What is Ontology? by gcpCOvQ

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


  O     OH
                                   O
        H                     O
 HO
                                       OH
         H
   H                          H    H
   HO    O
                              HO   O




                                                       Cellular Component
                                                       GO term: mitochondrion
Biological Process                                     GO id: GO:0005739
GO term: tricarboxylic acid                            Definition: A semiautonomous, self
cycle                                                  replicating organelle that occurs in
Synonym: Krebs cycle                                   varying numbers, shapes, and sizes in
Synonym: citric acid cycle                             the cytoplasm of virtually all eukaryotic
GO id:      GO:0006099                                 cells. It is notably the site of tissue
                                                       respiration.
    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".




                                                     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             chromosome                             mitochondrion

       Part_of                                                                               Part_of
     relationship                         Is_a relationships                               relationship

                    Nuclear                                                Mitochondrial
                  chromosome                                               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                         [i]x development
                                      ---[p] x morphogenesis
                                      ------[p] x formation
The process whose                     ------[p] x structural organization
specific outcome is the               ---[p] x maturation
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
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.)

								
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