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SPOT

SPOT. Samples, Phenotype, Ontology Team at EBI. 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. BioSamples database.

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SPOT

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

  2. SPOT • Consolidates • metadata integration • ontology development • tooling • Curation for ArrayExpressand BioSample database • Mouse phenotype data for biomedical community • GO - Uniprot • Helen Parkinson

  3. BioSamples database • 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

  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. Mouse Informatics • 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 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

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