Roberts u oxf_msc_200213


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Roberts u oxf_msc_200213

  1. 1. Biodiversity Informatics: small pieces, loosely joined. Dave Roberts Natural History Museum, London dmr@nomencurator.orgContemporary Issues in BiodiversityU. Oxford MSc in Conservation, Biodiversity and Management 20 Feb 2013
  2. 2. ViBRANT Virtual BiodiversityAddressing the challenges of taxonomy Goal ... Inventory the Earth’s species Document their relationships “Publish” & apply these data Data set ... 1.8 M described spp. (17M names) 300M pages (over last 250 years) 1.5-3B specimens People ... 4-6,000 taxonomists 30-40,000 “pro-amateurs” Many more citizen scientists?SEVENTH FRAMEWORK PROGRAMME -infrastructure
  3. 3. ViBRANT Virtual BiodiversitySEVENTH FRAMEWORK PROGRAMME -infrastructure
  4. 4. ViBRANT Virtual Biodiversity Biodiversity informatics landscape GenBank MorphBank Interactions Geospatial Census Biotic Genotype Phenotype Environment Human Effects Interactions Pop. data IUCN Niche & Pop. Biodiversity Ecology Loss TreeBase GBIF AquaMaps Phylogenetic Geographic Conservation & Trees Dsitributions management IPNI, Zoobank Extent of Occurrence AquaMaps Forecasts of Data Taxonomy Range Maps Change Products Key problems Systems Landscape is complex, fragmented & hard to navigate Many audiences (policy makers, scientists, amateurs, citizen scientists) Figure adapted from Many scales (global solutions to local problems) Peterson et al 2010SEVENTH FRAMEWORK PROGRAMME -infrastructure
  5. 5. ViBRANT Virtual Biodiversity 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. 2010SEVENTH FRAMEWORK PROGRAMME -infrastructure
  6. 6. ViBRANT Virtual Biodiversity Small pieces loosely joined Has many potential meanings: Joining contributors together to form communities Joining the data together that go towards forming a Scratchpad Joining Scratchpad content with the landscape of biodiversity informatics data on the webSEVENTH FRAMEWORK PROGRAMME -infrastructure
  7. 7. ViBRANT Virtual Biodiversity Can technology help?I The technology must largely embody the cause–effect relationship connecting problem to solution.II The effects of the technological fix must be assessable using relatively unambiguous or uncontroversial criteria.III Research and development is most likely to contribute decisively to solving a social problem when it focuses on improving a standardized technical core that already exists. Sarewitz and Nelson (2008) Three rules for technological fixes. Nature, 456: 871-872 SEVENTH FRAMEWORK PROGRAMME -infrastructure
  8. 8. ViBRANT Virtual BiodiversityIdentifiersA key to findsomething in adatabase.SEVENTH FRAMEWORK PROGRAMME -infrastructure
  9. 9. ViBRANT Virtual Biodiversity 10.4289/0013-8797.115.1.75SEVENTH FRAMEWORK PROGRAMME -infrastructure
  10. 10. ViBRANT Virtual Biodiversity FRAMEWORK PROGRAMME -infrastructure
  11. 11. ViBRANT Virtual Biodiversity FRAMEWORK PROGRAMME -infrastructure
  12. 12. ViBRANT Virtual Biodiversity FRAMEWORK PROGRAMME -infrastructure
  13. 13. ViBRANT Virtual Biodiversity FRAMEWORK PROGRAMME -infrastructure
  14. 14. ViBRANT Virtual BiodiversitySEVENTH FRAMEWORK PROGRAMME -infrastructure
  15. 15. ViBRANT Virtual BiodiversitySEVENTH FRAMEWORK PROGRAMME -infrastructure
  16. 16. ViBRANT Virtual Biodiversity Ecosystem state Herbivore cohort Abundance Carnivore cohort Omnivore cohort Body mass High biomass Ecological processes Low biomass Reproduction Metabolism Dispersal Eating Mortality OtherVariation in biomass across the world simulated by the Madingley model for terrestrial and marineecosystems. Fundamental ecological processes, encoded into simple computational forms,determine the abundance and body mass of organisms (grouped into cohorts for simplicity) andso indicate the state of ecosystems. Purves, D., Scharlemann, J. P. W., Harfoot, M., Newbold, T., Tittensor, D. P., Hutton, J. & Emmott, S. (2013). Ecosystems: Time to model all life on Earth. Nature 493: 295–297. DOI: 10.1038/493295a SEVENTH FRAMEWORK PROGRAMME -infrastructure
  17. 17. ViBRANT Virtual Biodiversity DOI:10.1038/493597a Length 85 cmMaturation 9 years t Weigh .1 kg Length 5 82 cmMat aturation 7.7 years We ight .6 kg Length 4 73 cm SHRINKING FISH 2000s For Northeast Arctic cod, the age, size and spawners have fallenMat aturation dramatically. 7 years We ight g 3.2 k Borrell, B. (2013). Ocean conservation: A big fight over little fish. Nature 493: 597–598. SEVENTH FRAMEWORK PROGRAMME -infrastructure
  18. 18. ViBRANT Virtual BiodiversityData mining.The abundant microorganismsin Earth’s soils perform myriadecosystem services, many ofwhich are still poorly understoodor remain unrecognized. Thebest ways of identifying andstudying these processes is atopic of debate in the ecologycommunity.Jansson, J. K. & Prosser, J. I. (2013). Nature 494: 40–41. doi: 10.1038/494040a SEVENTH FRAMEWORK PROGRAMME -infrastructure
  19. 19. ViBRANT Virtual Biodiversity 8 June 2012 14 June 2012Relman, D. (2012) Nature, 486,194–195 Number of microbial speciesdoi:10.1038/486194a Number of genes Modified from GBIF/GBIC –2-4 Jul 2012 –Copenhagen, ©2012, R. J. RobbinsSEVENTH FRAMEWORK PROGRAMME -infrastructure
  20. 20. ViBRANT Virtual Biodiversity FUNGI ARCHAEA BACTERIA ANIMALSIf the goal of biodiversitystudies is to understandall of the diversity in theEarth’s biosphere… PLANTSThen the notion that we can EUKARYAaccomplish that goal only bylooking here is just plain wrong. Modified from GBIF/GBIC –2-4 Jul 2012 –Copenhagen, ©2012, R. J. Robbins SEVENTH FRAMEWORK PROGRAMME -infrastructure