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

"an initiative to enable cross-platform data exchange and reuse through well-defined ontologies and a common XML-based framework."

"The goal of the Semantic Web initiative is to create a universal medium for the exchange of data where data can be shared and processed by automated tools as well as by people." [10]

• allows to model real things, not just documents or database tables (knowledge representation)
• 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
10. Semantic Web: interview with Tim Berners-Lee
11. W3C press release

Resource Description Framework (RDF)

Assertion of facts

<http://www.example.org/index.html>  has a creator whose value is John Smith

Resources

1. RDF Primer at W3C

RDF Schema

Vocabulary definitions

Web Ontology Language (OWL)

Relationships between vocabularies and other constraints

Ontologies

Controlled vocabulary of concepts and their relationships. Described using RDF Schema and OWL.

Examples:

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

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

Resources

1. GO annotation wiki (from Sri)

Contact: Ilya Sytchev