The Environment OntologyThe Environment Ontology

Barry Smithhttp://ontology.buffalo.edu/smith

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http://gensc.org/gc_wiki/index.php/GAZ_Project

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The problem

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what cellular component?

what molecular function?

what biological process?

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natural language labels designed for use in annotations

to make the data cognitively accessible to human beings

and algorithmically tractable to computers

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compare: legends for mapscompare: legends for maps

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compare: legends for mapscommon legends allow (cross-border) integration

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ontologies are legends for data

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compare: legends for diagrams

The Gene Ontology

The Gene Ontology

The GO Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

The GO Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

The GO Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity

15Karen Eilbecksong.sf.netproperties and features of

nucleic sequencesSequence Ontology

(SO)

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)

Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)

Protein Ontology Consortium(under development)protein types and

modificationsProtein Ontology

(PrO)

Michael Ashburner, Suzanna Lewis, Georgios Gkoutos

obo.sourceforge.net/cgi-bin/ detail.cgi?

attribute_and_valuequalities of biomedical entities

Phenotypic Quality Ontology

(PaTO)

Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes

Gene Ontology (GO)

FuGO Working Groupfugo.sf.netdesign, protocol, data

instrumentation, and analysis

Functional Genomics Investigation Ontology

(FuGO)

JLV Mejino Jr.,Cornelius Rosse

fma.biostr.washington.edu

structure of the human bodyFoundational Model of

Anatomy (FMA)

Melissa Haendel, Terry Hayamizu, Cornelius Rosse,

David Sutherland, (under development)

anatomical structures in human and model organisms

Common Anatomy Refer-

ence Ontology (CARO)

Paula Dematos,Rafael Alcantara

ebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)

Jonathan Bard, Michael Ashburner, Oliver Hofman

obo.sourceforge.net/cgi-bin/detail.cgi?cell

cell types from prokaryotes to mammals

Cell Ontology (CL)

CustodiansURLScopeOntology

TowardsTowards

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The Hole Story

Places are (in first approximation) holes

Places are holes

environmentplacesite

nichehabitatsettinghole

spatial regioninteriorlocation

Gibson’s theory of surface layout

‘a sort of applied geometry that is appropriate for the study of perception and behavior’ (1979, p. 33)

ground, open environment, enclosure, detached object, attached object, hollow object, place, sheet, fissure, stick, fiber, dihedral, etc.

The theory of surface layout as an anatomy of environments

systems of barriers, doors, pathways to which the behavior of organisms is specifically attuned,

temperature gradients, patterns of movement of air or water molecules

water holes, food sources (features)

apertures (mouths, sphincters ...)

Gibson:The terrestrial environment is [best] described in terms of a medium, substances, and the surfaces that separate them. (Gibson 1979, p. 16)

Double Hole Structure of the Occupied Niche

Medium (filling the environing hole)

Tenant (occupying the central hole)

Retainer (a boundary of some surrounding structure)

http://ontology.buffalo.edu/bio/niche-smith.htm

Tenant, medium and retainer

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 ...

The Empty Niche

Fiat boundary Physical boundary

Two Types of Boundary

Fiat boundary Physical boundary

Four Basic Niche Types(Niche as generalized hole)

1 2 3 4

1: a womb; an egg; a house (better: the interior thereof)2: a snail’s shell; 3: the niche of a pasturing cow; 4: the niche around a circling buzzard (fiat boundary)

Elton – niche as role

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.)

G.E. Hutchinson: niche as volume in a functionally defined space

the niche = an n-dimensional hyper-volume whose dimensions correspond to resource gradients over which species are distributed

G.E. Hutchinson (1957, 1965)

Hypervolume niche = a location in an attribute space

defined by a specific constellation of environmental variables such as degree of slope, exposure to sunlight, soil fertility, foliage density, salinity...

The Environment Ontology

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OBO FoundryGenomic Standards ConsortiumNational Environment Research Council (UK)Barcode of Life ProjectEncyclopedia of Life Project

EnvO

combines the spatial and Hutchinsonian perspectives to create a consensus controlled vocabulary for representing

macroscopic (geographical)

mesoscopic (behavioral)

microscopic (cellular, molecular …)

environments

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EnvO

cross-granular environments

e.g. infection = how the interior of one organism or organism part serves as environment for another organism

EnvO IDO (Infectious Disease Ontology)

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Applications of EnvO in biology

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Environment = totality of circumstances external to a living organism or group of

organisms

– pH– evapotranspiration– turbidity– available light– predominant vegetation– predatory pressure– nutrient limitation – …

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How EnvO currently works for information retrieval

Retrieve all experiments on organisms obtained from:– deep-sea thermal vents– arctic ice cores– rainforest canopy– alpine melt zone

Retrieve all data on organisms sampled from:– hot and dry environments– cold and wet environments– a height above 5,000 meters

Retrieve all the omic data from soil organisms subject to:– moderate heavy metal contamination

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Scale: From microbiological to geographic

Data on locations of organisms/samples, sources of museum artifacts ...

Environments have spatial locations

Data on organism interactions, e.g. on bacterial infection – how the interior of one organism or organism part serves as environment for another organism

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extending EnvO to the human realm

– neighborhood patterns• built environment, living conditions• climate• social networking• crime, transport• education, religion, work• health, hygiene

– disease patterns• patterns of disease transmission

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to enhance coordination of research

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a new type of patient data

a patient’s environmental history

use EnvO to mine relations between disease phenotypes and environmental patterns and patterns of community behavior

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The Environment Ontology

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OBO FoundryGenomic Standards ConsortiumNational Environment Research Council (UK)Barcode of Life ProjectEncyclopedia of Life Project

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