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. The idea of a Semantic Web data model seems to fit this goal. The success of developing a Synthetic Biology ontology depends in part on a good definition of the BioBricks abstraction hierarchy.

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”)

Resources

1. W3C Semantic Web Activity (links to RDF, OWL, etc)
2. Semantic Web primer from 2000 at xml.com
3. Berners-Lee - Semantic Web Life Sciences - BioIT World
4. Web Services - Semantic Web by Tim-Berners Lee
5. Introduction to the Semantic Web and RDF by A.M. Kuchling
6. Wikipedia article on Semantic Web
7. Semantic Web tutorials from W3C
8. Semantic Web tutorial using N3
9. Primer: Getting into RDF & Semantic Web using N3

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

Resources:

1. GO annotation wiki (from Sri)