Encyclopedia of Life

eol.org@eol

Cynthia Parr@cydparr

GSC15 23 April 2013

A webpage for every species

How EOL works

EOL

Crowds

Harvest

Third party applications

EOL

Plinian Core

DwCdescription

SPMinfoitem

usingDublin Core & Audubon Core for other metadataDarwin Core Archive flat files as transport mechanism

Sharing process adds semantics to content objects

EOL Today

Key Milestones in 2013

1.1 million species pages

240+ content providers

3 million unique visitors from 223 countries & territories

EOL

GBIF

NCBI

with Anne Bowser, University of Maryland

EOL connects hubs

BioNames

Rod PageRyan Schenk

iphylo.blogspot.com

Anatolia Zooarchaeology Case Study led by Alexandria Archive Institute

Research goals and outcomes:– Improve archaeological data collection /

documentation practices– Better understanding of gaps (spatial

and temporal)– Integrated biometrics show complex

patterns (introduction of domestic and continued use of wild animals by region)

– Aligning data to EOL taxon identifiers helps draw out patterns in relative proportion of taxa over time and space across many assemblages

EOL Computable Data Challenge1. 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/

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

Promote NLP text mining, crowdsourcing, standardizing

• Species Interaction Datasets—Integration, Visualization, and Analysis (Poelen and Mungall)

• Discovering EnvO habitat terms in EOL contents (Pafilis)

• Altitude Specificity of Flower Coloration (Wright)• Crowd-sourced data to examine morphological

impacts of extinction risk in ray-finned fishes (Chang)

• Macroecological patterns in butterfly-hostplant associations (Ferrer-Parris)

EOL GloBIGlobal Biotic Interactions

Challenge: Species interaction datasets are mostly buried in flat files & custom formats.

Plan: Build infrastructure for normalizing and aggregating species interaction datasets and make them accessible through flat files (Darwin Core Archive), web services, and semantic web endpoints (SPARQL).

Eventually: Publish biotic interaction ontology re-using existing ontologies, re-integrate with EOL

Enable semantic interoperability to allow for cross-functional analysis (e.g. How does a parasite regulate gene expression of host?

Poelen, Mungall, Simons, Reiz

http://globalbioticinteractions.wordpress.com/

14 datasets containing 25k taxa, 422k interactions, for 3k locations

alpha version of ingestion, normalization, aggegation

alpha version of web APIalpha version of data

exports

Dr. Katy Börner ledInformation Visualization MOOC

Easy access to analyzable trait data

“Are blue organisms more common in high altitudes?” “How can I predict vulnerability to climate change based on life history characteristics?” “What organisms should I collect to fill in gaps in genome quality tissue collections?”

• Look for data type, download for all taxa• Create a collection of taxa, download all data• Use Reol: an R interface to EOL (Banbury, Omeara)http://barbbanbury.info/barbbanbury/Reol.html• Find more specialized data repositories

Adding traits to EOL

Funded: Marine focus

<scientific name> <hasAvgBodyMass in g> <value><scientific name> <preysOn> <scientific name>

Harvest and display on data tabAdd high-level semantics from coarse SPM ontologyDownloads, fancy searchingMachine access

INSDC 900,000 species 4,000 genomes

60 million DNA sequence records

How are these related to traits?Next step: TraitBank

ThanksFunding & other contributionsSloan FoundationSmithsonian InstitutionDavid RubensteinMarine Biological LaboratoryHarvard UniversityOur content partnersThousands of individual contributors, and hundreds of volunteer curators

Image credits

Jenny from Taipei

University of Birmingham

Cynthia ParrChief Scientist @eol

@cydparr parrc@si.edu

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

Alexandria Archive: Sarah Kansa, Eric Kansa, 34 other zooarchaeologistsBioNames: Rod Page, Ryan SchenkMOOC: Katy Börner, Twy Bethard, Andrew Miles , Mattia Della Libera