1 introduction to allergy ontology barry smith rho, chapel hill, october 10, 2013

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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