1. Samples, Phenotype, Ontology Team at EBI SPOT Terry Meehan

2. 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

3. 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

4. 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/

5. 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

6. 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

7. 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

8. 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)

9. 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

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