1 Introduction to Allergy Ontology Barry Smith Rho, Chapel Hill, October 10, 2013

2 RDF: Collections of Triples (Subject – Predicate – Object) GenehasName“TrpA” GeneexpressesProtein hasNameTryptophan Synthetase ProteinhasSubstrateChemical from: Semantic Webs for Life Sciences, Bodenreider, Lussier, Stevens

3 Aggregation of Triples Gene “TrpA” Protein Tryptophan Synthetase Chemical hasName expresses hasName hasSubstrate

4 Uniprot Concept Acetoin BiosynthesisProtein 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

5 UniProt RDF

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 OntologyMultiple Data models Person Person Name First Name Last Name PersonSkill PersonName NetworkSkillProgrammingSkill Is-a Bearer-of Skill Last Name First Name Skill Person NameComputer Skill Programming Skill Network Skill

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. Source database Db2.Person, containing data about IT personnel and their skills: Source database Db3.ProgrSkill, containing data about programmers’ skills: PersonIDSkillID SkillIDNameDescription 222JavaProgramming IDSkillDescr 333SQL EmplIDSkillName 444Java

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12 T-helper 2 cell lineage commitment

Basic Formal Ontology continuant occurrent independent continuant dependent continuant organism 13

depends_on Continuant Occurrent process, event Independent Continuant thing Dependent Continuant quality temperature depends on bearer 14

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 15 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 coloranatomical structure is_a 16

BFO: The Very Top continuant independent continuant dependent continuant quality occurrent temperature 17

independent continuant dependent continuant quality temperature types instances organism John John’s temperature 18

independent continuant dependent continuant quality temperature types instances organism John John’s temperature 19

independent continuant dependent continuant quality temperature organism John John’s temperature occurrent process course of temperature changes John’s temperature history 20

independent continuant dependent continuant quality temperature organism John John’s temperature occurrent process life of an organism John’s life 21

BFO: The Very Top continuant occurrent independent continuant dependent continuant qualitydisposition 22

Disposition - of a glass vase, to shatter if dropped - of a human, to eat - of a banana, to ripen - of John, to anaphylactic shock 23

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) 24

independent continuant dependent continuant disposition disease disorder John’s IgE-mediated allergic disorder John’s allergic disease occurrent process course of disease course of John’s peanut allergy 25

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