What is Ontology? Dictionary:A branch of metaphysics concerned with the nature and relations of being. Barry Smith:The science of what is, of the kinds

What is Ontology?

• Dictionary:A branch of metaphysics concerned with the nature and relations of being.

• Barry Smith:The science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality.

16061700s

So what does that mean?From a practical view, ontology is the representation of something we know about. “Ontologies" consist of a representation of things, that are detectable or directly observable, and the relationships between those

things.

The GO is Actually Three Ontologies

Biological ProcessGO term: tricarboxylic acid cycleSynonym: Krebs cycleSynonym: citric acid cycleGO id: GO:0006099

Cellular ComponentGO term: mitochondrionGO id: GO:0005739Definition: A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Molecular FunctionGO term: Malate dehydrogenase. GO id: GO:0030060(S)-malate + NAD(+) = oxaloacetate + NADH.

H

O

H

O

O

H

O

H

O

H

H

O

O

H

O

H

O

H

H

O

NAD+NADH + H+

Seven Healthy Habits of Highly Effective Ontology Construction

• Univocity

• Positivity

• Objectivity

• Single Inheritance

• Create Good Definitions

• Distinguish Between Types & Instances

• Basis in Reality

GO Definitions: Each GO term has 2 Definitions

A definition written by a biologist:

necessary & sufficientconditions

written definition(not computable)

Graph structure: necessary conditions

formal(computable)

Appropriate Relationships to Parents

• GO currently has 2 relationship types– Is_a

• An is_a child of a parent means that the child is a complete type of its parent, but can be discriminated in some way from other children of the parent.

– Part_of• A part_of child of a parent means that the child is

always a constituent of the parent that in combination with other constituents of the parent make up the parent.

Placement in the Graph: Selecting Parents

• To make the most precise definitions, new terms should be placed as children of the parent that is closest in meaning to the term.

• To make the most complete definitions, terms should have all of the parents that are appropriate.

• In an ontology as complicated as the GO this is not as easy as it seems.

True Path Violations Create Incorrect Definitions

..”the pathway from a child term all the way up to its top-level parent(s) must always be true".

chromosome

Part_of relationship

nucleus

True Path Violations


chromosome

Mitochondrial chromosome

Is_a relationship



chromosome


Is_a relationship


nucleus

A mitochondrial chromosome is not part of a nucleus!



nucleus chromosome

Nuclear chromosome


Is_a relationshipsPart_of

relationship

mitochondrion


The Development Node

Organism/organ/tissue level

[i]x development ---[p] x morphogenesis ------[p] x formation ---------[p] y cell differentiation ------[p] x structural organization---[p] x maturation

Cell level

[i] y cell differentiation---[p] y cell fate commitment ------[p] y cell fate specification ------[p] y cell fate determination ---[p] y cell development ------[p] y cellular morphogenesis during differentiation ------[p] y cell maturation

Regulation terms

[i] y cell differentiation ---[p] regulation of y cell differentiation ------[i] positive regulation of y cell differentiation ------[i] negative regulation of y cell differentiation

x development

The process whose specific outcome is the progression of the x over time, from its formation to the mature structure.

zygote

http://www.dof.virginia.gov/images/http://hypertextbook.com/chaos/33.shtml

[i]x development---[p] x morphogenesis ------[p] x formation ------[p] x structural organization---[p] x maturation

x morphogenesis

The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.

http://www.campdevanol.com/blogger/archives/2005_05_01_campdevanol_archive.html


x formation

The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts.

http://www.sciencemuseum.org.uk/exhibitions/lifecycle/images/1-2-1-2-1-1-0-0-0-0-0.jpg

Limb bud


x structural organization

The process that contributes to creating the structural organization of x.This process pertains to the physical shaping of a rudimentary structure.

http://www.mun.ca/biology/desmid/brian/BIOL3530/DB_Ch05/fig5_20.jpg


x maturation

A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state. [description of x]

http://www.dof.virginia.gov/images/


y cell differentiation

The process whereby a relatively unspecialized cell acquires specialized features of a y cell.

http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cmed6.figgrp.41173

[i] y cell differentiation---[p] y cell fate commitment------[p] y cell fate specification------[p] y cell fate determination---[p] y cell development------[p] y cellular morphogenesis during differentiation------[p] y cell maturation

y cell fate commitment

The process whereby the developmental fate of a cell becomes restricted such that it will develop into a y cell.


y cell fate specification

The process whereby a cell becomes capable of differentiating autonomously into a y cell in an environment that is neutral with respect to the developmental pathway. Upon specification, the cell fate can be reversed.


y cell fate determination

The process whereby a cell becomes capable of differentiating autonomously into a y cell regardless of its environment; upon determination, the cell fate cannot be reversed.


y cell development

The process aimed at the progression of a y cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.

[i] y cell differentiation---[p] y cell fate commitment---[p] y cell development------[p] y cellular morphogenesis during differentiation------[p] y cell maturation

y cell morphogenesis during differentiation

The process by which the structures of a y cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a y cell.

[i] y cell differentiation---[p] y cell fate commitment---[p] y cell development------[p] y cellular morphogenesis during differentiation------[p] y cell maturation

http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg

y cell maturation

A developmental process, independent of morphogenetic (shape) change, that is required for a y cell to attain its fully functional state. [description of y]


is_a completeness

Logically, everything that exists is a sub-type of something else.

(There’s a prize if you can think of an exception.)

Documents

What is Ontology? Dictionary:A branch of metaphysics concerned with the nature and relations of being. Barry Smith:The science of what is, of the kinds