Synthetic Biology:Semantic web ontology: Difference between revisions

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#*Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
#*Namespace: ftp://ftp.geneontology.org/pub/go/xml/dtd/go.dtd
#*Properties: name, definition, isa, association, evidence
#*Properties: name, definition, isa, association, evidence
#Sequence Ontology: features on a nucleotide or protein sequence
#[http://song.sourceforge.net/so.shtml Sequence Ontology]: features on a nucleotide or protein sequence
#BioPAX: biological pathway data
#[http://www.biopax.org/ BioPAX]: biological pathway data
#UniProt (planning)
#[http://www.uniprot.org/ UniProt] (planning)
 
#[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum.
[http://sbml.org/documents/ SBML] uses [http://www.cellml.org/specifications/archive/metadata/20011102/cellml_metadata_specification.html CellML metadata] to describe its elements. See also a [http://www.sbml.org/forums/index.php?t=msg&goto=1435&rid=0#msg_1435 message] on SBML forum.
#[http://biomodels.net/ BioModels] database and Systems Biology Ontologies (SBO) project
 
Biomodels database and Systems Biology Ontologies (SBO) project
http://biomodels.net/
 


[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]]).
GO (terms describing process)
DAG-Edit - ontology viewer
https://sourceforge.net/projects/geneontology/
BioPAX


References:
References:

Revision as of 16:01, 15 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.

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”)

Ontology

Controlled vocabulary of concepts and their relationships.

Examples of ontologies:

  1. Dublin Core
  2. Gene Ontology
  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

GO annotation wiki (from Sri).

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
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