Ontology and the Future of Biomedical Research Barry Smith .
The Environment Ontology Barry Smith 1.
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Transcript of The Environment Ontology Barry Smith 1.
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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natural language labels designed for use in annotations
to make the data cognitively accessible to human beings
and algorithmically tractable to computers
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
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 ...
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
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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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
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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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