Transcript Relationships - Gene Ontology

Building Biomedical
Ontologies
Jennifer Clark, GO Editorial Office
Clark et al., 2005
is_a
part_of
Clark et al., 2005
"encyclopaedia of Flemish children's games“ BRUEGEL
classes
GO terms, types, kinds, universals
instances
annotated gene product attributes,
tokens, individuals, particulars
Domain of Ontology
•
•
•
•
biological process
Loggerhead nesting
evidence codes
NCBI organismal classification
Relationships
• is_a
• part_of
• develops_from
part_of
•
•
•
•
no necessity
necessarily is part
necessarily has part
necessarily is part and necessarily
has part
How to define A is_a B
A is_a B =def.
1. A and B are names of universals
(natural kinds, types) in reality
2. all instances of A are as a matter of
biological science also instances of B
Easy term request:
Please add
• leucophore differentiation,
• erythrophore differentiation
• cyanophore differentiation
• neuron differentiation
cellular process
Is_a
cell differentiation
part_of
cell fate
specification
cell
development
cell differentiation
is_a
osteoblast
differentiation
neuron
differentiation
adipocyte
differentiation
keratinocyte
differentiation
garland cell
differentiation
‘X cell differentiation’
Essence = Genus + Differentiae
Genus: differentiation
Differentiae: a neuron (or x cell)
X cell differentiation
X cell differentiation
Differentiation of an x cell.
X cell differentiation
The process whereby
a relatively unspecialized cell
acquires specialized features
of an x cell.
[List characteristics of x cell.]
[Term]
id: GO:0030182
name: neuron differentiation
namespace: biological_process
def: "The process whereby a relatively unspecialized cell
acquires specialized features of a neuron." [GO:mah]
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0048699 ! neurogenesis
[Term]
id: CL:0000540
name: neuron
def: "The basic cellular unit of nervous tissue. Each neuron
consists of a body\, an axon\, and dendrites. Their purpose
is to receive\, conduct\, and transmit impulses in the
nervous system." [MESH:A.08.663]
xref_analog: FBbt:00005106
xref_analog: FBbt:00005146
is_a: CL:0000393 ! electrically responsive cell
is_a: CL:0000404 ! electrically signaling cell
relationship: develops_from CL:0000031 ! neuroblast
http://cancerweb.ncl.ac.uk
• neuron
• An excitable cell specialised for the transmission of
electrical signals over long distances. Neurons receive
input from sensory cells or other neurons and send
output to muscles or other neurons. Neurons with
sensory input are called sensory neurons, neurons with
muscle outputs are called motoneurons, neurons that
connect only with other neurons are called interneurons.
Neurons connect with each other via synapses. Neurons
can be the longest cells known, a single axon can be
several metres in length. Although signals are usually
sent via action potentials, some neurons are nonspiking.
Stedman's Online Medical
Dictionary
• neuron (noor on)
• The morphologic and functional unit of the
nervous system, consisting of the nerve
cell body, the dendrites, and the axon.
Syn: neurone Syn: neurocyte, nerve cell
[Term]
id: GO:0030182
name: neuron differentiation
namespace: biological_process
def: "The process whereby a relatively unspecialized cell
acquires specialized features of a neuron. The basic cellular
unit of nervous tissue. Each neuron consists of a body\, an
axon\, and dendrites. Their purpose is to receive\, conduct\,
and transmit impulses in the nervous system."
[MESH:A.08.663, GO:mah]
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0048699 ! neurogenesis
[Term]
id: GO:0030182
name: neuron differentiation
namespace: biological_process
def: "The process whereby a relatively unspecialized cell
acquires specialized features of a neuron. The basic cellular
unit of nervous tissue. Each neuron consists of a body\, an
axon\, and dendrites. Their purpose is to receive\, conduct\,
and transmit impulses in the nervous system."
[MESH:A.08.663, GO:mah]
is_a: GO:0030154 ! cell differentiation
relationship: part_of GO:0048699 ! neurogenesis
intersection_of: is_a GO:0030154 ! cell differentiation
intersection_of: has_participant CL:0000540 ! neuron
Difficult term request
• Reconcile plant trichomes and insect
trichomes.
Plant trichome
http://bib18.ulb.ac.be/Botanique_I/image/6703873062005_trichome_arabidopsis.jpg
http://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg
Insect trichome
http://www.grisda.org/tstandish/images/animalia/arthropoda/Wildtype-D.-melanogaster-EM.jpg
• If a plant trichome is a hair cell, and an
insect trichome is a cell hair, then plant
trichome differentiation would be an is_a
of hair cell differentiation. And insect
trichome formation could be a part_of hair
cell differentiation.
Becky Foulger 2004-08-04
Discussion…
5000 words
25 A4 pages.
[ 956691 ] hair/trichome formation
https://sourceforge.net/tracker/index.php?func=detail&aid
=956691&group_id=36855&atid=440764
Difficult term request
• All the metamorphosis terms should be
changed to morphogenesis terms.
http://www.kellscraft.com/Butterflies/butter69.jpg
Standard structure
[i]x development
---[p] x morphogenesis
------[p] x formation
---------[p] y cell differentiation
------[p] x structural organization
---[p] x maturation
Standard definitions
• x development
• The process whose specific outcome is the progression of the x over
time, from its formation to the mature structure.
• x morphogenesis
• The process by which the anatomical structures of x are generated
and organized. Morphogenesis pertains to the creation of form.
• x formation
• The process that gives rise to x. This process pertains to the initial
formation of a structure from unspecified parts.
• 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.
morphogenesis terms
• x morphogenesis
• The process by which the anatomical
structures of x are generated and
organized. Morphogenesis pertains to the
creation of form.
metamorphosis terms
'leg disc metamorphosis' ; GO:0007478
def: The transformation of a leg imaginal
disc from a monolayered epithelium in the
larvae of holometabolous insects into
recognizable adult structures including the
leg, coxa and ventral thoracic pleura.
Rules
Changes can be made to terms:
• Annotations must still be true afterwards.
•
•
•
•
Name needs changed. Do it.
Definition wording needs changed. Do it.
Position in the graph needs changed. Do it.
Definition meaning needs changed. Obsolete
the term.
x morphogenesis
starting structure
x mature structure
The process by which the
anatomical structures of x are
generated and organized.
Morphogenesis pertains to the
creation of form.
gene products act here
x metamorphosis
multiple mature structures
The transformation of a
leg imaginal disc from a
monolayered epithelium in
the larvae of
holometabolous insects
into recognizable adult
structures including the
leg, coxa and ventral
thoracic pleura.
x starting structure
gene products act here
http://www.aardman.com
Gromit morphogenesis
blob of plasticine
Gromit
‘gene products’ act here
Aardman plasticine
metamorphosis
All the individual characters in the cast
of Wallace and Gromit films
huge ball
of plasticine
Wallace
Gromit
Killer penguin
Shaun the sheep
‘gene products’ act here
after
before
Fixed metamorphosis terms
• leg disc morphogenesis
• Def: The process by which the anatomical
structures derived from the leg disc are
generated and organized. Morphogenesis
pertains to the creation of form.
[description]
• exact_synonym: leg disc metamorphosis
Discussion:
10,000 words
53 A4 pages
[ 1228979 ] metamorphosis terms
https://sourceforge.net/tracker/index.php?func=detail&aid
=1228979&group_id=36855&atid=440764
Some more
ontology thoughts…
Basis in Reality:
When building or maintaining an
ontology, always think carefully
about how classes relate to
instances in reality
molecular function
Ontology
binding
tetrapyrrole binding
cofactor binding
is_a
chlorophyll
binding
PSBI
Annotations
heme
binding
coenzyme
binding
quinone
binding
PSBI
Catwoman
strength,
speed,
agility
and ultra-keen senses of a cat.
http://home.austarnet.com.au/davekimble/catwoman.jpg
superman
strength
flight
x-ray vision
leaps over tall buildings in a single bound
http://www.uncleodiescollectibles.com/doesnotcompute/2004-10-11/Actor%20Christoper%20Reeve.jpg
Ontology
cartoon character super power ontology
super senses
super physical powers
is_a
x-ray
vision
Annotations
cat
senses
super
leaping
super
strength
Ontology
cartoon character super power ontology
super senses
super physical powers
is_a
x-ray
vision
Superman
cat
senses
super
leaping
Catwoman
Catwoman
Superman
Annotations
super
strength
Ontology
cartoon character super power ontology
super senses
super physical powers
is_a
x-ray
vision
Superman’s
X-ray vision
Annotations
cat
senses
Catwoman’s
cat senses
super
leaping
Superman’s
super leaping
super
strength
Catwoman’s
super strength
Ontology
cartoon character super power ontology
is_a
super senses
Superman’s
X-ray vision
Annotations
Catwoman’s
cat senses
super physical powers
Superman’s
super leaping
Catwoman’s
super strength
molecular function
Ontology
binding
tetrapyrrole binding
cofactor binding
is_a
chlorophyll
binding
PSBI
Annotations
heme
binding
coenzyme
binding
quinone
binding
PSBI
molecular function
Ontology
binding
tetrapyrrole binding
cofactor binding
is_a
chlorophyll
binding
PSBI’s chlorophyll
binding function
Annotations
heme
binding
coenzyme
binding
quinone
binding
PSBI’s quinone
binding function
3 Objectivity:
The existence of classes
is not dependent
on our biological knowledge.
‘unlocalised’
‘unknown’
‘unclassified’
http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm
do not designate biological
natural kinds.
Task:
Annotate
molecular function
of 10-4,
a gene from Drosophila melanogaster
Molecular function ontology
Annotations
molecular function
is_a
molecular function
unknown
10-4
Molecular function ontology
molecular function
is_a
molecular function
unknown
Annotations
10-4
Molecular function ontology
molecular function
is_a
molecular function
unknown
Annotations
10-4
With thanks…
For slides:
Barry Smith
David Hill
For everything:
The Gene Ontology Consortium