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How the Encyclopedia of Life is wrangling organismal attribute data

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Lightning talk presented at iEvoBio 2013 in Snowbird, Utah

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How the Encyclopedia of Life is wrangling organismal attribute data

  1. 1. eol.org@eol@cydparrHow the Encyclopedia of Life iswrangling organismal attribute data
  2. 2. How EOL worksEOLCrowdsHarvestThird party applications
  3. 3. EOL TodayKey Milestones in 20131.1 million species pages240+ content providers3.3 million unique annualvisitors from 235countries
  4. 4. 0 100000 200000 300000 400000 500000 600000 700000 800000DistributionMolecularBiologyMultiple topicsTypeInformationHabitatConservationStatusThreatsMorphologyConservationManagementTrendsSizeAssociationsUsesTrophicStrategyCyclicity & Life CyclePopulationBiologyReproductionMigrationTaxonomyLifeExpectancyIdentificationBehaviourEcologyDiseasesNumber of text objectsSubjectoftextobject
  5. 5. Text mining, crowdsourcing, standardizingsee http://eol.org/info/fellowsCo-occurrence, term extraction &linked dataThessen & DevriesEnvO habitat terms Pafilis et al.Altitude Specificity of FlowerColorationWrightMorphological impacts of extinctionrisk in fishChangButterfly-hostplant associations Ferrer-Parris et al.Species Interactions Poelen & Mungallet al.
  6. 6. 14 datasets containing 25ktaxa, 422kinteractions, for 3klocationsalpha version ofingestion, normalization,aggregationalpha version of web APIalpha version of dataexportsDr. Katy Börner ledInformation VisualizationMOOCGLoBI http://globalbioticinteractions.wordpress.com/
  7. 7. EOL TraitBankFunded: Marine focusVirtuoso triple store, re-using URIs where possible5 datasets 128,050 data points for 20,896 taxaHarvest and display on data tabDownloads, fancy searchingMachine access
  8. 8. Uploads & harvests will be by spreadsheetand Darwin Core ArchiveSupport for annotation and curationPlease contact me to be part of the private beta
  9. 9. Easy access to analyzable trait data“Are blue organisms more common in high altitudes?”“Does the evolution of mammalian bacula appear to berelated to the pattern of promiscuous mating?”“What organisms should I collect to fill in gaps in genomequality tissue collections?”• Look for trait, download for all taxa• Create a collection of taxa, download all data• Use Reol: an R interface to EOL (Banbury, O’Meara)http://reolblog.wordpress.com/• Find more specialized data repositories
  10. 10. But also . . .
  11. 11. ThanksFunding & other contributionsSloan FoundationSmithsonian InstitutionDavid RubensteinMarine Biological LaboratoryHarvard UniversityOur content partnersThousands of individualcontributors, and hundreds ofvolunteer curatorsImage creditsJenny from TaipeiCynthia ParrChief Scientist @eol@cydparr parrc@si.eduAlexandria Archive: Sarah Kansa, Eric Kansa, 34 othezooarchaeologistsGLoBI: Jorrit Poelen (lead/software), Chris Mungall(ontologies), James Simons (biologist) and RobertReiz (software). Datasets shared by: Peter D.Roopnarine, Rachel Hertog, Carlos García-Robledo, James Simons, Jenny L. Wrast, C.Barnes, International Council for the Exploration ofthe Sea (ICES), Jose R. Ferrer Paris, SenolAkin, Malcolm Storey (BioInfo.org.uk), Ivy E.Baremore, Joel Sachs (SPIRE), Colt W. Cook, David A.Blewett
  12. 12. Quick mathIn Phenoscape57 publications had 565,158 anatomical traitdescriptions for 2,527 kinds of organisms= 223 traits/organismIn ZFIN38,189 trait descriptions for 4,727 genes for ZebraFish1.9 million species on the planet= LOTS OF TRAITS
  13. 13. Anatolia Zooarchaeology Case Study led byAlexandria Archive Institute1. 14 different sites2. 34+ zooarchaeologists3. Decoding, cleanup, metadata documentation4. 220,000+ specimens5. 450 entities linked to 143 EOL taxon concepts6. Anatomical entities linked to Uberon.org7. Biometrics linked to measurement ontology8. Collaborative analysishttp://opencontext.org/

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