What is Ontology? 1606 1700s 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.

So what does that mean? is part of 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. is part of

The GO is Actually Three Ontologies Molecular Function GO term: Malate dehydrogenase. GO id: GO:0030060 (S)-malate + NAD(+) = oxaloacetate + NADH. Cellular Component GO term: mitochondrion GO id: GO:0005739 Definition: 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. Biological Process GO term: tricarboxylic acid cycle Synonym: Krebs cycle Synonym: citric acid cycle GO id: GO:0006099

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 & sufficient conditions 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". Part_of relationship nucleus chromosome

Mitochondrial chromosome True Path Violations ..”the pathway from a child term all the way up to its top-level parent(s) must always be true". chromosome Mitochondrial chromosome Is_a relationship

True Path Violations ..”the pathway from a child term all the way up to its top-level parent(s) must always be true". Part_of relationship nucleus A mitochondrial chromosome is not part of a nucleus! chromosome Mitochondrial chromosome Is_a relationship

Mitochondrial chromosome True Path Violations ..”the pathway from a child term all the way up to its top-level parent(s) must always be true". nucleus chromosome Nuclear chromosome Mitochondrial chromosome Is_a relationships Part_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. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation zygote http://www.dof.virginia.gov/images/ http://hypertextbook.com/chaos/33.shtml

x morphogenesis The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation 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. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation Limb bud http://www.sciencemuseum.org.uk/exhibitions/lifecycle/images/1-2-1-2-1-1-0-0-0-0-0.jpg

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. [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation http://www.mun.ca/biology/desmid/brian/BIOL3530/DB_Ch05/fig5_20.jpg

---[p] x morphogenesis ------[p] x formation x maturation A developmental process, independent of morphogenetic (shape) change, that is required for x to attain its fully functional state. [description of x] [i]x development ---[p] x morphogenesis ------[p] x formation ------[p] x structural organization ---[p] x maturation http://www.dof.virginia.gov/images/

y cell differentiation The process whereby a relatively unspecialized cell acquires specialized features of a y cell. [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 http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=cmed6.figgrp.41173

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

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.)