Transcript hasName
Introduction to Allergy Ontology Barry Smith Rho, Chapel Hill, October 10, 2013 1 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 2 Aggregation of Triples hasName “TrpA” Gene expresses hasName Tryptophan Synthetase Protein hasSubstrate Chemical 3 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/ 4 UniProt RDF 5 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/ 10 11 T-helper 2 cell lineage commitment 12 Basic Formal Ontology continuant independent continuant occurrent dependent continuant organism http://www.ifomis.org/bfo 13 depends_on Continuant Independent Continuant Dependent Continuant thing quality Occurrent process, event temperature depends on bearer .... ..... ....... 14 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) 15 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) 16 BFO: The Very Top continuant independent continuant occurrent dependent continuant quality temperature 17 independent continuant dependent continuant quality organism John temperature types John’s temperature instances 18 independent continuant dependent continuant quality organism John temperature types John’s temperature instances 19 independent continuant organism John dependent continuant occurrent quality process temperature John’s temperature course of temperature changes John’s temperature history 20 independent continuant organism John dependent continuant occurrent quality process temperature John’s temperature life of an organism John’s life 21 BFO: The Very Top continuant independent continuant occurrent dependent continuant quality disposition 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 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 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