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

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#[http://www.bioinfo.de/isb/2002/02/0017/main.html Ontologies for molecular biology and bioinformatics]
#[http://www.bioinfo.de/isb/2002/02/0017/main.html Ontologies for molecular biology and bioinformatics]
#[http://mged.sourceforge.net/ontologies/ Microarray Gene Expression Society (MGED) Ontology]
#[http://mged.sourceforge.net/ontologies/ Microarray Gene Expression Society (MGED) Ontology]
#[http://www.schemaweb.info/ RDF Schemas directory]
#[http://www.co-ode.org/ontologies/ CO-ODE ontology examples]
#[http://www.co-ode.org/ontologies/ CO-ODE ontology examples]
#*[http://smi-protege.stanford.edu:8080/KnowledgeZone/ KnowledgeZone] - peer reviewed ontology library


Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]):
Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the [http://parts2.mit.edu/r/parts/partsdb/index.cgi Registry website]):
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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]])
#[http://www.schemaweb.info/ RDF Schemas directory]
#[http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html Ontology Development 101: A Guide to Creating Your First Ontology] - what is an ontology and why we need it
#[http://protege.stanford.edu/publications/ontology_development/ontology101-noy-mcguinness.html Ontology Development 101: A Guide to Creating Your First Ontology] - what is an ontology and why we need it
#[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)
#[http://www.co-ode.org/downloads/pizzafinder/ Manchester Pizza Finder]
#[http://www.co-ode.org/downloads/pizzafinder/ Manchester Pizza Finder]
#[http://bioontology.org/ National Center for Biomedical Ontology]
#[http://bioontology.org/ National Center for Biomedical Ontology]

Revision as of 15:44, 3 January 2006

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 protein sequence and annotation data in RDF format. UniProt OWL Ontology
  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
  12. RDF Schemas directory
  13. CO-ODE ontology examples

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

Resources

  1. GO annotation wiki (from Sri)
  2. Ontology Development 101: A Guide to Creating Your First Ontology - what is an ontology and why we need it
  3. Protégé OWL Tutorial (PDF)
  4. Manchester Pizza Finder
  5. National Center for Biomedical Ontology