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Introduction to Allergy Ontology
Barry Smith
Rho, Chapel Hill, October 10, 2013
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RDF: Collections of Triples
(Subject – Predicate – Object)
Gene
hasName
“TrpA”
Gene
expresses
Protein
Protein
hasName
Tryptophan Synthetase
Protein hasSubstrate Chemical
from: Semantic Webs for Life Sciences, Bodenreider, Lussier, Stevens
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Aggregation of Triples
hasName
“TrpA”
Gene
expresses
hasName
Tryptophan Synthetase
Protein
hasSubstrate
Chemical
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Uniprot Keywords in RDF
rdf:comment
Acetoin Biosynthesis
rdf:type
Protein involved in the
synthesis of acetoin
owl:sameAs
Uniprot Concept
urn:lsid:uniprot.org:go:45151
After Eric Jain
http://www.isb-sib.ch/~ejain/rdf/
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UniProt RDF
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http://www.isb-sib.ch/~ejain/rdf/intro.html
OWL: Web Ontology Language
(RDF + Reasoning)
from: Ian Horrocks, OWL 2: The Next Generation
Saturation-based Technique (basics)
Example:
Ontology vs. Data-Model
Single Ontology
Multiple Data models
Person
Person
Skill
Person
Name
Computer
Skill
PersonName
NetworkSkill
ProgrammingSkill
PersonSkill
Last Name
Last
Name
Programming Network
Skill
Skill
Is-a
Bearer-of
First
Name
First Name
Skill
Skill
Person Name
Computer Skill
Ontology provides a comprehensive hierarchical view of a
domain as opposed to a flat and partial representation of
a data-model
Ontology annotates Data Model
Source database Db1, with tables Db1.Person and Db1.Skill,
containing person data and data pertaining to skills of
different kinds, respectively.
PersonID
SkillID
111
222
SkillID Name
222
Java
Description
Programming
Source database Db2.Person, containing data about IT
personnel and their skills:
ID
333
SkillDescr
SQL
Source database Db3.ProgrSkill, containing data about
programmers’ skills:
EmplID
444
SkillName
Java
http://amigo.geneontology.org/
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T-helper 2 cell lineage commitment
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Basic Formal Ontology
continuant
independent
continuant
occurrent
dependent
continuant
organism
http://www.ifomis.org/bfo
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depends_on
Continuant
Independent
Continuant
Dependent
Continuant
thing
quality
Occurrent
process, event
temperature depends
on bearer
.... ..... .......
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the universal red
instantiates
the universal eye
instantiates
this particular case depends_on an instance of eye
of redness (of a
(in a particular fly)
particular fly eye)
Phenotype Ontology (PATO)
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color
anatomical structure
is_a
is_a
red
instantiates
the particular case
of redness (of a
particular fly eye)
eye
instantiates
depends on
an instance of an
eye (in a particular
fly)
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BFO: The Very Top
continuant
independent
continuant
occurrent
dependent
continuant
quality
temperature
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independent
continuant
dependent
continuant
quality
organism
John
temperature
types
John’s
temperature
instances
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independent
continuant
dependent
continuant
quality
organism
John
temperature
types
John’s
temperature
instances
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independent
continuant
organism
John
dependent
continuant
occurrent
quality
process
temperature
John’s
temperature
course of
temperature
changes
John’s
temperature history
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independent
continuant
organism
John
dependent
continuant
occurrent
quality
process
temperature
John’s
temperature
life of an
organism
John’s
life
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BFO: The Very Top
continuant
independent
continuant
occurrent
dependent
continuant
quality
disposition
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Disposition
- of a glass vase, to shatter if dropped
- of a human, to eat
- of a banana, to ripen
- of John, to anaphylactic shock
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peanut allergy
peanut allergy disorder = mast cells and basophils with
peanut allergen-specific IgE bound to their membranes
peanut allergy disease: IgE-mediated hypersensitivity to
peanut allergen(s)
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independent
continuant
disorder
John’s
IgE-mediated
allergic disorder
dependent
continuant
occurrent
disposition
process
disease
course of
disease
John’s
allergic disease
course of John’s
peanut allergy
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terms for an allergy ontology
allergic reaction
acute urticaria (hives)
allergic angioedema
allergic rhinitis
allergic asthma
anaphylaxis
mast cell/basophil degranulation
peanut allergy
milk allergy
ragweed allergy
dust mite allergy