principles for building biomedical ontologies
DESCRIPTION
Principles for Building Biomedical Ontologies. Talk delivered by Jennifer Clark, GO Editorial Office. Clark et al ., 2005. is_a. part_of. Clark et al ., 2005. Slides and content by:. Barry Smith http://ifomis.de Rama Balakrishnan, David Hill, Jennifer Clark. http://www.geneontology.org. - PowerPoint PPT PresentationTRANSCRIPT
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Principles for Building Biomedical Ontologies
Talk delivered by Jennifer Clark, GO Editorial Office
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Clark et al., 2005
part_of
is_a
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Clark et al., 2005
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•formal ontology
•information science
•special reference to the bio-medical domain.
Barry Smith
http://ifomis.de
Rama Balakrishnan, David Hill, Jennifer Clark.
http://www.geneontology.org
Slides and content by:
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The Rules
1. Univocity
2. Positivity
3. Objectivity
4. Single Inheritance
5. Intelligibility of Definitions
6. Basis in Reality
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classes
GO terms, types, kinds, universals
instances
annotated gene product attributes,
tokens, individuals, particulars
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1 Univocity:
Terms should have the same meanings on every occasion of use
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= bud initiation
= bud initiation
= bud initiation
The Challenge of Univocity: People use the same words to describe different things
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Bud initiation? How is a computer to distinguish?
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= bud initiation
sensu Metazoa
= bud initiation
sensu Saccharomyces
= bud initiation
sensu Viridiplantae
Univocity: GO adds “sensu” descriptors to discriminate among organisms
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Tactile senseTactionTactition
?
The Challenge of Univocity:People call the same thing by different names
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Tactile senseTactionTactition
perception of touch ; GO:0050975
Univocity: GO uses 1 term and many characterized synonyms
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‘is at times part of’ antlers part_of red deer
‘necessarily is_part’ Seed dormancy part_of seed development
‘necessarily has_part’ Plant embryo part_of seed
Univocity in part_of relation
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2 Positivity:
The complements of classes are not themselves classes.
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Vertebrates
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
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Vertebratesnon-vertebrates
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
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Vertebratesnon-vertebrates
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
http://www.digibarn.com/collections/systems/canon-cat/Image53.jpg
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Vertebratesnon-vertebratesSet of
all things
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
http://www.digibarn.com/collections/systems/canon-cat/Image53.jpg
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VertebratesSet of
all organisms
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
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VertebratesInvertebratesSet of
all organisms
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
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VertebratesInvertebratesSet of
all organisms
http://www.artalyst.com/files/userimages/user70/21088058-O.preview.jpg
http://www.cucco.org/CatPictures/Cat%20Nap.jpg
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membrane-bound organelle
GO:0043227
V. Not a membrane bound organelle
Non-membrane bound organelle
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A centrosome is not a membrane bound organelle,but it still may be considered an organelle.
Non-membrane bound organelles
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3 Objectivity:
The existence of classesis not dependenton our biological knowledge.
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do not designate biological natural kinds.
‘unlocalised’‘unknown’ ‘unclassified’
http://news.bbc.co.uk/1/hi/sci/tech/4501152.stm
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Task:
Annotate
molecular function
of 10-4,
a gene from Drosophila melanogaster
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molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
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molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
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molecular function
molecular function unknown
is_a
10-4
Molecular function ontology Annotations
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4 Single Inheritance:
No class in a classificationhierarchy should have morethan one is_a parent on theimmediate higher level
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Clark et al., 2005
part_of
is_a
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Rule of Single Inheritance
no diamonds:
C
is_a2
B
is_a1
A
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Problems with multiple inheritance
B C
is_a1 is_a2
A
‘is_a’ no longer univocal
(univocal: having only one meaning)
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Is_a diamond in GO Process
behavior
locomotory behavior larval behavior
larval locomotory behavior
is_a
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behavior
locomotory behavior larval behavior
larval locomotory behavior
behavior of a thingdescriptive
behavior
is_a
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Is_a diamond in GO Process
behavior
locomotory behavior
larval behavior
larval locomotory
behavior
is_a1 is_a2
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5 Intelligibility of Definitions:
The terms used in a definition should be simplerthan the term to be defined
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cellular process
cell differentiation
cell fate cell
Specification development
Is_a
part_of
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cell differentiation
osteoblast neuron keratinocyte differentiation differentiation differentiation
adipocyte garland celldifferentiation differentiation
‘X cell differentiation’
is_a
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Essence = Genus + Differentiae
Genus: differentiation
Differentiae: a neuron (or x cell)
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X cell differentiation
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X cell differentiation
Differentiation of an x cell.
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X cell differentiation
The process whereby
a relatively unspecialized cell
acquires specialized features
of an x cell.
[List characteristics of x cell.]
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cone cell fate commitment retinal_cone_cell
keratinocyte differentiation keratinocyte
adipocyte differentiation fat_cell
dendritic cell activation dendritic_cell
Process ontology Cell Ontology
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[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
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[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
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[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 differentiationintersection_of: is_a GO:0030154 ! cell differentiationintersection_of: has_participant CL:0000540 ! neuron
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Other Ontologies that can be aligned with GO
Chemical ontologies 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Anatomy ontologies metanephros development
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But Eventually…
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Building Ontology
Improve
Collaborate and Learn
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6 Basis in Reality:
When building or maintaining an ontology, always think carefullyabout how classes relate to instances in reality
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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
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cartoon character super power ontology
super senses super physical powers
x-ray cat super supervision senses leaping strength
is_a
Annotations
Ontology
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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
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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
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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
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molecular function
binding
tetrapyrrole binding cofactor binding
chlorophyll heme coenzyme quinonebinding binding binding binding
is_a
PSBI
Annotations
Ontology
PSBI
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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
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The Rules1. Univocity: Terms should have the same meanings
on every occasion of use2. Positivity: Terms such as ‘non-mammal’ or ‘non-
membrane’ do not designate genuine classes.3. Objectivity: Terms such as ‘unknown’ or
‘unclassified’ or ‘unlocalized’ do not designate biological natural kinds.
4. Single Inheritance: No class in a classification hierarchy should have more than one is_a parent on the immediate higher level
5. Intelligibility of Definitions: The terms used in a definition should be simpler (more intelligible) than the term to be defined
6. Basis in Reality: When building or maintaining an ontology, always think carefully about how classes relate to instances in reality
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END
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spare slides follow.
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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
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True path violationWhat is it?
chromosome
Mitochondrial chromosome
Is_a relationship
Part_of relationship
nucleus
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True path violationWhat is it?
nucleus chromosome
Nuclear chromosome
Mitochondrial chromosome
Is_a relationshipsPart_of relationship
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The Importance of synonyms for utility:How do we represent the function of tRNA?
Molecular_function
Triplet_codon amino acid adaptor activity
GO Definition: Mediates the insertion of an amino acid at the correct point in the sequence of a nascent polypeptide chain during protein synthesis.
Synonym: tRNA
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Main obstacle to integration
Current ontologies do not deal well with Time and Space and Instances (particulars)
Our definitions should link the terms in the ontology to instances in spatio-temporal reality
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7 Distinguish Universals and Instances
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Don’t forget instances when defining relations
part_of as a relation between classes versus part_of as a relation between instances
nucleus part_of cell your heart part_of you
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•formal ontology
•information science
•special reference to the bio-medical domain.
Barry Smith
http://ifomis.de
Rama Balakrishnan, David Hill, Jennifer Clark.
http://www.geneontology.org
Slides and content by: