The Environment Ontology Barry Smith 1

The Spatial-Structural Niche A Hole Story

4 Places are holes

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DIGESTIVE SYSTEM the interior of your gut: an environment for more than10 13 microorganisms

10 Positive and negative parts positive part negative part or hole (made of matter) (not made of matter)

J. J. Gibson The terrestrial environment is [best] described in terms of a medium, substances, and the surfaces that separate them. The Ecological Approach to Visual Perception, 1979, p. 16

A site intuitively: a spatial entity that can contain a material entity 12

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 13

14 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

15 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 16

17 Double hole structure of a Spatial Environment

18 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...

20 Two Types of Boundary

21 Niche as function … John found his niche as a mid-level accounts manager in a small-town bank …

22 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.)

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. 25

continuant systemecosystembiome environmental feature site pond mountain slope … object organism spatial region 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

continuant system ecosystembiome habitat environmental feature site pond mountain slope … object organism spatial region 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)

continuant system ecosystembiome habitatniche environmental feature site pond mountain slope … object organism spatial region Aligning EnvO to the Basic Formal Ontology part_of

Hutchinsonian niche dimensions –pH –evapotranspiration –turbidity –available light –predominant vegetation –predatory pressure –nutrient limitation –… 33

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 –… 36

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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ph ⨯ temperature ⨯ time ⨯ space 43 time

niche #1 44 time niche #2 niche #1 timehe #2