eol.org@eol@cydparr
How the Encyclopedia of Life is wrangling organismal attribute data
How EOL works
EOL
Crowds
Harvest
Third party applications
EOL Today
Key Milestones in 2013
1.1 million species pages
240+ content providers
3.3 million unique annual visitors from 235 countries
DistributionMolecularBiology
Multiple topicsTypeInformation
HabitatConservationStatus
ThreatsMorphology
ConservationManagement
TrendsSize
AssociationsUses
TrophicStrategyCyclicity & Life Cycle
PopulationBiologyReproduction
MigrationTaxonomy
LifeExpectancyIdentification
BehaviourEcology
Diseases
0 100000 200000 300000 400000 500000 600000 700000 800000
Number of text objectsSu
bjec
t of t
ext o
bjec
t
Text mining, crowdsourcing, standardizing see http://eol.org/info/fellows
Co-occurrence, term extraction & linked data
Thessen & Devries
EnvO habitat terms Pafilis et al.Altitude Specificity of Flower Coloration
Wright
Morphological impacts of extinction risk in fish
Chang
Butterfly-hostplant associations Ferrer-Parris et al.
Species Interactions Poelen & Mungall et al.
14 datasets containing 25k taxa, 422k interactions, for 3k locations
alpha version of ingestion, normalization, aggregation
alpha version of web APIalpha version of data
exports
Dr. Katy Börner ledInformation Visualization MOOC
GLoBI http://globalbioticinteractions.wordpress.com/
EOL TraitBank
Funded: Marine focus
Virtuoso triple store, re-using URIs where possible5 datasets 128,050 data points for 20,896 taxa
Harvest and display on data tabDownloads, fancy searchingMachine access
Uploads & harvests will be by spreadsheetand Darwin Core Archive
Support for annotation and curation
Please contact me to be part of the private beta
Easy access to analyzable trait data
“Are blue organisms more common in high altitudes?”
“Does the evolution of mammalian bacula appear to be related to the pattern of promiscuous mating?”
“What organisms should I collect to fill in gaps in genome quality 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
But also . . .
ThanksFunding & other contributionsSloan FoundationSmithsonian InstitutionDavid RubensteinMarine Biological LaboratoryHarvard UniversityOur content partnersThousands of individual contributors, and hundreds of volunteer curators
Image credits
Jenny from Taipei
Cynthia ParrChief Scientist @eol
@cydparr [email protected]
Alexandria Archive: Sarah Kansa, Eric Kansa, 34 other zooarchaeologists
GLoBI: Jorrit Poelen (lead/software), Chris Mungall (ontologies), James Simons (biologist) and Robert Reiz (software). Datasets shared by: Peter D. Roopnarine, Rachel Hertog, Carlos García-Robledo, James Simons, Jenny L. Wrast, C. Barnes, International Council for the Exploration of the Sea (ICES), Jose R. Ferrer Paris, Senol Akin, Malcolm Storey (BioInfo.org.uk), Ivy E. Baremore, Joel Sachs (SPIRE), Colt W. Cook, David A. Blewett
Quick math
In Phenoscape57 publications had 565,158 anatomical trait descriptions for 2,527 kinds of organisms= 223 traits/organism
In ZFIN 38,189 trait descriptions for 4,727 genes for Zebra Fish
1.9 million species on the planet
= LOTS OF TRAITS
Anatolia Zooarchaeology Case Study led by Alexandria 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 ontology 8. Collaborative analysis
http://opencontext.org/