Synthetic Biology:Semantic web ontology: Difference between revisions
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This is a part of the effort to provide a standardized, extensible, scalable and '''machine-processable''' interface for the [http://parts.mit.edu/ Registry of Standard Biological Parts]. | This is a part of the effort to provide a standardized, extensible, scalable and '''machine-processable''' interface for the [http://parts.mit.edu/ 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 | BioBricks abstraction hierarchy]]. | ||
==Semantic Web== | ==Semantic Web== | ||
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*identifies every resource with a globally unique URI: don't say "color", say <http://example.com/2005/std6#col> | *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”) | *allows “serendipitous reuse”: integration with data sources in other fields (“web join”) | ||
===Resources=== | |||
#[http://www.xml.com/lpt/a/2000/11/01/semanticweb/index.html Semantic Web primer] from 2000 at xml.com | |||
#[http://www.w3.org/2005/Talks/0517-boit-tbl/ Berners-Lee - Semantic Web Life Sciences - BioIT World] | |||
#[http://www.w3.org/2003/Talks/05-gartner-tbl/ Web Services - Semantic Web by Tim-Berners Lee] | |||
#[http://www.amk.ca/talks/2004-12-02/ Introduction to the Semantic Web and RDF by A.M. Kuchling] | |||
==Ontology== | ==Ontology== | ||
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Resources: | Resources: | ||
#[http://dimer.tamu.edu/GO/wiki GO annotation wiki] (from [[User:Skosuri|Sri]]) | #[http://dimer.tamu.edu/GO/wiki GO annotation wiki] (from [[User:Skosuri|Sri]]) | ||
Revision as of 10:17, 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
- 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”)
Resources
- 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
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 uses CellML metadata to describe its elements. See also a message on SBML forum.
- BioModels database and Systems Biology Ontologies (SBO) project
Resources:
- GO annotation wiki (from Sri)
