1 Introduction to Allergy Ontology Barry Smith Rho, Chapel Hill, October 10, 2013.
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Transcript of 1 Introduction to Allergy Ontology Barry Smith Rho, Chapel Hill, October 10, 2013.
1
Introduction to Allergy Ontology
Barry SmithRho, 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
Gene
“TrpA”
Protein
Tryptophan Synthetase
Chemical
hasName
expresseshasName
hasSubstrate
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Uniprot Concept
Acetoin Biosynthesis Protein involved in the synthesis of acetoin
urn:lsid:uniprot.org:go:45151
rdf:type owl:sameAs
rdf:comment
Uniprot Keywords in RDF
After Eric Jain http://www.isb-sib.ch/~ejain/rdf/
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UniProt RDF
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
Ontology provides a comprehensive hierarchical view of a domain as opposed to a flat and partial representation of a data-model
Computer Skill
Single Ontology Multiple Data modelsPersonPerson
Person Name
First Name
Last Name
PersonSkill
PersonName NetworkSkill ProgrammingSkill
Is-a Bearer-of
Skill
Last Name First Name Skill
Person Name Computer SkillProgrammingSkill
NetworkSkill
Skill
Ontology annotates Data ModelSource database Db1, with tables Db1.Person and Db1.Skill,
containing person data and data pertaining to skills of different kinds, respectively.
Source database Db2.Person, containing data about IT personnel and their skills:
Source database Db3.ProgrSkill, containing data about programmers’ skills:
PersonID SkillID
111 222
SkillID Name Description
222 Java Programming
ID SkillDescr
333 SQL
EmplID SkillName
444 Java
http://amigo.geneontology.org/
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12T-helper 2 cell lineage
commitment
Basic Formal Ontology
continuant occurrent
independentcontinuant
dependentcontinuant
organism
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http://www.ifomis.org/bfo
depends_on
Continuant Occurrent
process, eventIndependentContinuant
thing
DependentContinuant
quality
.... ..... .......temperature dependson bearer
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this particular case of redness (of a particular fly eye)
the universal red
instantiates
an instance of eye (in a particular fly)
the universal eye
instantiates
depends_on
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Phenotype Ontology (PATO)
the particular case of redness (of a particular fly eye)
red
instantiates
an instance of an eye (in a particular fly)
eye
instantiates
depends on
color anatomical structure
is_a is_a
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BFO: The Very Top
continuant
independentcontinuant
dependentcontinuant
quality
occurrent
temperature17
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature 18
independentcontinuant
dependentcontinuant
quality
temperature types
instances
organism
John John’s
temperature
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independentcontinuant
dependentcontinuant
quality
temperatureorganism
John John’s
temperature
occurrent
process
course of temperature
changes
John’s temperature history
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independentcontinuant
dependentcontinuant
quality
temperatureorganism
John John’s
temperature
occurrent
process
life of an organism
John’s life
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BFO: The Very Top
continuant occurrent
independentcontinuant
dependentcontinuant
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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independentcontinuant
dependentcontinuant
disposition
diseasedisorder
John’s IgE-mediated
allergic disorder
John’s allergic disease
occurrent
process
course of 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