Slides from ENVO flash talk at GSC 2015

1. The Environment Ontology
goes for GOLD
Suzanna Lewis
Chris Mungall
Pier Luigi Buttigieg

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

3. http://worldwildlife.org/biomes

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.  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. 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. Marine epipelagic biomeMarine neritic epipelagic biome
Biome level

8. Marine subtidal rocky reef
Feature level

9. Coastal water
Material level

10. Marine neritic epipelagic biome
Marine subtidal rocky reef
Coastal water

11. ENVO’s main hierarchies:
biome, environmental feature, and
environmental material

12. material entity
system
environmental systemseamount
determined by
is a
seamount environment
ecological
community
ecological
population
PCO
BFO
ENVO
habitat
biome

13. Buttigiegetal.(2013)JBiomedSemant4:43.

15. Any material entity can act as a feature,
determining an environmental system
around it

16. A mucus microbiome
from an individual’s
frontal sinus

17. ENVO: urban biome
UBERON: frontal sinus
ENVO: mucus

18. 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

19. http://www.environmentontology.org/

20. http://www.environmentontology.org/

22. 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