Synthetic Biology:Semantic web ontology

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:

1. Dublin Core
   • Namespace: http://purl.org/dc/elements/1.1/
   • Properties: title, creator, publisher, identifier
2. Gene Ontology
   • 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 (planning)
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

GO annotation wiki (from Sri).

References:

1. Berners-Lee - Semantic Web Life Sciences - BioIT World
2. Web Service - Semantic Web by Tim-Berners Lee
3. Introduction to the Semantic Web and RDF by A.M. Kuchling