MGED Ontology

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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
:


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:


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:


Restriction


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:


intersectionOf



Datatypes


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


(applied to class expressions)


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


http://en.wikipedia.org/wiki/Web_Ontology_Language



OWL Web Ontology Language Guide


http://www.w
3
.org/TR/owl
-
guide/



OWL Web Ontology Language Overview


http://www.w
3
.org/TR/owl
-
features/



OWL Web Ontology Language

Reference


http://www.w
3
.org/TR/owl
-
ref/


OWL Web Ontology Language Semantics and Abstract Syntax


http://www.w
3
.org/TR/owl
-
semantics/syntax.html



Ontology Working Group


http://mged.sourceforge.net/ontologies/


http://www.w
3
.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