Warwick 2003

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BiodiversityWorldthe biologists goals
The University of ReadingFrank Bisby, Alistair
Culham, Neil Caithness, Tim Sutton, Peter Brewer,
Chris Yesson Cardiff UniversityAlec Gray, Andrew
Jones, Richard White, Nick Fiddian, Xuebiao Xu,
Mikhaila Burgess, Jaspreet Singh Pahwa The
Natural History MuseumMalcolm Scoble, Paul
Williams, Shonil Bhagwat Bristol UniversityPaul
Valdes (The University of Southampton)
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Major challenges in Biodiversity Science

• How to access Global Biodiversity?
• To see and aggregate data from all round the
  world
• To synthesise a global view
• To move from description to real analysis
• Ultimately to bring the totality onto the
  Internet at a level of abstraction above that
  achieved by individual travel and fieldwork
• What GBIF calls Digital Biodiversity Science

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Major challenges in Biodiversity Science

• First steps towards a Systems Biology for the
  behaviour of global biodiversity
• To access an aggregated and synthesised view of
  the factual base
• To build hypotheses with a sound basis
• To model outcomes based on the hypotheses
• To test the modelled outcomes

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Major challenges in Biodiversity Science

• To a large extent these challenges are convergent
  with the goals of the UKe-Science Initiative
• indeed, it has been said that analysing global
  biodiversity is one of the clearest application
  areas
• e-Science is about global collaboration in key
  areas of science, and the next generation of
  infrastructure that will enable it (John Taylor,
  02)
• We certainly qualify as e-Science
• We certainly need distributed computing, possibly
  combining needs for the GRID and for the
  Semantic Web.

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Our Vision for the BDWorld GRID

• a distributed problem-solving environment
• giving access to a wide array of the worlds data
  sources and analytical tools
• providing an integrated and flexible environment
  for analysis of global scale patterns in
  biodiversity

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Our Vision for the BDWorld GRID

• And suitable for addressing some difficult
  Biodiversity questions
• - where might a species be expected to occur,
  under past, present, or predicted climatic
  conditions?
• - where should conservation efforts be
  concentrated?
• - to what extent is biogeography reflected in
  phylogeny?

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What are the technical goals of BDWorld?

• Extensible problem solving environment for global
  biodiversity analysis
• Employ GRID technology because
• (i) Distributed computing
• (ii) Distributed resources
• (iii) Semantic mediation
• Resource location
• Workflow design validation

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START
Distributed Array of GSDs
Enquiry name(s)
Species 2000 Catalogue of Life
STAGE 1
Returns list of accepted taxa, synonyms and
common names
Enquiry select data for taxon set
Distributed array of thematic data sources
STAGE 2
Return dataset composed ofhomologous responses
from multiple thematic data sources
Analytical Toolbox
Reference to Abiotic datasets
STAGE 3
Presentation and storage of results
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Architecture
BDWorld ResourcesData sets Analytical tools
Resource Wrappers
BGIBDWorld GRID Interface
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Bioclimatic Modelling

• Predicting species distributions under past,
  present and future climate scenarios.
• Models
• GARP (Genetic Algorithms for Rule-set Production)
• CSM (Climate Space Models)
• Bioclim

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Case Study - Leucaena leucocephala

• Leucaena leucocephala (Lam.) De Wit
• Native of Central America
• Widely introduced around the tropics
• Widely utilised around the globe for
• - Wood
• - Forage
• - Soil enrichment and erosion control
• Regarded as an invasive weed in some areas

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Distribution Data

• Area data from ILDIS
• Point data from private databases and herbaria

Point data of Leucaena leucocephala from Hughes
(1998)
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Example of Modelling
Model of Leucaena leucocephala - for
exploring- in which countries may further
introductions be made? - has the species become
invasive by adapting to new niches?- how will
the distribution change under global warming
scenarios?
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Leucaena leucocephala future predictions

• Hadley Circulation Model - HadCM3 IS92a
  ScenarioPopulation rises to 11.3 billion by
  2100 and economic growth averages 2.3 per annum
  between 1990 and 2100 with a mix of conventional
  and renewable energy sources being used. Global
  view

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Workflow Design
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Biodiversity Richness Conservation Evaluation

• Which areas represent an optimal conservation
  area network?
• What compromises can be made in such a selection
  process?

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• Phylogenetic Analysis Biogeography

• Does a combined analysis of climate and character
  data enhance the robustness of a phylogenetic
  analysis?

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A strict consensus of 1024 most parsimonious
trees for Pelargonium
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Some relevant resource types

• Data sources
• Taxonomic Verification and Synonymic Indexing
  Species 2000 ITIS Catalogue of Life
• Species Information Sources (SISs)
• Species geography Species bank databases
• Descriptive data Species bank databases
• Specimen distribution (BioCASE, AVH,
  SpeciesAnalyst, RDG, MBG...DIGIR,ABCD etc)
• Geographical
• Boundaries of geographical political units
• Climate surfaces (Hadley, Paul Valdes'
  Palaeoclimate Data)
• Modelled Climate progressions past and future
• Genetic sequences (EMBL/GenBank, local data)
• Analytic tools
• Biodiversity richness assessment (WorldMap)
• Bioclimatic modelling (Garp, CSM, Bioclim)
• Phylogenetic analysis (Paup, clustalw, etc)

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What does this mean for data management - data
sets?

• Functionality and integrity
• Accurate access by taxonomy
• Synonymic indexing in taxonomic verification
  systems
• Accurate identification and names in other data
  sets
• Accurate access by geographical distribution
• Accurate geospatial data for specimen and
  observational datasets
• Also a role for political units in synthetic
  datasets
• Accurate access via metadata and semantic
  mediation
• Semantic inference using metadata and ontology

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What does this mean for data management - systems?

• Global Connectivity
• Need for physical connectivity
• WWW, GRID, Semantic Web..
• Need for Semantic Standards
• TDWG (IUBS Taxonomic Databases Working Group)
• GBIF
• Need for generic solutions to resource location,
  metadata and packaging of biodiversity objects.
  

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BiodiversityWorldthe biologists goals
The University of ReadingFrank Bisby, Alistair
Culham, Neil Caithness, Tim Sutton, Peter Brewer,
Chris Yesson Cardiff UniversityAlec Gray, Andrew
Jones, Richard White, Nick Fiddian, Xuebiao Xu,
Mikhaila Burgess, Jaspreet Singh Pahwa The
Natural History MuseumMalcolm Scoble, Paul
Williams, Shonil Bhagwat Bristol UniversityPaul
Valdes (The University of Southampton)