads to deliver and “integrated user experience” - a one stop shop for all the products of ViBRANT. Two - work is broken down into a triad of components - networking, service and research.
  • Here is the breakdown in a little more details. Activities are split into workpackages divided up under the banner of networking, service and research. Funds are relatively evenly split between these activities. In practical terms let me go through some of the highlights of each workpackage…
  • WP3. Training courses, online support, FAQ’s, engagiung with user communities; A new feedback mechanism (tightly integrated into the system - this will replace Uservoice).; Sociological user study, to differentiate what users tell us they are doing, from what they are actually doing.

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

  • 1. 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
  • 2. 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
  • 3. 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…
  • 4. 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?
  • 5. 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
  • 6. 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
  • 7. Macro Structure - Delivery Components 7 of 14 Networking (WP3, 4, & 8) Service (WP5 & 6) Research (WP2 & 7)
  • 8. 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
  • 9. 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
  • 10. 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
  • 11. 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
  • 12. Service Activities
    • WP5. (1,013,430 €), 5 partners
    • Interaction and data services
    • WP6. (268,463 €), 2 partners
    • Scholarly Publishing
    10 of 14
  • 13. Service Activities
    • WP5. (1,013,430 €), 5 partners
    • Interaction and data services
    • WP6. (268,463 €), 2 partners
    • Scholarly Publishing
    10 of 14
  • 14. Research Activities 11 of 14
    • WP2. (908,416 €), 2 partners
    • Technical architecture
    • WP7. (644,291 €), 4 partners
    • Biodiversity literature data access & data mining
  • 15. Research Activities 11 of 14
    • WP2. (908,416 €), 2 partners
    • Technical architecture
    • WP7. (644,291 €), 4 partners
    • Biodiversity literature data access & data mining
  • 16. 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
  • 17. 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”
  • 18. 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”
  • 19. Practical Value Added - an example “ get published through your Scratchpad” Write the title & abstract
  • 20. Practical Value Added - an example “ get published through your Scratchpad” Define who you want to see / coauthor the manuscript
  • 21. Practical Value Added - an example “ get published through your Scratchpad” Define the structure of the paper
  • 22. Practical Value Added - an example drag-&-drop the content
  • 23. Practical Value Added - an example Preview the manuscript
  • 24. Practical Value Added - an example Submit the manuscript for review (sent as XML)
  • 25. Practical Value Added - an example Get published after peer review PDF HTML XML
  • 26. Practical Value Added - an example Zookeys special issue
  • 27. Questions?
  • 28.  
  • 29. 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”