Building Biomedical Ontologies Jennifer Clark, GO Editorial Office
Dec 28, 2015
Building Biomedical Ontologies
Jennifer Clark, GO Editorial Office
Clark et al., 2005
part_of
is_a
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
• is_a
• part_of
• develops_from
Relationships
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
cell differentiation
Is_a
part_of
cell fate cell
specification development
cell differentiation
osteoblast neuron keratinocyte differentiation differentiation differentiation
adipocyte garland celldifferentiation differentiation
‘X cell differentiation’
is_a
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:0030182name: neuron differentiationnamespace: biological_process
def: "The process whereby a relatively unspecialized cell acquires specialized features of a neuron." [GO:mah]
is_a: GO:0030154 ! cell differentiationrelationship: part_of GO:0048699 ! neurogenesis
[Term]id: CL:0000540name: neuron
def: "The basic cellular unit of nervous tissue. Each neuronconsists of a body\, an axon\, and dendrites. Their purposeis to receive\, conduct\, and transmit impulses in the nervous system." [MESH:A.08.663]
xref_analog: FBbt:00005106xref_analog: FBbt:00005146is_a: CL:0000393 ! electrically responsive cellis_a: CL:0000404 ! electrically signaling cellrelationship: 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:0030182name: neuron differentiationnamespace: 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 differentiationrelationship: part_of GO:0048699 ! neurogenesis
[Term]id: GO:0030182name: neuron differentiationnamespace: 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 differentiationrelationship: part_of GO:0048699 ! neurogenesisintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000540 ! neuron
Difficult term request
• Reconcile plant trichomes and insect trichomes.
Plant trichomehttp://bib18.ulb.ac.be/Botanique_I/image/6703873062005_trichome_arabidopsis.jpg
http://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg
Insect trichomehttp://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 words25 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.
starting structure x mature structure
x morphogenesis
gene products act here
x metamorphosis multiple mature structures
gene products act here
x starting structure
The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.
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.
http://www.aardman.com
blob of plasticine Gromit
Gromit morphogenesis
‘gene products’ act here
Aardman plasticine metamorphosis
All the individual characters in the cast of Wallace and Gromit films
‘gene products’ act here
huge ball of plasticine Wallace
Gromit
Killer penguin
Shaun the sheep
before
after
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 words53 A4 pages
[ 1228979 ] metamorphosis termshttps://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 carefullyabout how classes relate to instances in reality
molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI
Annotations
Ontology
PSBI
supermanstrengthflightx-ray visionleaps over tall buildings in a single bound
Catwomanstrength,speed,agilityand ultra-keen senses of a cat.
http://www.uncleodiescollectibles.com/doesnotcompute/2004-10-11/Actor%20Christoper%20Reeve.jpg
http://home.austarnet.com.au/davekimble/catwoman.jpg
cartoon character super power ontology
super senses super physical powers
x-ray cat super supervision senses leaping strength
is_a
Annotations
Ontology
cartoon character super power ontology
super senses super physical powers
x-ray cat super supervision senses leaping strength
is_a
Catwoman Catwoman
Annotations
Ontology
Superman
Superman
cartoon character super power ontology
super senses super physical powers
x-ray cat super supervision senses leaping strength
is_a
Catwoman’scat senses
Catwoman’ssuper strength
Annotations
Ontology
Superman’sX-ray vision
Superman’ssuper leaping
cartoon character super power ontology
super senses super physical powers
is_a
Catwoman’scat senses
Catwoman’ssuper strength
Annotations
Ontology
Superman’sX-ray vision
Superman’ssuper leaping
molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI
Annotations
Ontology
PSBI
molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI’s quinone binding function
Annotations
Ontology
PSBI’s chlorophyll binding function
3 Objectivity:
The existence of classesis not dependenton our biological knowledge.
do not designate biological natural kinds.
‘unlocalised’‘unknown’ ‘unclassified’
http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm
Task:
Annotate
molecular function
of 10-4,
a gene from Drosophila melanogaster
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
With thanks…
For slides:
Barry SmithDavid Hill
For everything:
The Gene Ontology Consortium