Synthetic Biology:Semantic web ontology/Examples: Difference between revisions
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#[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence | #[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence | ||
#[http://www.biopax.org/ BioPAX]: biological pathway data | #[http://www.biopax.org/ BioPAX]: biological pathway data | ||
#[http://www. | #[http://www.isb-sib.ch/~ejain/rdf/ UniProt] protein sequence and annotation data in RDF format. | ||
#[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum. | #[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum. | ||
#[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project | #[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project |
Revision as of 15:23, 5 December 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 protein sequence and annotation data in RDF format.
- 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):