Synthetic Biology:Semantic web ontology: Difference between revisions
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Assertion of facts | Assertion of facts | ||
'''<http://www.example.org/index.html>''' has a '''creator''' whose value is '''John Smith''' | '''<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=== | ===Resources=== | ||
#[http://www.w3.org/TR/rdf-primer/ RDF Primer at W3C] | #[http://www.w3.org/TR/rdf-primer/ RDF Primer at W3C] | ||
Revision as of 13:01, 16 September 2005
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
- W3C Semantic Web Activity (links to RDF, OWL, etc)
- Semantic Web primer from 2000 at xml.com
- Berners-Lee - Semantic Web Life Sciences - BioIT World
- Web Services - Semantic Web by Tim-Berners Lee
- Introduction to the Semantic Web and RDF by A.M. Kuchling
- Wikipedia article on Semantic Web
- Semantic Web tutorials from W3C
- Semantic Web tutorial using N3
- Primer: Getting into RDF & Semantic Web using N3
- Semantic Web: interview with Tim Berners-Lee
- W3C press release
Resource Description Framework (RDF)
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
RDF Schema
Vocabulary definitions
Resources
Web Ontology Language (OWL)
Relationships between vocabularies and other constraints
Resources
Ontologies
Controlled vocabulary of concepts and their relationships. Described using RDF Schema and OWL.
Examples:
- 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 uses CellML metadata to describe its elements. See also a message on SBML forum.
- 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
- GO annotation wiki (from Sri)
Contact: Ilya Sytchev
