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 and RDF Schema

Semantic Web

• 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)

SBML (http://sbml.org/documents/) uses CellML metadata http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html to describe its elements. http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435

http://dimer.tamu.edu/GO/wiki GO annotation wiki GO (terms describing process) DAG-Edit - ontology viewer https://sourceforge.net/projects/geneontology/ BioPAX

Biomodels database and Systems Biology Ontologies (SBO) project http://biomodels.net/

Architecture http://www.w3.org/2005/Talks/0517-boit-tbl/#[19]

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