1. Ontology Notes are from:
- Fall 2006, BIO/CS311 Bioinformatics – Lecture 24
- Alton’s Slides – “What is Ontology” - - -

2. 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

3. 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)

4. 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):

5. 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

6. 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.

7. 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).

8. 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.

9. 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

10. XML Examples Format XML with CSS Displaying XML with XSL
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.

11. 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)

12. 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

13. 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 " (note that a property value can be another resource)

14. RDF Example & RDFS
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.

15. CARO
CARO reference ontology of anatomy, combining FMA (Foundational Model of Anatomy) and model organism anatomical ontologies.
NCBO anatomy workshop in September, 06, Seattle

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