Synthetic Biology:Semantic web ontology/Examples

Ontology - essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.

Examples:

1. Dublin Core provides a vocabulary to describe bibliographic metadata
   • Namespace: http://purl.org/dc/elements/1.1/
   • Properties: title, creator, publisher, identifier
2. Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism. GO terms are organized in directed acyclic graphs (DAGs), which differ from hierarchies in that a 'child' (more specialized term) can have many 'parents' (less specialized terms). GO terms are connected by 'is a' (generalizations) and 'part of' (composition) relationships.
   • Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
   • Properties: name, definition, isa, association, evidence
3. Sequence Ontology: features on a nucleotide or protein sequence
4. BioPAX: biological pathway data
5. UniProt protein sequence and annotation data in RDF format. UniProt OWL Ontology
6. SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
7. BioModels database and Systems Biology Ontologies (SBO) project
8. Open Biomedical Ontologies
9. Bio-Ontologies
10. Ontologies for molecular biology and bioinformatics
11. Microarray Gene Expression Society (MGED) Ontology

Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):

Resources

1. GO annotation wiki (from Sri)
2. RDF Schemas directory
3. Ontology Development 101: A Guide to Creating Your First Ontology
4. Protégé OWL Tutorial (PDF)
5. National Center for Biomedical Ontology