the environment ontology barry smith ontology.buffalo/smith
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The Environment Ontology Barry Smith http://ontology.buffalo.edu/smith. The Spatial-Structural Niche A Hole Story. Places are holes. DIGESTIVE SYSTEM. the interior of your gut: an environment for more than 10 13 microorganisms. Positive and negative parts. negative part. or hole. - PowerPoint PPT PresentationTRANSCRIPT
The Environment OntologyThe Environment Ontology
Barry Smithhttp://ontology.buffalo.edu/smith
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The Spatial-Structural NicheA Hole Story
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Places are holes
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DIGESTIVE SYSTEM
the interior of your gut: an environment for more than1013 microorganisms
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Positive and negative parts
positivepart
negativepart
or hole
(made of matter)
(not made of matter)
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: 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
1 2 3 4
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Mobile Sites
1 2 3 4
1: a womb; a spaceship2: a snail’s shell; a 3: the home range of a migrating herd of buffalo; 4: the niche around a flying buzzard
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
Medium (filling the environing hole)
Tenant (occupying the central hole)
Retainer (a boundary of some surrounding structure)
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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
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 ...
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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.)
……… (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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Aligning EnvO to the Basic Formal Ontology
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
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
part_of
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?
3. quality axis – the corresponding determinable universal (e.g temperature, within some range)
recall our treatment of the truthmakers of a time-series graph
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time
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time
ph ⨯ temperature ⨯ time ⨯ space
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time
niche #1
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time
niche #2
niche #1
timehe #2