behavior ontology workshop princeton
DESCRIPTION
Presented at 2014 Animal Behavior Ontology workshop at Princeton, NJ in association with the Animal Behavior Society annual meeting.TRANSCRIPT
![Page 1: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/1.jpg)
Why should we care?
Cyndy ParrEOL Chief Scientist
Photo by Rita Willaert
![Page 2: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/2.jpg)
![Page 3: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/3.jpg)
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.”
![Page 4: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/4.jpg)
Journal data sharing requirements for supplementary data
![Page 5: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/5.jpg)
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
![Page 6: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/6.jpg)
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)
![Page 7: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/7.jpg)
2008
text, media, literature
all species, genera, etc.
names infrastructure
data curation
human/machine interfaces
5 million visitors per year
eol.org
![Page 8: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/8.jpg)
GenBank 60 million DNA sequence records
900,000 species 4,000 genomes
How are these related to traits?
![Page 9: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/9.jpg)
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
![Page 10: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/10.jpg)
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
![Page 11: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/11.jpg)
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
![Page 12: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/12.jpg)
TraitBank
~7 million records326 traits 1.2 million taxa40+ datasetshttp://eol.org/collections/97700
![Page 13: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/13.jpg)
TraitBank Quick facts
![Page 14: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/14.jpg)
TraitBank Data tab
![Page 15: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/15.jpg)
TraitBank Metadata
![Page 16: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/16.jpg)
TraitBank Search & download
![Page 17: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/17.jpg)
TraitBank Search & download
![Page 18: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/18.jpg)
TraitBank Data glossaryhttp://eol.org/data_glossary
![Page 19: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/19.jpg)
Download
![Page 20: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/20.jpg)
TraitBank Uploading Darwin Core Archives
Common names | Taxa | References | MeasurementsOrFacts | Associations | Events | Occurrences
![Page 22: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/22.jpg)
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
![Page 23: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/23.jpg)
Annotation of an observation record
![Page 24: Behavior ontology workshop princeton](https://reader034.vdocument.in/reader034/viewer/2022042623/5405f13b8d7f729e768b4f1d/html5/thumbnails/24.jpg)
EOL-BHL Research Sprint