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://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:
- Dublin Core provides a vocabulary to describe bibliographic metadata
- Namespace: http://purl.org/dc/elements/1.1/
- Properties: title, creator, publisher, identifier
- 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.
- 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 protein sequence and annotation data in RDF format. UniProt OWL Ontology
- SBML uses CellML metadata to describe its elements. See also a message on SBML forum.
- BioModels database and Systems Biology Ontologies (SBO) project
- Open Biomedical Ontologies
- Bio-Ontologies
- Ontologies for molecular biology and bioinformatics
- Microarray Gene Expression Society (MGED) Ontology
- RDF Schemas directory
- CO-ODE ontology examples
- KnowledgeZone - peer reviewed ontology library
Diagram of synthetic biology ontology v0.01 (developed using existing terminology described on the Registry website):
Resources
- GO annotation wiki (from Sri)
- Ontology Development 101: A Guide to Creating Your First Ontology - what is an ontology and why we need it
- Protégé OWL Tutorial (PDF)
- Manchester Pizza Finder
- National Center for Biomedical Ontology