文档介绍：MGED Ontology: An Ontology of Biomaterial Descriptions for Microarrays
Microarray Data Analysis and Management:
Bio-ontologies for Microarrays
EMBL-EBI, Hinxton, Cambridge, UK
Dec. 5, 2001
Chris Stoeckert, U. Penn
Ontology Usage for Genes in EpoDB
EpoDB is a prototype system of genes expressed during erythropoiesis
Built before microarrays were readily available
Illustrate usage of an ontology of gene parts and controlled vocabularies of gene (and gene family) names
EpoDB “Gene Ontology”
.edu/EpoDB
Stoeckert, Salas, Brunk, Overton (1999) Nucl. Acids Res. 26:288
EpoDB Gene Landmark Query
What is an ontology? (In puter science not philosophy sense)
An ontology is a specification of concepts that includes the relationships between those concepts.
Removes ambiguity. Provides semantics and constraints.
Allows putational inferences and parisons
Types of Ontologies
Taxonomy
Tree structure. IS-A hierachy
Variants - Gene Ontology (DAG)
Frame-based (object-oriented)
Classes and attributes
EcoCyc
Description logic (DL)
Reasoning about concept (class) bine terms with constraints (sanctioning)
GRAIL (GALEN, TAMBIS)
Ontology Inference Layer (OIL)
Combines Frames and DLs
Uses Web standards XML and RDF
Taxonomy
Terms mon usage
Homo sapiens, not human, not homo sapeins
NCBI ID = 9606
Hierarchy provides unambiguous levels of equivalence
Homo sapiens and Mus musculus are of the class Mammalia but Drosophila melanogaster is not.
Can use taxonomic hierarchies for other types of information
., Human Developmental Anatomy (U. of Edinburgh)
Microarray Information to be Captured
Figure from:
David J. Duggan et al. (1999) Expression Profiling using cDNA microarrays. Nature ics 21: 10-14
Tables Describing Samples in RAD (RNA Abundance Database)
Experiment
ExpGroups
Groups
RelExperiments
ControlGenes
Hybridization
Conditions
Label
Sample
Treatment
Disease
Devel. Stage
ExperimentSample
Taxon
Anatomy