Resource Description Framework and Ontology

1. Resource Description Framework and Ontology Cungen Cao Knowledge Acquisition & Sharing Group Institute of Computing Technology Chinese Academy of Sciences March 25, 2002

2. AI Ontology

3. T. Gruber’s Definition An ontology is a formal explicit specification of a shared conceptualization

4. Necessary Conditions for “Something” to Be Called an Ontology • Exhaustive • Everything must be stated • Explicit • Everything must be stated explicitly • Formal • Everything must be stated formally • Consensual • Everything stated is consensus

5. defcategory Basic-Entity { attribute: full-name :type String attribute: abbreviated-name :type String attribute: informal-definition :type Text attribute: formal-definition :type First-Order-Formula relation: is-instance :type Concept relation: has-part :type Instance …… } Geographical Ontology

6. defcategory Location { relation: in-east-of :type PhysicalEntity relation: in-south-of : type PhysicalEntity relation: in-west-of : type PhysicalEntity relation: in-north-of : type PhysicalEntity relation: in-middle-of : type PhysicalEntity }

7. defcategory Region inherits Basic-Entity; includes Location { attribute: population :type Integer :facet time attribute: land-area :type Real :unit km2 attribute: average-summer-whether :type Real :unit ℃ … }

8. defcategory City inherits Region { relation: geographical-part-of :type GeographicalEntity attribute: city-flower :type PlantEntity … } defcategory Country inherits Region { attribute: capital-city :type GeographicalEntity attribute: first-regional-division :type GeographicalEntity attribute: national-flower :type GeographicalEntity attribute: number-of-nationalities :type Integer … }

9. Axiom 1. geographical entities X and Y, in-east-of(X,Y)  in-west-of(Y,X). Axiom 1. geographical entities X and Y, in-east-of(X,Y)  in-west-of(Y,X)  in-northwest-of (Y,X)  in-southwest-of (Y,X). Axiom 2. city X, country Y, geographical-part-of(X,Y)  population(X)  population(Y). Axiom 3. city X country Y, geographical-part-of(X,Y)  number-of-nationalities(X)  number-of-nationalities(Y). Axiom 4. city X, country Y, capital-city(X,Y)geographical-part-of(X,Y) Geographical Axioms

10. Steps in Ontology Building • Which domain? • What purposes? • What categories? • What attributes for each category? • How are categories interrelated? • How are relationships constrained?

11. Standard Universal Ontology? • Is there any universal ontology covering everything? • Most probably no! • Every enterprise has his own preferences • Ontology translation is a necessity

12. Resource Description Framework

13. Web Information Retrieval • Agent-based Search Engines • E.g. Altavista, Infoseek, Excite • Brute force • Metadata-based Search Engines • E.g. Yahoo • Man-generated categories & subject labels

14. Metadata-Based Information Retrieval • Metadata • Book • Author, Title, Publisher, Date of Publication, Subject • lookup information: Bai Shuo, Li Guojie • Person • Name, Surname, First Name, Gender, Date of Birth, Date of Place, etc. • Geographic Entity • Name, Location, Population, Nationalities, etc.

15. Resource Description Framework • RDF is a common framework for representing metadata for Web resources between different applications • RDF descriptions can be exchanged without loss of semantics! • A resource is anything that can have a URI • E.g. my electronic paper Ontology whose URL is http://www.nki.net.cn/ontology.htm

16. Resource Description Framework • Resources are specified by properties • Title, author, date of last modification, etc. • See Dublin Core Metadata • A property is a resource having a name, URI, and it own properties • You can define your own properties! • Properties defined by you can be searched, manipulated and sold like any other resource!

17. Resource Description Framework • A statement (Resource, Property, Value) or (Subject, Predicate, Object) is a resource • You can define metadata for statements!

18. Why Is XML Better Than RDF? • Advantages of XML • A device for inventing tags freely to structure your documents • E.g. The company <name> IBM </name> …

19. Why Is XML Better Than RDF? • Disadvantages of XML • XML is a serial language, Maintaining such an order over Internet may not be time-consuming • When you represent general XML documents in computer memory, you get weird data structures that mix trees, graphs, and character strings. In general, these are hard to handle in even moderate amounts, let alone by the billion

20. XML Is the Foundation of RDF • RDF relies on the support of XML, and XML syntax is only one possible syntax for RDF • RDF uses XML to exchange descriptions of resources RDFS RDF XHTML XML HTML

21. Is RDF Enough? • RDF itself does not have an inference engine • the RDF data model does not provide any mechanism for declaring specific classes of resources, or for declaring which properties may be applicable to which classes of resources.

22. We Need RDF Schemas • A Type System • An RDF schema defines the properties of a resource (title, author, subject, size, color, etc.) • An RDF schema defines the types of resources (e.g. Web pages, animals and geographical entities) which the properties can be applicable. • An RDF schema defines properties in terms of the classes of resource to which they apply. • Domain and range constraints on the properties

23. RDF Schemas • RDFS Classes • rdfs: Class • rdfs: Resource • rdf: Property • rdfs:ContrainstProperty • rdfs: Literal

24. RDF Schemas • RDF Properties (Instances of rdf: Property) • rdf: type. (R, rdf:type, C)R is an instance of C • rdfs: subClassOf. (C, rdfs: subClassOf, rdf:type rdfs: Class) • rdfs: subPropertyOf • rdfs: domain • Domain constraints define the applicability of properties • rdfs: range • Range constraints are only applied to properties • Value of a range constraints is a class

25. rdfs: label • rdfs: comment • rdfs: seeAlso • rdfs: isDefinedBy • rdfs: subPropertyOf rdfs: seeAlso

26. Discussion

27. OIL: Ontology Inference Layer • An ontology infrastructure for semantic Web • Vrije, Manchester, Stanford, Bell lab, … • Frame Formalism + Description Logic • For OIL ontology semantics • Ontology design reasoning support • (FaCT by Manchester)

28. OIL Layered Architecture • Core OIL • Compatible with RDFS • Standard OIL • Heavy OIL

29. Gene Ontology • GO (Gene Ontology) is a controlled vocabulary used to describe the biology of a gene product in any organism. • A gene product has one or many molecular functions • A gene product may be used in one or many biological processes • A gene product may appear in several cellular component

30. Gene Ontology • Purpose: Common Language for Annotating Gene Products • Useful Internet Resources • http://www.geneontology.com/ • http://genome-www.stanford.edu/GO • http://www.ebi.ac.uk/interpro/QuickGo

31. Gene Ontology • GO has 3 independent ontologies in DAG • molecular function describes tasks done by gene products at molecular level • biological process describes broad biological goals accomplished by ordered assemblies of molecular functions • cellular component describes subcellular structures, locations, and macromolecular complexes

32. GO Process Ontology