The Environment Ontology Barry Smith 1

2 oject

3 The problem

4 what cellular component? what molecular function? what biological process?

5 natural language labels designed for use in annotations to make the data cognitively accessible to human beings and algorithmically tractable to computers

6 compare: legends for maps

7 common legends allow (cross-border) integration

8 ontologies are legends for data

9 compare: legends for diagrams

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

15 Karen Eilbecksong.sf.net properties and features of nucleic sequences Sequence Ontology (SO) RNA Ontology Consortium(under development) three-dimensional RNA structures RNA Ontology (RnaO) Barry Smith, Chris Mungallobo.sf.net/relationshiprelations Relation Ontology (RO) Protein Ontology Consortium(under development) protein types and modifications Protein Ontology (PrO) Michael Ashburner, Suzanna Lewis, Georgios Gkoutos obo.sourceforge.net/cgi -bin/ detail.cgi? attribute_and_value qualities of biomedical entities Phenotypic Quality Ontology (PaTO) Gene Ontology Consortiumwww.geneontology.org cellular components, molecular functions, biological processes Gene Ontology (GO) FuGO Working Groupfugo.sf.net design, protocol, data instrumentation, and analysis Functional Genomics Investigation Ontology (FuGO) JLV Mejino Jr., Cornelius Rosse fma.biostr.washington. edu structure of the human body Foundational 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 entities Chemical 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

Towards 16

The Hole Story

Places are (in first approximation) holes

Places are holes

environment place site niche habitat setting hole spatial region interior location

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

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

Two Types of Boundary

Four Basic Niche Types (Niche as generalized hole) 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 39 OBO Foundry Genomic Standards Consortium National Environment Research Council (UK) Barcode of Life Project Encyclopedia 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 40

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) 41

42 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 –… 45

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 46

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 51

to enhance coordination of research 52

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 53

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The Environment Ontology 55 OBO Foundry Genomic Standards Consortium National Environment Research Council (UK) Barcode of Life Project Encyclopedia of Life Project

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