Samples, Phenotype, Ontology Team at EBI

SPOT

Terry Meehan

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

• 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

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/RaceAll free text!!!

http://humanfoodproject.com/americangut/

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

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

• 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

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)

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

Acknowledgements

Funding: -NIH KOMP2 common fund U54 HG006370- EU and other NIH funding (GWAS