Synthetic Biology:Semantic web ontology/Examples: Difference between revisions

Revision as of 13:13, 19 October 2005

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

Examples:

Dublin Core provides a vocabulary to describe bibliographic metadata
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
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
Sequence Ontology: features on a nucleotide or protein sequence
BioPAX: biological pathway data
UniProt (planning)
SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
BioModels database and Systems Biology Ontologies (SBO) project
Open Biomedical Ontologies
Bio-Ontologies
Ontologies for molecular biology and bioinformatics
Microarray Gene Expression Society (MGED) Ontology

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

Ontology editors
- Protégé is a free, open source ontology editor and knowledge-base framework
- OilEd is an ontology editor allowing the user to build ontologies using DAML+OIL
- Ontolingua
- Chimaera is a software system that supports users in creating and maintaining distributed ontologies on the web

@@ Line 17: / Line 17: @@
 #[http://anil.cchmc.org/Bio-Ontologies.html Bio-Ontologies]
 #[http://www.bioinfo.de/isb/2002/02/0017/main.html Ontologies for molecular biology and bioinformatics]
+#[http://mged.sourceforge.net/ontologies/ Microarray Gene Expression Society (MGED) Ontology]
 Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]):