Samples, Phenotype, Ontology Team at EBI SPOT Terry Meehan
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SPOT Consolidates metadata integration ontology development
tooling Curation for ArrayExpress and BioSample database Mouse
phenotype data for biomedical community GO - Uniprot Helen
Parkinson Mouse Informatics BioSamples Functional Genomics Gene
Ontology
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What is the research area? Capture and represent samples used
in assays ENCODE cell lines, HipSci, individual samples in ENA What
role do you see environmental ontologies playing? Important
metadata to distinguish samples Uses ENVO, GAZ (Geolocation),
UBERON What are the hurdles? Environmental factors from medical
questionaires BioSamples database
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BioSamples example - American Gut Project About 100 metadata
parameters collected Primary carb Primary vegetable Nutritional
Supplements Cosmetics Drinking water source (e.g. well) Deodorant
use Travel Ethnicity/Race All free text!!!
http://humanfoodproject.com/americangut/
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Functional Genomics What is the research area? Application
ontology for capturing experimental variables gene expression NHGRI
GWAS catalogue What role do you see environmental ontologies
playing? EFO uses many ontologies Deconvulating traits in the GWAS
catalogue What are the hurdles? Not sure which ontologies to
use
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Human GWAS trait example- Sleepiness Genome-wide association of
sleep and circadian phenotypes. BMC Med Genet. 2007 Sep 19 Epworth
Sleepiness Scale (ESS) Chance of Dozing (1-4) Sitting and reading
Watching TV Sitting inactive in a public place As a passenger in a
car Lying down to rest in the afternoon Sitting and talking to
someone Sitting quietly after a lunch without alcohol In a car,
while stopped for a few minutes in traffic
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What is the research area? IMPC- measuring 200+ biophysical
parameters in 20,000 knockout mouse Dozen research centers
Reference strain across centers What role do you see environmental
ontologies playing? Mammalian phenotype ontology Classifying center
specific differences in phenotypes What are the hurdles? Capturing
laboratory environmental factors Mouse Informatics The ARRIVE
(Animal Research: Reporting In Vivo Experiments)
http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000412
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Example- Housing and Husbandry Survey Over 60 questions about
humidity in rooms drinking water treatment Environmental
enhancements (e.g. toys) air ventilation methods light intensity
(Lux) bedding in cages diet (14 different commercial diets)
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Conclusions SPOT has a translational focus Environmental
factors we would like represented reflect this Human made
environments (work places, Labs, homes) Often captured in
questionnaires and guidelines
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Acknowledgements Funding: -NIH KOMP2 common fund U54 HG006370 -
EU and other NIH funding (GWAS