quasar
PRESENTED BY
10 SLIDES
351 VUES
100 LIKES

SPOT

DESCRIPTION

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.

1 / 10

Télécharger la présentation

SPOT

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related