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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.
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The Environment Ontology Barry Smith http://ontology.buffalo.edu/smith
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)
A site • intuitively: a spatial entity that can contain a material entity
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
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
Mobile Sites 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
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
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 ...
Niche as function • … John found his niche as a mid-level accounts manager in a small-town bank …
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 …)
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.
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
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...
Hutchinsonian niche dimensions • pH • evapotranspiration • turbidity • available light • predominant vegetation • predatory pressure • nutrient limitation • …
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...
Hutchinsonian niche dimensions • pH • evapotranspiration • turbidity • available light • predominant vegetation • predatory pressure • nutrient limitation • …
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
timehe #2 niche #1 niche #2 time niche #1
