The University of Reading Frank Bisby, Alistair Culham, Neil Caithness, Tim Sutton, Peter Brewer, Chris Yesson Cardiff University Alec Gray, Andrew Jones, Richard White, Nick Fiddian, Xuebiao Xu, Mikhaila Burgess, Jaspreet Singh Pahwa The Natural History Museum Malcolm Scoble, Paul Williams, Shonil Bhagwat Bristol University Paul Valdes (The University of Southampton) BiodiversityWorld the biologist’s goals

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’

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

Major challenges in Biodiversity Science To a large extent these challenges are convergent with the goals of the UK e-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.

Our Vision for the BDWorld GRID: a distributed problem-solving environment giving access to a wide array of the world’s data sources and analytical tools providing an integrated and flexible environment for analysis of global scale patterns in biodiversity

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?

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

START STAGE 1 STAGE 2 STAGE 3 Analytical Toolbox Reference to Abiotic datasets Species 2000 Catalogue of Life Distributed Array of GSD’s Enquiry name(s) Returns list of accepted taxa, synonyms and common names Distributed array of thematic data sources Enquiry: select ‘data’ for ‘taxon set’ Return dataset composed of homologous responses from multiple thematic data sources Presentation and storage of results

Architecture GRID BGI BDWorld GRID Interface Resource Wrappers BDWorld Resources Data sets & Analytical tools

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

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 Case Study - Leucaena leucocephala

Distribution Data Area data from ILDIS Point data from private databases and herbaria Point data of Leucaena leucocephala from Hughes (1998) October 2001

Example of Modelling October 2001 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?

 Hadley Circulation Model - HadCM3 – IS92a Scenario “Population 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 Global view Leucaena leucocephala – future predictions

Workflow Design

Biodiversity Richness & Conservation Evaluation Which areas represent an optimal conservation area network? What compromises can be made in such a selection process?

Does a combined analysis of climate and character data enhance the robustness of a phylogenetic analysis? 3.Phylogenetic Analysis & Biogeography:

A strict consensus of 1024 most parsimonious trees for Pelargonium

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)

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

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.

The University of Reading Frank Bisby, Alistair Culham, Neil Caithness, Tim Sutton, Peter Brewer, Chris Yesson Cardiff University Alec Gray, Andrew Jones, Richard White, Nick Fiddian, Xuebiao Xu, Mikhaila Burgess, Jaspreet Singh Pahwa The Natural History Museum Malcolm Scoble, Paul Williams, Shonil Bhagwat Bristol University Paul Valdes (The University of Southampton) BiodiversityWorld the biologist’s goals