Niches - Ontology

Niches - Ontology

The Mouth Barry Smith http://ontology.buffalo.edu/smith Preamble: Biomedical Ontology in Buffalo ORG

Ontology Research Group Werner Ceusters Lou Goldberg Barry Smith NCBO National Center for Biomedical Ontology Stanford Medical Informatics Cambridge University Department of Genetics Berkeley National Laboratories

Mayo Clinic San Francisco Medical Center University of Oregon Institute of Neuroscience UB Department of Philosophy OBO Open Biological Ontologies Consortium GO (Gene Ontology) FuGO (Functional Genomics Investigation Ontology)

Phenotype Ontology Sequence Ontology Cell Ontology Mouse Anatomy Ontology GO: asymmetric protein localization involved in cell fate commitment

Anatomical Structure Organ Serous Sac Cavity Subdivision Serous Sac

Cavity Serous Sac Organ Component Parietal Parietal Pleura

Pleura Mediastinal Mediastinal Pleura Pleura Organ Part Organ Subdivision

Pleural PleuralSac Sac Pleural Pleural Cavity Cavity

Interlobar Interlobar recess recess is_a Tissue Pleura(Wall

Pleura(Wall ofofSac) Sac) Visceral Visceral Pleura Pleura Mesothelium Mesothelium

ofofPleura Pleura of Organ Cavity t_

Organ Cavity Subdivision pa r Anatomical Space OBO OBO Relation Ontology

OBO-UBO (Upper Biomedical Ontology) From controlled vocabulary to reasoning tool From single granularity to cross-granularity From single-study to all biological experiments and all clinical trials Smith B et al. Relations in biomedical ontologies. Genome Biology 2005, 6:R46 NIH Ontology Efforts NCBO / NCBC Roadmap Centers

caBIG NCI Thesaurus Pre-NCIT NECTAR (National Electronics Clinical Trials and Research Network) BIRN (Biomedical Informatics Research Network) BIRN Ontology Workshop (NIH) Stanford, February 28-March 1 NIAID Immunology Ontology Workshop (NIH) Gaithersburg, March 21-22 2006

Image Ontology Workshop Stanford, March 24-25 2006 Gene Ontology Workshop St. Croix, March 31-April 3 2006 Training Course in Biomedical Ontology Dagstuhl, Germany, May 21-24 2006 Anatomy Ontology Workshop Seattle, September 8-9 2006 Disease Ontology Workshop Baltimore, November 6-7 2006

Interoperability of Biomedical Ontologies Dagstuhl, Germany, March 27-30 2007 The Mouth OBO-UBO Places are holes A hole in the ground

Solid physical boundaries at the floor and walls but with a fiat lid: hole Holes involve two kinds of boundaries bona fide boundaries which exist independently of our demarcating acts

fiat boundaries which exist only because we put them there niches, environments are holes Armchair Ontology Positive and negative parts positive

part (made of matter) negative part or hole (not made of matter) niches, environments are holes

environment place niche habitat setting hole spatial region interior

Ecological Niche Concepts niche as particular place or subdivision of an environment that an organism or population occupies vs. niche as function of an organism or population within an ecological community Elton 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 animals place in the community to which it belongs, just as if he had said there goes the vicar (Elton 1927, pp. 63f.) ity

hu mi d foliage density The Niche as Hypervolume temperature

ity hu mi d foliage density The Niche as Hypervolume temperature

ity hu mi d foliage density The Niche as Hypervolume

temperature ity hu mi d foliage density The Niche as Hypervolume

temperature Hypervolume niche is 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... John found his niche as a mid-level

accounts manager in a small-town bank But every hypervolume niche must be realized in some specific spatial location Niche type must be tokenized in space Your mouth is a tokenized niche (or perhaps a constantly changing sum of tokenizations of different niche types) niche topology: Smith B, Varzi AC, The niche, Nous, 1999;33:198222.

J. J. Gibsons theory of surface layout systems of barriers, doors, pathways to which the behavior of organisms of given types is specifically attuned, temperature gradients, patterns of movement of air or water molecules or bacteria

Double Hole Structure Retainer (a boundary of some surrounding structure) Medium (filling the environing hole) Tenant (occupying the central hole) The Structure of Niches

media and retainers the medium of the bears niche is a circumscribed body of air Two Types of Boundary Fiat boundary Physical boundary

Four Basic Niche Types 1 2 1: a womb; 2: a snails shell; 3: the niche of a pasturing cow; 4: the niche around a buzzard

3 4 Types of Niches a pond, a nest, a cave, a hut, an airconditioned apartment building the history of evolution as a history of the development of niches

Four Basic Niche Types 1 2 1: a house; 2: a snails shell; 3: the niche of a pasturing cow; 4: the earths atmosphere

3 4 stationary niches 1: your office when the door is closed; 2: a rabbit hole; 3: a seat at Yankee stadium; 4: the Klingon Empire

Four Basic Niche Types 1 2 1: a womb; 2: a snails shell; 3: the niche of a pasturing cow; 4: the niche around a buzzard

3 4 all vacant niches must have a retainer generic dependence of niche on tenant(s) Niche Construction Lewontin: niches normally arise in symbiosis with

the activities of organisms or groups of organisms; they are not already there, like vacant rooms in a gigantic evolutionary hotel, awaiting organisms who would evolve into them. ecosystem engineering maintenance of niches (screwdrivers, paintings) niches on different levels of the food chain

a. at the bottom of the hiearchy is the saprophytic chain, in which micro-organisms live on dead organic matter; b. above this is the primary relation between animals and the plants they consume; c. above this is the predator chain, in which animals of one sort eat smaller animals of another sort; d. crosscutting all of these is the parasite chain, in which a smaller organism consumes part of a

larger host organism. Token Science selection theory is concerned with phenomena at the level of populations; it is concerned with what properties are selected for and against in a population. We do not describe single organisms and their physical constituents one by one. genotypes vs. genotokens

niche theory and set theory Fiat Boundaries fish and bird niches as volumes of space demarcatory vs. behavioral fiat boundaries Varieties of Controlled Airspace Apertures, Mouths, and Sphincters

security vs. freedom of movement plants barnacles and snails fish and birds skin or hide Security vs. Freedom the mouth of the bear, the mouth of the bears cave, the threshold of your office freedom of movement and fiat boundaries

(of niches and of organisms) the alimentary canal: hole or part ? Double Hole Structure Retainer (a boundary of some surrounding structure) Medium (filling the environing hole) Tenant

(occupying the central hole) The Medium for Life a medium is a medium only relative to a given type of niche a medium requires either a retainer (in the case of a vacant niche) or a tenant (in the case of an occupied niche) when a tenant leaves its niche the gap left by the tenant is filled immediately by the surrounding

medium Michelangelos David examples of media: air, smoke, water Mixed Media mixed media (including radioactive impurities, as well as as bacterial films, vitamins, amino acids, salts, and sugars) Scrooge, crowds, plastic balls every medium is maximal

Towards an Environment Ontology Substances (Anatomy, Cellular Components) Qualities, Roles, Functions Processes Environments (of Organisms, of Populations, of Proteins, ...) UN Assessment of Ecosystem Health Gewin V (2005) Eco-Defense against Invasions.

PLoS Biol 3(12): e429.

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