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:
- Dublin Core
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
- Gene Ontology
- Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
- Properties: name, definition, isa, association, evidence
- Sequence Ontology: features on a nucleotide or protein sequence
- BioPAX: biological pathway data
- 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:
