the environment ontology barry smith ontology.buffalo/smith

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