What is an Ontology?

An ontology is a specification of a conceptualization that is designed for reuse across multiple applications and

implementations. …a specification of a conceptualization is a written, formal description of a set of concepts and

relationships in a domain of interest.

Peter Karp (2000) Bioinformatics 16:269

Ontologies Working Group Goals

• Collect controlled vocabularies for sample descriptions.

• Define microarray concepts and their relationships.

• Provide bridge to ontologies from other knowledge domains.

Ontologies in Gene Expression Databases

• Controlled vocabulary– Define relationships through hierarchy (e.g., taxonomy)

• Schema– Concepts as objects or relational tables– Attributes and data types provide specification– Relationships specified through subclassing (objects) or foreign

keys (relational tables)

• Knowledge representation– Link to other domains (gene sequence annotation, gene and

protein roles, pathways)– Facilitate data exchange by mapping common concepts

Anatomy Hierarchy

RelExperiments

Experiment Tables

Experiment

ExpGroupsGroups

Exp.ControlGenes

ControlGenes

HybridizationConditions

Label

Sample

TreatmentDiseaseDevel. Stage

ExperimentSample

Anatomy

Taxon

MAML DTD -> UML mapping:Array platform

Other Domains• Gene descriptions (Gene Ontology)

– Molecular function– Biological process– Subcellular localization

• Cellular and biochemical pathways (EcoCyc)• Literature (MeSH)• Phenotypes • Others …

Requires common set of terms (semantic mapping) Or shared usage of identifiers (e.g. GenBank accessions)

Ontology Working Group Progress

• Critical concepts identified– Alternative relationships discussed

• Web site for information– Beginnings of central repository

• Application to sample descriptions– Different species

www.mged.org

http://www.cbil.upenn.edu/Ontology

Example Sample Descriptions

• Human

• Mouse

• Arabidopsis

• Issues:– qualifier/value-> qualifier/ID/value/source– Expand “treatment”

Experiment

Examine gene expression changes in response to atherogenic diet incongenic strains that are susceptible or resistant to atherosclerosis.

Strain: B6.SPRET-Ath1r

Relevant phenotypic trait: - resistant to atherosclerosis(to atherogenic diet)

Relevant trait parameters: - increased levels of HDL; protocol(as defined by) - resistant to aortic lesions; protocol

Strain: B6.SJL-Ath9s

Relevant phenotypic trait: - susceptible to atherosclerosis(to atherogenic diet)

Relevant trait parameters: - unchanged levels of HDL; protocol- susceptible to aortic lesions;

protocol

Treatment: diet: atherogenic diet; protocol

Treatment 1

Type: Diet: atherogenetic diet; description of diet and/or reference

Age of mouse at begin of treatment

Time of the day at begin of treatment: N/A

Date: ? (seasonal effects)

Duration of treatment: 6 weeks

Treatment 2

Type: food deprivation

Time of day at begin of treatment: 6am

Duration of treatment: 4 hours

Treatment 3:

Type: Tissue harvesting

Time of day at begin of treatment: 10am

Duration of treatment: 1 hours

Protocol of treatment or reference

MIAME Ontology

Define MIAME concepts and their relationships incorporating MAML.

The goal is to generate a document that will provide a clear and common understanding of what should be reported and how.

The tables are a draft to form the basis for such a document.Located at Ontology Working Group home page.

Ontology Working Group Plans• Restructure ontology/ controlled vocabulary repository

– Organize by concept– Indicate species relevance– Incorporate reviews (pros/cons)

• Integrate sample descriptions of human (TT), mouse (MR), and plant (CS).– Post current documents

• Assignment to group members– Each do their own example sample description

• Next meeting– Try to get together at ISMB. Copenhagen July, 2001.