what is an ontology? an ontology is a specification of a conceptualization that is designed for...
Post on 03-Jan-2016
229 Views
Preview:
TRANSCRIPT
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
RelExperiments
Experiment Tables
Experiment
ExpGroupsGroups
Exp.ControlGenes
ControlGenes
HybridizationConditions
Label
Sample
TreatmentDiseaseDevel. Stage
ExperimentSample
Anatomy
Taxon
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
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.
top related