1. 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.

2. 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

3. The GO is Actually Three Ontologies
Molecular Function
GO term: Malate dehydrogenase.
GO id: GO:
(S)-malate + NAD(+) = oxaloacetate + NADH.
Cellular Component
GO term: mitochondrion
GO id: GO:
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:

4. Seven Healthy Habits of Highly Effective Ontology Construction
Univocity
Positivity
Objectivity
Single Inheritance
Create Good Definitions
Distinguish Between Types & Instances
Basis in Reality

5. 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)

6. 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.

7. 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.

8. 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

9. 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

10. 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

11. 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

12. The Development Node

13. Organism/organ/tissue level
[i]x development
---[p] x morphogenesis
------[p] x formation
[p] y cell differentiation
------[p] x structural organization
---[p] x maturation

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. ---[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

21. 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

22. 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

23. 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

24. 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

25. 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

26. 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

27. 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

28. 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.)