Synthetic Biology:Semantic web ontology/Examples: Difference between revisions

From OpenWetWare
Jump to navigationJump to search
No edit summary
Line 27: Line 27:
#[http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html Ontology Development 101: A Guide to Creating Your First Ontology]
#[http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html Ontology Development 101: A Guide to Creating Your First Ontology]
#[http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf Protégé OWL Tutorial] (PDF)
#[http://www.co-ode.org/resources/tutorials/ProtegeOWLTutorial.pdf Protégé OWL Tutorial] (PDF)
===Software===
*Ontology editors
**[http://protege.stanford.edu Protégé] is a free, open source ontology editor and knowledge-base framework
**[http://oiled.man.ac.uk/ OilEd] is an ontology editor allowing the user to build ontologies using DAML+OIL
**[http://ontolingua.stanford.edu/ Ontolingua]
**[http://www.ksl.stanford.edu/software/chimaera/ Chimaera] is a software system that supports users in creating and maintaining distributed ontologies on the web

Revision as of 13:03, 8 November 2005

Ontology - essentially, a formal description of objects and their interrelationships Described using RDF Schema and/or OWL.

Examples:

  1. Dublin Core provides a vocabulary to describe bibliographic metadata
  2. Gene Ontology provides a controlled vocabulary to describe gene and gene product attributes in any organism. GO terms are organized in directed acyclic graphs (DAGs), which differ from hierarchies in that a 'child' (more specialized term) can have many 'parents' (less specialized terms). GO terms are connected by 'is a' (generalizations) and 'part of' (composition) relationships.
  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
  8. Open Biomedical Ontologies
  9. Bio-Ontologies
  10. Ontologies for molecular biology and bioinformatics
  11. Microarray Gene Expression Society (MGED) Ontology

Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):

Resources

  1. GO annotation wiki (from Sri)
  2. RDF Schemas directory
  3. Ontology Development 101: A Guide to Creating Your First Ontology
  4. Protégé OWL Tutorial (PDF)
Retrieved from "https://openwetware.org/mediawiki/index.php?title=Synthetic_Biology:Semantic_web_ontology/Examples&oldid=10022"