Behavior ontology workshop princeton
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Why should we care? Cyndy Parr EOL Chief Scientist Photo by Rita Willaert
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Presented at 2014 Animal Behavior Ontology workshop at Princeton, NJ in association with the Animal Behavior Society annual meeting.
Transcript of Behavior ontology workshop princeton
Why should we care?
Cyndy ParrEOL Chief Scientist
Photo by Rita Willaert
US Federal Agencies Must Have Open Data
February 22, 2013 Office of Science and Technology Policy MemorandumIncreasing Access to the Results of Federally Funded Scientific Research
May 09, 2013
Executive OrderMaking Open and Machine Readable the New Default for Government Information
“As one vital benefit of open government, making information resources easy to find, accessible, and usable can fuel entrepreneurship, innovation, and scientific discovery that improves Americans' lives and contributes significantly to job creation.”
Journal data sharing requirements for supplementary data
Even better reasons
A researcher may use an ontology to: 1) expand a query to discover all studies or other resources (videos, images, web discussions) 2) annotate papers with standardized terms describing results related to her hypotheses 3) standardize datasets so that they can be assembled for re-analysis, meta-analysis or phylogenetic analysis
Standardize datasets for re-analysis, meta-analysis or phylogenetic analysis
• Cross-species, cross-domainEvolution of development of lateralization in both brain and behavior
• Within-species, cross-researcher, over timeChanges in reproductive behavior in red-winged blackbirds due to global warming.
• Cross-species cross-domainUnderstanding parasite manipulation of host behaviors (e.g. by Toxoplasma gondii)
2008
text, media, literature
all species, genera, etc.
names infrastructure
data curation
human/machine interfaces
5 million visitors per year
eol.org
GenBank 60 million DNA sequence records
900,000 species 4,000 genomes
How are these related to traits?
Why TraitBankIn Phenoscape
57 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 Zebrafish
1.9 million species on the planet
= LOTS OF TRAITS & no central repository
TraitBank data sourceshttp://eol.org/traitbank launched January 2014Numeric data (measurements)
Categorical data (controlled vocabulary)
Species interactions
Mostly summaries
From: Databases LiteratureNatural History CollectionsLegacy/unpublished data
Search & Download
Data Sources
Data Summaries on EOL Taxon
Pages
Which plants grow well in acidic soil?
What do water bears eat?
What is the biggest species of whale?
Structured Data
TraitBank
JSON-LD API
TraitBank
~7 million records326 traits 1.2 million taxa40+ datasetshttp://eol.org/collections/97700
TraitBank Quick facts
TraitBank Data tab
TraitBank Metadata
TraitBank Search & download
TraitBank Search & download
TraitBank Data glossaryhttp://eol.org/data_glossary
Download
TraitBank Uploading Darwin Core Archives
Common names | Taxa | References | MeasurementsOrFacts | Associations | Events | Occurrences
Text miningEnvironments-EOLEvangelos Pafilis, Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Crete, Greece
491,616 habitat terms for 136,548 taxa
Annotation of an observation record
EOL-BHL Research Sprint
