building biomedical ontologies
DESCRIPTION
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, - PowerPoint PPT PresentationTRANSCRIPT
![Page 1: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/1.jpg)
Building Biomedical Ontologies
Jennifer Clark, GO Editorial Office
![Page 2: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/2.jpg)
Clark et al., 2005
part_of
is_a
![Page 3: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/3.jpg)
Clark et al., 2005
![Page 4: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/4.jpg)
"encyclopaedia of Flemish children's games“ BRUEGEL
![Page 5: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/5.jpg)
![Page 6: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/6.jpg)
![Page 7: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/7.jpg)
classes
GO terms, types, kinds, universals
instances
annotated gene product attributes,
tokens, individuals, particulars
![Page 8: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/8.jpg)
Domain of Ontology
• biological process
• Loggerhead nesting
• evidence codes
• NCBI organismal classification
![Page 9: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/9.jpg)
• is_a
• part_of
• develops_from
Relationships
![Page 10: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/10.jpg)
part_of
• no necessity
• necessarily is part
• necessarily has part
• necessarily is part and necessarily has part
![Page 11: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/11.jpg)
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
![Page 12: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/12.jpg)
![Page 13: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/13.jpg)
Easy term request:
Please add
• leucophore differentiation,
• erythrophore differentiation
• cyanophore differentiation
• neuron differentiation
![Page 14: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/14.jpg)
cellular process
cell differentiation
Is_a
part_of
cell fate cell
specification development
![Page 15: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/15.jpg)
cell differentiation
osteoblast neuron keratinocyte differentiation differentiation differentiation
adipocyte garland celldifferentiation differentiation
‘X cell differentiation’
is_a
![Page 16: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/16.jpg)
Essence = Genus + Differentiae
Genus: differentiation
Differentiae: a neuron (or x cell)
![Page 17: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/17.jpg)
X cell differentiation
![Page 18: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/18.jpg)
X cell differentiation
Differentiation of an x cell.
![Page 19: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/19.jpg)
X cell differentiation
The process whereby
a relatively unspecialized cell
acquires specialized features
of an x cell.
[List characteristics of x cell.]
![Page 20: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/20.jpg)
[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
![Page 21: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/21.jpg)
[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
![Page 22: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/22.jpg)
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.
![Page 23: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/23.jpg)
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
![Page 24: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/24.jpg)
[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
![Page 25: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/25.jpg)
[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
![Page 26: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/26.jpg)
Difficult term request
• Reconcile plant trichomes and insect trichomes.
![Page 27: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/27.jpg)
Plant trichomehttp://bib18.ulb.ac.be/Botanique_I/image/6703873062005_trichome_arabidopsis.jpg
http://www.innovations-report.de/bilder_neu/40879_szymanski.trichomeLO.jpg
![Page 28: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/28.jpg)
Insect trichomehttp://www.grisda.org/tstandish/images/animalia/arthropoda/Wildtype-D.-melanogaster-EM.jpg
![Page 29: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/29.jpg)
![Page 30: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/30.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
![Page 31: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/31.jpg)
![Page 32: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/32.jpg)
Discussion…
5000 words25 A4 pages.
[ 956691 ] hair/trichome formation
https://sourceforge.net/tracker/index.php?func=detail&aid=956691&group_id=36855&atid=440764
![Page 33: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/33.jpg)
Difficult term request
• All the metamorphosis terms should be changed to morphogenesis terms.
![Page 34: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/34.jpg)
http://www.kellscraft.com/Butterflies/butter69.jpg
![Page 35: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/35.jpg)
![Page 36: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/36.jpg)
Standard structure
[i]x development
---[p] x morphogenesis
------[p] x formation
---------[p] y cell differentiation
------[p] x structural organization
---[p] x maturation
![Page 37: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/37.jpg)
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.
![Page 38: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/38.jpg)
morphogenesis terms
• x morphogenesis
• The process by which the anatomical structures of x are generated and organized. Morphogenesis pertains to the creation of form.
![Page 39: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/39.jpg)
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.
![Page 40: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/40.jpg)
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.
![Page 41: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/41.jpg)
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.
![Page 42: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/42.jpg)
http://www.aardman.com
![Page 43: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/43.jpg)
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
![Page 44: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/44.jpg)
before
after
![Page 45: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/45.jpg)
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
![Page 46: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/46.jpg)
Discussion:
10,000 words53 A4 pages
[ 1228979 ] metamorphosis termshttps://sourceforge.net/tracker/index.php?func=detail&aid=1228979&group_id=36855&atid=440764
![Page 47: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/47.jpg)
Some more ontology thoughts…
![Page 48: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/48.jpg)
Basis in Reality:
When building or maintaining an ontology, always think carefullyabout how classes relate to instances in reality
![Page 49: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/49.jpg)
molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI
Annotations
Ontology
PSBI
![Page 50: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/50.jpg)
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
![Page 51: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/51.jpg)
cartoon character super power ontology
super senses super physical powers
x-ray cat super supervision senses leaping strength
is_a
Annotations
Ontology
![Page 52: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/52.jpg)
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
![Page 53: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/53.jpg)
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
![Page 54: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/54.jpg)
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
![Page 55: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/55.jpg)
molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI
Annotations
Ontology
PSBI
![Page 56: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/56.jpg)
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
![Page 57: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/57.jpg)
3 Objectivity:
The existence of classesis not dependenton our biological knowledge.
![Page 58: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/58.jpg)
do not designate biological natural kinds.
‘unlocalised’‘unknown’ ‘unclassified’
http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm
![Page 59: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/59.jpg)
Task:
Annotate
molecular function
of 10-4,
a gene from Drosophila melanogaster
![Page 60: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/60.jpg)
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
![Page 61: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/61.jpg)
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
![Page 62: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/62.jpg)
molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
![Page 63: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/63.jpg)
With thanks…
For slides:
Barry SmithDavid Hill
For everything:
The Gene Ontology Consortium
![Page 64: Building Biomedical Ontologies](https://reader030.vdocuments.us/reader030/viewer/2022033103/56814446550346895db0e37c/html5/thumbnails/64.jpg)