What is an ontology and Why should you care? Barry Smith ontology.buffalo/smith
What is an Ontology?
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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
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Ontologies Working Group Goals
• Collect controlled vocabularies for sample descriptions.
• Define microarray concepts and their relationships.
• Provide bridge to ontologies from other knowledge domains.
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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
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Anatomy Hierarchy
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RelExperiments
Experiment Tables
Experiment
ExpGroupsGroups
Exp.ControlGenes
ControlGenes
HybridizationConditions
Label
Sample
TreatmentDiseaseDevel. Stage
ExperimentSample
Anatomy
Taxon
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MAML DTD -> UML mapping:Array platform
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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)
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Ontology Working Group Progress
• Critical concepts identified– Alternative relationships discussed
• Web site for information– Beginnings of central repository
• Application to sample descriptions– Different species
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www.mged.org
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http://www.cbil.upenn.edu/Ontology
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Example Sample Descriptions
• Human
• Mouse
• Arabidopsis
• Issues:– qualifier/value-> qualifier/ID/value/source– Expand “treatment”
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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
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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
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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.
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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.