MGEDOntologyWorkingGroupReport.pptVIP

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” /EpoDB EpoDB Gene Landmark Query What is an ontology?(In the computer 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 for computational inferences and reliable comparisons 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) relationships Combine terms with constraints (sanctioning) GRAIL (GALEN, TAMBIS) Ontology Inference Layer (OIL) Combines Frames and DLs Uses Web standards XML and RDF Taxonomy Terms for common 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 e.g., Human Developmental Anatomy (U. of Edinburgh) Microarray Information to be Captured Tables Describing Samples in RAD (RNA Abundance Database) CBIL Anatomy Hierarchy Anatomy Table Used by RAD Standardisation of Microarray Data and Annotations -MGED Group MGED Working Groups Annotation: Experiment description and data representation standards (Alvis Brazma, EMBL-EBI) Format: Microarray data XML exchange format (Paul Spellman, UC Berkeley) Ontology: Ontologies for sample description (Chris Stoeckert, U Penn) Norm