Presented by Amr Ali AL-Hossary (M.B.,B.Ch) MGED Ontology Presented by Amr Ali AL-Hossary (M.B.,B.Ch)

Agenda Ontology OWL RDF MAGE MGED Current Work

Ontology Def: ontology is a formal representation of a set of concepts within a domain and the relationships between those concepts. Origin: philosophy, metaphysics

Components of Ontology Individuals: instances or objects (the basic or "ground level" objects) Classes: sets, collections, concepts, types of objects, or kinds of things. Attributes: aspects, properties, features, characteristics, or parameters that objects (and classes) can have Relations: how classes and individuals are related to one another Restrictions: formally stated descriptions of what must be true in order for some assertion to be accepted as input Events: the changing of attributes or relations

Components of Ontology (contd.) Function terms: complex structures formed from certain relations that can be used in place of an individual term in a statement. Rules: statements in the form of an if-then (antecedent-consequent) sentence that describe the logical inferences that can be drawn from an assertion in a particular form Axioms: assertions (including rules) in a logical form that together comprise the overall theory that the ontology describes in its domain of application. This definition differs from that of "axioms" in generative grammar and formal logic. In those disciplines, axioms include only statements asserted as a priori knowledge. As used here, "axioms" also include the theory derived from axiomatic statements.

Ontology Languages OWL: Web Ontology Language An ontology language is a formal language used to encode the ontology. Web Ontology Language (OWL) is a family of knowledge representation languages for authoring ontologies. Acronym : OWL instead of WOL. Proposed as an easy pronounced acronym  good logos, suggest wisdom, and honor William A. Martin's “One World Language” Follow-on from RDF and RDFS, + earlier ontology language projects (OIL, DAML and DAML+OIL). Considered one of the fundamental technologies underpinning Semantic Web. All its elements (classes, properties and individuals) are defined as RDF resources, and identified by URIs.

OWL sublanguages OWL Lite: OWL DL: OWL Full: support those users primarily needing a classification hierarchy and simple constraints. OWL DL: provide maximum expressiveness possible retaining computational completeness (all conclusions are guaranteed to be computed), decidability (all computations will finish in finite time), and the availability of practical reasoning algorithms. OWL Full: Based on a different semantics. designed to preserve some compatibility with RDF Schema ( e.g. a class can present a collection of individuals & as an individual itself). Every legal OWL Lite ontology is a legal OWL DL ontology. Every legal OWL DL ontology is a legal OWL Full ontology. Every valid OWL Lite conclusion is a valid OWL DL conclusion. Every valid OWL DL conclusion is a valid OWL Full conclusion.

OWL lite RDF Schema Features: Class (Thing, Nothing) rdfs:subClassOf rdf:Property rdfs:subPropertyOf rdfs:domain: source object rdfs:range : values Individual

OWL lite (In)Equality: Property Characteristics: equivalentClass: have the same instances (synonymous classes) equivalentProperty sameAs: other names for individuals differentFrom AllDifferent distinctMembers Property Characteristics: ObjectProperty DatatypeProperty inverseOf TransitiveProperty SymmetricProperty FunctionalProperty: only one value for individual InverseFunctionalProperty: the inverse of the property is functional

OWL lite Property Restrictions: Restricted Cardinality: onProperty allValuesFrom someValuesFrom Restricted Cardinality: minCardinality (only 0 or 1) maxCardinality (only 0 or 1) cardinality (only 0 or 1) Header Information: Ontology imports

OWL lite Class Intersection: Datatypes Versioning: intersectionOf xsd datatypes Versioning: versionInfo priorVersion backwardCompatibleWith incompatibleWith DeprecatedClass DeprecatedProperty

OWL lite Annotation Properties: rdfs:label rdfs:comment rdfs:seeAlso rdfs:isDefinedBy AnnotationProperty OntologyProperty

OWL DL & OWL Full Class Axioms: oneOf, dataRange disjointWith equivalentClass (applied to class expressions) rdfs:subClassOf

OWL DL & OWL Full Arbitrary Cardinality: minCardinality maxCardinality Cardinality Boolean Combinations of Class Expressions: unionOf complementOf intersectionOf Filler Information: hasValue

Part II MAGE

MAGE group Stands for “MicroArray and Gene Expression” group The group aims to provide a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems. MAGE-OM: Microarray Gene Expression - Object Model (data exchange model) expressed in UML MAGE-ML: Microarray Gene Expression - Markup Language (data exchange format) expressed in XML MAGEstk (or MAGE Software Toolkit) collection of packages acting as converters between MAGE-OM and MAGE-ML under various programming platforms.

MAGE-OM sections Experiment Bioassay ArrayDesign DesignElement Biomaterial BioAssayData QuantitationType Array Bioevent Protocol AuditAndSecurity Description HigherLevelAnalysis

Minimum Information About a Microarray Experiment - MIAME needed to enable interpretation of experiment results unambiguously potentially to reproduce the experiment. Six critical data Raw data for each hybridisation (e.g., CEL or GPR files) The final processed data (normalised) for the set of hybridisations in the experiment (study) Essential annotation including experimental factors and their values Experimental design including sample data relationships (e.g., which raw data file relates to which sample, which hybridisations are technical, which are biological replicates) Sufficient annotation of the array (e.g., gene identifiers, genomic coordinates, probe oligonucleotide sequences or reference commercial array catalog number) protocols (e.g., what normalisation method has been used to obtain the final processed data)

MGED provides standard terms for the annotation of microarray experiments. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed. The terms will be provided in the form of an ontology which means that the terms will be organized into classes with properties and will be defined. A standard ontology format will be used. For descriptions of biological material (biomaterial) and certain treatments used in the experiment, terms may come from external resources that are specified in the Ontology. Software programs utilizing the Ontology are expected to generate forms for annotation, populate databases directly, or generate files in the established MAGE-ML format. Thus, the Ontology will be used directly by investigators annotating their microarray experiments as well as by software and database developers and therefore will be developed with these very practical applications in mind. 

References Web Ontology Language OWL Web Ontology Language Guide http://en.wikipedia.org/wiki/Web_Ontology_Language OWL Web Ontology Language Guide http://www.w3.org/TR/owl-guide/ OWL Web Ontology Language Overview http://www.w3.org/TR/owl-features/ OWL Web Ontology Language Reference http://www.w3.org/TR/owl-ref/ OWL Web Ontology Language Semantics and Abstract Syntax http://www.w3.org/TR/owl-semantics/syntax.html Ontology Working Group http://mged.sourceforge.net/ontologies/ http://www.w3.org/2007/OWL/wiki/OWL_Working_Group Recommendations for Microarray Data Standards, Annotations, Ontologies and Databases http://www.mged.org/Workgroups/MIAME/ Protégé-OWL http://protegewiki.stanford.edu/index.php/Protege-OWL