The Environment Ontology
Barry Smith
http://ontology.buffalo.edu/smith
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The Spatial-Structural Niche
A Hole Story
Places are holes
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5
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DIGESTIVE
SYSTEM
the interior of your gut: an
environment for more
than1013 microorganisms
Positive and negative parts
negative
part
or hole
(not made
of matter)
positive
part
(made of matter)
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A site
intuitively: a spatial entity that can contain
a material entity
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A spatial environment
is a site that
1. contains a medium (air, water)
2. can contain an organism or a population
of organisms
Some sites are supported and demarcated
by some solid object
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Stationary Sites
1
2
3
4
1: your office when the door is closed; a closed
mouth
2: a rabbit hole; an open mouth
3: the surface of a leaf
4: the Klingon Empire
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Mobile Sites
1
2
3
4
1: a womb; a spaceship
2: a snail’s shell; a
3: the home range of a migrating
herd of buffalo;
4: the niche around a flying buzzard
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At any given instant
a site is coincident with some spatial region
But because there are mobile sites
not: site  spatial region
For stationary sites we can associate
latitute/longitude specifications
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Double hole structure of a
Spatial Environment
Retainer
(a boundary of some
surrounding structure)
Medium
(filling the environing hole)
Tenant
(occupying the central hole)
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Retainer
the retainer of the bear’s niche is the cave
walls and floor plus the surfaces created
by the germs, vegetation, … therein
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Medium
the medium of the bear’s niche is a
circumscribed body of air
medium might be body of water, cytosol,
nasal mucosa, epithelium, endocardium,
synovial tissue ...
Two Types of Boundary
Fiat boundary
Physical boundary
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Niche as function
… John found his niche as a mid-level
accounts manager in a small-town bank …
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Niche as Function
the ‘niche’ of an animal means
its place in the biotic environment, its
relations to food and enemies.
When an ecologist says ‘there goes a badger’
he should include in his thoughts some
definite idea of the animal’s place in the
community to which it belongs, just as if he
had said ‘there goes the vicar’
(Elton 1927, pp. 63f.)
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biome
environmental
feature
environmental
material
…
…
… (soil, cheese …)
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Biome =def. An ecosystem which contains
populations adapted to the environmental
conditions conserved over its spatial
extent.
Microbiome =def. A biome which contains
the totality of microscopic organisms, their
genetic elements, and interactions in a
given environment.
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continuant
Aligning EnvO to the Basic Formal Ontology
system
ecosystem
biome
object
organism
pond
environmental
feature
site
mountain slope
spatial region
…
habitat
Habitat =def. An ecosystem which can
support the life of a given organism,
population, or community
Realized niche =def. An ecosystem which
is that part of a habitat which supports the
life of a given organism, population or
community
Aligning EnvO to the Basic Formal Ontology
ecosystem
biome
system
continuant
habitat
object
organism
pond
environmental
feature
site
mountain slope
spatial region
…
Hutchinsonion niche
(niche as volume in a functionally
defined hyperspace)
=def. an n-dimensional hyper-volume
whose dimensions correspond to resource
gradients over which species are
distributed
– degree of slope, exposure to sunlight, soil
fertility, foliage density, salinity...
G.E. Hutchinson (1957, 1965)
Aligning EnvO to the Basic Formal Ontology
ecosystem
biome
system
continuant
habitat
part_of
niche
object
organism
pond
environmental
feature
site
mountain slope
spatial region
…
Hutchinsonian niche dimensions
– pH
– evapotranspiration
– turbidity
– available light
– predominant vegetation
– predatory pressure
– nutrient limitation
–…
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Hutchinsonion niche
(niche as volume in a functionally
defined hyperspace)
=def. an n-dimensional hyper-volume
whose dimensions correspond to resource
gradients over which species are
distributed
– degree of slope, exposure to sunlight, soil
fertility, foliage density, salinity...
G.E. Hutchinson (1957, 1965)
Hutchinsonian niche dimensions
– pH
– evapotranspiration
– turbidity
– available light
– predominant vegetation
– predatory pressure
– nutrient limitation
–…
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Gigantic evolutionary hotel
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How to deal with the Hutchinsonian
niche in BFO terms?
recall our treatment of the
truthmakers of a time-series
graph
3. quality axis – the corresponding determinable universal
(e.g temperature, within some range)
time
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time
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ph ⨯ temperature ⨯ time ⨯ space
time
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timehe #2
niche #1
niche #2
niche #1
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