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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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Presentation Transcript
slide1

SPOT

Samples, Phenotype, Ontology Team at EBI

Terry Meehan

slide2
SPOT
  • Consolidates
    • metadata integration
    • ontology development
    • tooling
  • Curation for ArrayExpressand BioSample database
  • Mouse phenotype data for biomedical community
  • GO - Uniprot
  • Helen Parkinson
slide3

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
biosamples example american gut project
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/

functional genomics
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
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
slide7

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

example housing and husbandry survey
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
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
Acknowledgements
  • Funding:
  • -NIH KOMP2 common fund U54 HG006370
  • - EU and other NIH funding (GWAS