Ontology Notes are from: - Fall 2006, BIO/CS311 Bioinformatics – Lecture 24 - Alton’s Slides – “What is Ontology” - http://www.wikipedia.org/ - http://www.w3schools.com/ - http://www.w3.org/TR/owl-ref/

Ontology definition… “A formal vocabulary that describes the basic categories of being by defining entities, types of entities, and the relationships among them” – BIO/CS311 (In CS) an ontology is a data model that represents a set of concepts within a domain and the relationships between those concepts. It is used to reason about the objects within that domain. - wikipedia

Ontology Languages Ontology must be expressed in a formal language. An ontology language needs to allow specification of terms, relationships, properties OBO (Open Biomedical Ontologies) - Flat-file structure OWL (Ontology Web Language) - Semantic markup language (like XML)

Elements of an Ontology Instances (Individuals) Classes Attributes (properties) Relationships Most important type is subsumption: "is_a"; Most commonly used are "is_a" and "part_of" Hierarchical structure Note: Problems with Partonomy (classification based on part-of relation):

Other ways to represent knowledge Controlled Vocabulary: classes only, no attributes, no relationships, no hierarchy Anatomical Dictionary: classes and attributes, no hierarchy, no relationships Taxonomy: classes, hierarchy, and relationships, no attributes

OBO Open Biomedical Ontologies, OBO, forms part of the resources of the National Center for Biomedical Ontology. An effort to create controlled vocabularies for shared use across different biological and medical domains. Flat-file structure. OBO does not include all features of OWL.

OWL Ontology Web Language , OWL, is a markup language for publishing and sharing data using ontologies on the Internet. OWL is built on top of RDF. OWL is written in XML. To learn OWL, we need to know XML (EXtensible Markup Language) and RDF (Resource Description Framework).

OWL OWL is for processing information on the web (instead of displaying it). OWL has three sublanguages OWL Lite OWL DL (includes OWL Lite) OWL Full (includes OWL DL) OWL is a part of the "Semantic Web Vision" - a future where: Web information has exact meaning. Web information can be processed by computers. Computers can integrate information from the web.

XML (EXtensible Markup Language) XML is a metamarkup language for text documents Is NOT (presentation language, programming language, network transport protocol, database.) Parse XML & Store XML Data Client software Server software Database Retrieve data & format XML

XML Examples Format XML with CSS Displaying XML with XSL http://www.leeleong.com/OtherWork/Ontology/index.htm Format XML with CSS Displaying XML with XSL XML Data Embedded in HTML XML Praser: To manipulate an XML document, you need an XML parser.

XML XML can be generated on a server without installing any XML controls. (e.g. generate XML with ASP) XML can be generated from a database without any installed XML software. (e.g. with ASP)

RDF (Resource Description Framework) RDF is a framework for describing resources on the web RDF is written in XML RDF is a part of the W3C's Semantic Web Activity RDF descriptions are not designed to be displayed on the web

RDF RDF identifies things using Web identifiers (URIs), and describes resources with properties and property values A Resource is anything that can have a URI A Property is a Resource that has a name, such as "author" or "homepage" A Property value is the value of a Property, such as "Jan Egil Refsnes" or "http://www.w3schools.com" (note that a property value can be another resource)

RDF Example & RDFS http://www.leeleong.com/OtherWork/Ontology/index.htm 2. Example + graph 7. Collection – Example + graph 8. RDF Schema (RDFS) is an extension to RDF RDF describes resources with classes, properties, and values. RDF Schema provides the framework to describe application-specific classes and properties. 9. The Dublin Core Metadata Initiative (DCMI) has created some predefined properties for describing documents.

CARO http://www.bioontology.org/wiki/index.php/CARO:Main_Page CARO reference ontology of anatomy, combining FMA (Foundational Model of Anatomy) and model organism anatomical ontologies. NCBO anatomy workshop in September, 06, Seattle

University of Missouri-Rolla End of Slides University of Missouri-Rolla © 2006 Curators of University of Missouri