Transcript What is Ontology?

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?
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
Molecular Function
GO term: Malate dehydrogenase.
GO id: GO:0030060
(S)-malate + NAD(+) = oxaloacetate + NADH.
NAD+
O
HO
H
HO
NADH + H+
OH
O
H
O
OH
H
H
H
HO
O
O
Biological Process
GO term: tricarboxylic acid
cycle
Synonym: Krebs cycle
Synonym: citric acid cycle
GO id:
GO:0006099
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.
Seven Healthy Habits of Highly
Effective Ontology Construction
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•
•
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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".
nucleus
Part_of relationship
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
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
A mitochondrial chromosome is not part of a nucleus!
Part_of relationship
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
Part_of
relationship
Nuclear
chromosome
chromosome
Is_a relationships
mitochondrion
Part_of
relationship
Mitochondrial
chromosome
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
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
http://www.nature.com/ncb/journal/v6/n8/images/ncb0804-707-I1.jpg
---[p] y cell development
------[p] y cellular morphogenesis during differentiation
------[p] y cell maturation
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.)