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
-OR-
SUBJECT -> PREDICATE -> OBJECT

• 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
12. Design Issues @ W3C - web architecture and metadata

Resource Description Framework (RDF)

Used for assertion of facts

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

the RDF terms for the various parts of the statement are:

• the subject is the URL <http://www.example.org/index.html>
• the predicate is the word "creator"
• the object is the phrase "John Smith"

Resources

1. RDF Primer at W3C
2. Wikipedia page
3. RDF @ W3C - a lot of links to resources
4. RDF Made Easy - a short tutorial
5. Intro to RDF and Jena RDP API
6. RDF Tutorial @ W3C - a lengthy presentation
7. Practical RDF - O'Reilly book, decent but not great
8. RDF FAQ @ W3C
9. RDF Data Access Use Cases and Requirements
10. Relational Databases on the Semantic Web
11. RDF Tutorial from the University of Lyon

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