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Slides from ENVO flash talk at GSC 2015

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  1. 1. The Environment Ontology goes for GOLD Suzanna Lewis Chris Mungall Pier Luigi Buttigieg
  2. 2. animal- associated soil marine plant- associated sediment aquatic hot spring food cultured freshwater hydrothermal vent terrestrial sludge waste water extreme organism- associated air microbial mat lite 5255 genome projects
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  4. 4. Why not just use string-matching? Class A Class B Mapped? Useful? FMA: extensor retinaculum of wrist MouseAnatomy: retina Yes No Vivo: legal decision Cognitive Atlas: decision Yes No PlantOntology: Pith MouseAnatomy: medulla Yes No TaxRank: domain NCI: protein domain Yes No ZfishAnat: hypophysis MouseAnatomy: pituitary No Yes TAO:fossa AdverseReactions: depression Yes No FMA: colon GAZ: Colón, Panama Yes No Quality: male Chebi: maleate 2(-) Yes No String matching for mapping can lead to spurious results and semantics of mappings and provenance are not always clear
  5. 5.  what kinds of things exist?  what are the relationships between these things? Alkaline hot spring [ENVO:00002991] Microbial mat [ENVO:01000008] Hot spring [ENVO:00000051] alkaline is_a located_in has_quality Biological ontology: A machine interpretable representation of some aspect of biological reality
  6. 6. What is an environment? “The environment is everything that isn’t me” – A. Einstein An inherently slippery concept which can be defined at many levels of granularity
  7. 7. Marine epipelagic biomeMarine neritic epipelagic biome Biome level
  8. 8. Marine subtidal rocky reef Feature level
  9. 9. Coastal water Material level
  10. 10. Marine neritic epipelagic biome Marine subtidal rocky reef Coastal water
  11. 11. ENVO’s main hierarchies: biome, environmental feature, and environmental material
  12. 12. material entity system environmental systemseamount determined by is a seamount environment ecological community ecological population PCO BFO ENVO habitat biome
  13. 13. Buttigiegetal.(2013)JBiomedSemant4:43.
  14. 14. Any material entity can act as a feature, determining an environmental system around it
  15. 15. A mucus microbiome from an individual’s frontal sinus
  16. 16. ENVO: urban biome UBERON: frontal sinus ENVO: mucus
  17. 17. Objectives for EnvO (Dagstuhl) Environmental qualities • Water/Humidity/Aridity • Nutrient level • Temperature • Pressure & gravity • Light • Toxins • Predators/Pathogens/Competitors • Population of its own species • Time of year/Time of day • pH • Salinity • Surface angle(?) • Current/flow rate From S. Gilbert
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  20. 20. Acknowledgements Norman Morrison Barry Smith Chris Mungall Michael Ashburner Dawn Field Phenotype RCN lite Pier Luigi Buttigieg Max Planck Institute for Marine Microbiology ENVO Consortium and collaborators