Synthetic Biology:Semantic web ontology
From OpenWetWare
This is a part of the effort to provide a standardized, extensible, scalable and machine-processable interface for the Registry of Standard Biological Parts.
Semantic Web
RDF/XML, RDF Schema and OWL
- allows to model real things, not just documents or database tables
- consists of statements about resources in the form of triples:
SUBJECT -> PROPERTY -> VALUE
- identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col>
- allows “serendipitous reuse”: integration with data sources in other fields (“web join”)
Ontology
Controlled vocabulary of concepts and their relationships.
Examples of ontologies:
- Dublin Core
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
- Gene Ontology
- 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
GO annotation wiki (from Sri).
References: